@article{IBB_ID_54042, author={Riccardi C, Musumeci D, Capuozzo A, Irace C, King S, Russo Krauss I, Paduano L, Montesarchio D}, title={"dressing up" an Old Drug: An Aminoacyl Lipid for the Functionalization of Ru(III)-Based Anticancer Agents}, date={2018}, journal={Acs Biomater Sci Eng (ISSN: 2373-9878)}, year={2018}, fullvolume={196}, volume={196}, pages={163--174}, url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85037865210&doi=10.1021%2facsbiomaterials.7b00547&partnerID=40&md5=7fd37b83067d714cc9deb55d9773d19a}, abstract={In the search for more efficient anticancer treatments, Ru(III) complexes have attracted much interest among metal-based candidate drugs, showing marked antitumor and antimetastatic activity associated with lower systemic toxicity. Remarkable examples are the Ru(III) complexes NAMI-A and KP1019, which have reached advanced clinical evaluation. In order to improve the in vivo stability of Ru(III)-based drugs, as well as their cellular uptake and effectiveness, a new approach has been proposed by our research group, based on the incorporation of the active, NAMI-A-like Ru(III) complex into highly functionalized nucleolipidic structures, i.e., hybrid molecules containing a nucleoside or nucleotide central core derivatized with a lipid chain, ensuring both efficient protection against extracellular degradation and high cellular internalization of the metal. Aiming at expanding the chemical diversity of available amphiphilic Ru(III) complexes, we here selected a trifunctional α-amino acid to replace the nucleosidic core of previously prepared nucleolipid-based Ru(III) complexes. The amino acidic scaffold, linked to the Ru(III) complex, is decorated with both hydrophilic and lipophilic moieties, conferring high propensity to form stable aggregates in water, which is required to obtain a suitable nanocarrier for the drug delivery. Following this approach, a novel compound, indicated here as compound I, was successfully prepared and characterized, then studied in coformulation with the biocompatible cationic lipid 1,2-dioleyl-3-trimethylammoniumpropane chloride (DOTAP) by dynamic light scattering (DLS), small angle neutron scattering (SANS), and UV-vis analysis. Evaluated in vitro on a panel of human and nonhuman cell lines, it showed good antiproliferative activity on cancer cells, with IC50 values in the μM range, and no relevant cytotoxicity on the healthy cells used as control. © 2017 American Chemical Society.}, keywords={Amphiphilic Amino Acid, Anticancer Agents, Antiproliferative Activity, Nanoaggregates, Ru(iii) Complexes, Biocompatibility, Cell Culture, Chlorine Compounds, Cytotoxicity, Dynamic Light Scattering, Neutron Scattering, Ruthenium, Anti-Cancer Agents, Anti-Proliferative Activities, Anticancer Treatment, Cellular Internalization, Efficient Protections, Systemic Toxicities, Ruthenium Compounds, 2 Dioleoyl 3 Trimethylammoniopropane, Ruthenium Complex, Water, 3t3-L1 Cell Line, Antineoplastic Activity, Article, Biological Activity, C6 Cell Line (glioma), Controlled Study, Drug Delivery System, Drug Formulation, Female, Hacat Cell Line, Hela Cell Line, Human, Human Cell, Hydrophilicity, In Vitro Study, Lipophilicity, Mcf-7 Cell Line, Nonhuman, Photon Correlation Spectroscopy, Priority Journal, Ultraviolet Spectroscopy, }, references={Rademaker-Lakhai, J.M., Van Den Bongard, D., Pluim, D., Beijnen, J.H., Schellens, J.H.M., A phase i and pharmacological study with imidazolium-trans-DMSO-imidazole-tetrachlororuthenate, a novel ruthenium anticancer agent (2004) Clin. 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Chem., 17 (1), pp. 29-39}, document_type={Journal Article, }, affiliation={Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia 21, Napoli, 80126, Italy CNR, Istituto di Biostrutture e Bioimmagini, Via Mezzocannone 16, Napoli, 80134, Italy Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, Napoli, 80131, Italy ISIS Facility Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, United Kingdom CSGI, Consorzio Interuniversitario per Lo Sviluppo Dei Sistemi A Grande Interfase, Via della Lastruccia 3, Sesto Fiorentino, (Florence), 50019, Italy Istituto per l'Endocrinologia e l'Oncologia Gaetano Salvatore, Consiglio Nazionale Delle Ricerche (CNR), Via Pansini 5, Napoli, 80131, Italy}, ibbaffiliation={1}, } @article{IBB_ID_53420, author={Pica A, Russo Krauss I, Parente V, Tateishi-karimata H, Nagatoishi S, Tsumoto K, Sugimoto N, Sica F}, title={Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers}, date={2016 Nov 28}, journal={Nucleic Acids Res (ISSN: 0305-1048, 1362-4962)}, year={2016}, fullvolume={210}, volume={210}, pages={N/D--N/D}, url={}, abstract={Aptamers directed against human thrombin can selectively bind to two different exosites on the protein surface. The simultaneous use of two DNA aptamers, HD1 and HD22, directed to exosite I and exosite II respectively, is a very powerful approach to exploit their combined affinity. Indeed, strategies to link HD1 and HD22 together have been proposed in order to create a single bivalent molecule with an enhanced ability to control thrombin activity. In this work, the crystal structures of two ternary complexes, in which thrombin is sandwiched between two DNA aptamers, are presented and discussed. The structures shed light on the cross talk between the two exosites. The through-bond effects are particularly evident at exosite II, with net consequences on the HD22 structure. Moreover, thermodynamic data on the binding of the two aptamers are also reported and analyzed.}, keywords={, }, references={}, document_type={Journal Article, }, affiliation={Department of Chemical Sciences, University of Naples Federico II, Via Cintia, I-80126 Naples, Italy., Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone, 16, I-80134 Naples, Italy., Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan., Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113- 8656, Japan., Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan sugimoto@konan-u.ac.jp., Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan., Department of Chemical Sciences, University of Naples Federico II, Via Cintia, I-80126 Naples, Italy filosica@unina.it., }, ibbaffiliation={1}, } @article{IBB_ID_53214, author={Ferraro G, Pica A, Russo Krauss I, Pane F, Amoresano A, Merlino A}, title={Effect of temperature on the interaction of cisplatin with the model protein hen egg white lysozyme}, date={2016}, journal={J Biol Inorg Chem (ISSN: 0949-8257, 1432-1327electronic, 0949-8257print)}, year={2016}, fullvolume={248}, volume={248}, pages={1--10}, url={https://www2.scopus.com/inward/record.uri?eid=2-s2.0-84962145344&partnerID=40&md5=4da59018e31bc36a7100526355df83d8}, abstract={The products of the reaction between cisplatin (CDDP) and the model protein hen egg white lysozyme (HEWL) at 20, 37 and 55 °C in pure water were studied by UV–Vis absorption spectroscopy, intrinsic fluorescence and circular dichroism, dynamic and electrophoretic light scattering and inductively coupled plasma mass spectrometry. X-ray structures were also solved for the adducts formed at 20 and 55 °C. Data demonstrate that high temperature facilitates the formation of CDDP-HEWL adducts, where Pt atoms bind ND1 atom of His15 or NE2 atom of His15 and NH1 atom of Arg14. Our study suggests that high human body temperature (fever) could increase the rate of drug binding to proteins thus enhancing possible toxic side effects related to CDDP administration. © 2016 SBIC}, keywords={Cisplatin, Hen Egg White Lysozyme, Metallodrugs, Platinum-Based Drugs, Protein–ligand Interactions, }, references={}, document_type={Journal Article, }, affiliation={Department of Chemical Sciences, University of Naples Federico II, via Cintia, Naples, Italy CNR Institute of Biostructure and Bioimages, via Mezzocannone 16, Naples, Italy}, ibbaffiliation={1}, } @article{IBB_ID_52752, author={Merlino A, Caterino M, Russo Krauss I, Vergara A}, title={Missing gold atoms in lysozyme crystals used to grow gold nanoparticles}, date={2015}, journal={Nat Nanotechnol (ISSN: 1748-3387)}, year={2015}, fullvolume={310}, volume={310}, pages={285--285}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84927164388&partnerID=40&md5=ab5ecb96d19f87b4da44f06c3422eb4a}, abstract={}, keywords={Gold, Gold Nanoparticle, Lysozyme, Atom, Crystal Structure, Crystallization, Electron, Hypothesis, Letter, Molecular Recognition, Priority Journal, Transmission Electron Microscopy, }, references={}, document_type={Letter, Journal Article, }, affiliation={Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, Naples, Italy Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Naples, Italy}, ibbaffiliation={1}, } @article{IBB_ID_52753, author={Picone D, Donnarumma F, Ferraro G, Russo Krauss I, Fagagnini A, Gotte G, Merlino A}, title={Platinated oligomers of bovine pancreatic ribonuclease: Structure and stability}, date={2015}, journal={J Chem Res (ISSN: 0162-0134, 1873-3344, 0162-0134print)}, year={2015}, fullvolume={414}, volume={414}, pages={37--43}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84924260246&partnerID=40&md5=a57781077a03413b74fcbdb83268b3f8}, abstract={The reaction between cis-diamminedichloroplatinum(II) (CDDP), cisplatin, a common anticancer drug, and bovine pancreatic ribonuclease (RNase A), induces extensive protein aggregation, leading to the formation of one dimer, one trimer and higher oligomers whose yields depend on cisplatin/protein ratio. Structural and functional properties of the purified platinated species, together with their spontaneous dissociation and thermally induced denaturation, have been characterized. Platinated species preserve a significant, although reduced, ribonuclease activity. The high resistance of the dimers against dissociation and the different thermal unfolding profiles suggest a quaternary structure different from those of the well-known swapped dimers of RNase A. © 2015 Elsevier Inc. All rights reserved.}, keywords={Cisplatin, Platinated Ribonucleases, Protein Aggregation, Protein-Metal Interactions, Ribonuclease Oligomers, Dimer, Pancreatic Ribonuclease, Article, Crystal Structure, Crystallization, Dissociation, Enzyme Activity, Enzyme Analysis, Enzyme Denaturation, Enzyme Purification, Enzyme Stability, Enzyme Structure, Protein Folding, Protein Quaternary Structure, Protein Unfolding, X Ray Diffraction, Bovinae, }, references={Comess, K.M., Lippard, S.J., (1993) Molecular Aspects of Platinum-DNA Interactions in Molecular Aspects of Anticancer Drug-DNA Interactions, pp. 134-168. , S. Neidle, M. Waring, Macmillan Londo Jamieson, E.R., Lippard, S.J., (1999) Chem. Rev., 99, pp. 2467-2498 Takahara, P.M., Rosenzweig, A.C., Frederick, C.A., Lippard, S.J., (1995) Nature, 377, pp. 649-652 Kartalou, M., Essigmann, J.M., (2001) Mutat. Res., 478, pp. 1-21 Che, C.-M., Siu, F.M., (2010) Curr. Opin. Chem. 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Chem., 116, pp. 89-95}, document_type={Journal Article, }, affiliation={Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario DiMonte sant'Angelo, Via Cintia, Naples, Italy Institute of Biostructures and Bioimages, CNR, Via Mezzocannone 16, Naples, Italy Department of Life and Reproduction Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, Verona, Italy}, ibbaffiliation={1}, } @article{IBB_ID_11789, author={Merlino A, Russo Krauss I, Castellano I, Ruocco MR, Capasso A, De Vendittis E, Rossi B, Sica F}, title={Structural and denaturation studies of two mutants of a cold adapted superoxide dismutase point to the importance of electrostatic interactions in protein stability}, date={2014 Mar}, journal={Bba-Gen Subjects (ISSN: 0925-4439, 0006-3002, 1570-9639)}, year={2014}, fullvolume={487}, volume={487}, pages={632--640}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84893303686&partnerID=40&md5=a004ba1ff29471b9cf928bd5e6207301}, abstract={A peculiar feature of the psychrophilic iron superoxide dismutase from Pseudoalteromonas haloplanktis (PhSOD) is the presence in its amino acid sequence of a reactive cysteine (Cys57). To define the role of this residue, a structural characterization of the effect of two PhSOD mutations, C57S and C57R, was performed. Thermal and denaturant-induced unfolding of wild type and mutant PhSOD followed by circular dichroism and fluorescence studies revealed that C -> R substitution alters the thermal stability and the resistance against denaturants of the enzyme, whereas C57S only alters the stability of the protein against urea. The crystallographic data on the C57R mutation suggest an involvement of the Arg side chain in the formation of salt bridges on protein surface. These findings support the hypothesis that the thermal resistance of PhSOD relies on optimization of charge-charge interactions on its surface. Our study contributes to a deeper understanding of the denaturation mechanism of superoxide dismutases, suggesting the presence of a structural dimeric intermediate between the native state and the unfolded state. This hypothesis is supported by the crystalline and solution data on the reduced form of the enzyme. (C) 2014 Elsevier B.V. All rights reserved.}, keywords={Crystal Structure, Mutants, Psychrophilic Enzyme, Superoxide Dismutase, Thermal Stability, Unfolding, Arginine, Cysteine, Iron Superoxide Dismutase, Sodium Chloride, Amino Acid Sequence, Article, Bacterial Mutation, Circular Dichroism, Crystallography, Enzyme Denaturation, Enzyme Stability, Enzyme Structure, Fluorescence, Heat Tolerance, Nonhuman, Priority Journal, Protein Interaction, Pseudoalteromonas, Pseudoalteromonas Haloplanktis, Static Electricity, Substitution Reaction, Thermostability, Cold Temperature, X-Ray, Models, Molecular, Protein Conformation, Protein Denaturation, Protein Stability, Spectrometry, }, references={D'Amico, S., Collins, T., Marx, J.C., Feller, G., Gerday, C., Psychrophilic microorganisms: Challenges for life (2006) EMBO Rep., 7, pp. 385-38 Feller, G., Life at low temperatures: Is disorder the driving force? 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Acta, 1784, pp. 1865-1872 Siddiqui, K.S., Cavicchioli, R., Cold-adapted enzymes (2006) Annual Review of Biochemistry, 75, pp. 403-433. , DOI 10.1146/annurev.biochem.75.103004.142723 De Vendittis, E., Castellano, I., Cotugno, R., Ruocco, M.R., Raimo, G., Masullo, M., Adaptation of model proteins from cold to hot environments involves continuous and small adjustments of average parameters related to amino acid composition (2008) Journal of Theoretical Biology, 250 (1), pp. 156-171. , DOI 10.1016/j.jtbi.2007.09.006, PII S0022519307004249 Merlino, A., Russo Krauss, I., Castellano, I., De Vendittis, E., Rossi, B., Conte, M., Vergara, A., Sica, F., Structure and flexibility in cold-adapted iron superoxide dismutases: The case of the enzyme isolated from Pseudoalteromonas haloplanktis (2010) J. Struct. Biol., 172, pp. 343-352 Castellano, I., Di Maro, A., Ruocco, M.R., Chambery, A., Parente, A., Di Martino, M.T., Parlato, G., De Vendittis, E., Psychrophilic superoxide dismutase from Pseudoalteromonas haloplanktis: Biochemical characterization and identification of a highly reactive cysteine residue (2006) Biochimie, 88 (10), pp. 1377-1389. , DOI 10.1016/j.biochi.2006.04.005, PII S0300908406000551 Miller, A.F., Superoxide dismutases: Ancient enzymes and new insights (2012) FEBS Lett., 586, pp. 585-595 Perry, J.J., Shin, D.S., Getzoff, E.D., Tainer, J.A., The structural biochemistry of the superoxide dismutases (2010) Biochim. Biophys. Acta, 1804, pp. 245-262 Castellano, I., Ruocco, M.R., Cecere, F., Di Maro, A., Chambery, A., Michniewicz, A., Parlato, G., De Vendittis, E., Glutathionylation of the iron superoxide dismutase from the psychrophilic eubacterium Pseudoalteromonas haloplanktis (2008) Biochim. Biophys. 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C., Blaise, V., Collins, T., D'Amico, S., Delille, D., Gratia, E., Hoyoux, A., Gerday, C., A perspective on cold enzymes: Current knowledge and frequently asked questions (2004) Cell. Mol. Biol. (Noisy-le-grand), 50, pp. 643-655 Huston, A. L., Haeggstrom, J. Z., Feller, G., Cold adaptation of enzymes: Structural, kinetic and microcalorimetric characterizations of an aminopeptidase from the Arctic psychrophile Colwellia psychrerythraea and of human leukotriene A (4) hydrolase (2008) Biochim. Biophys. Acta, 1784, pp. 1865-1872 Siddiqui, K. S., Cavicchioli, R., Cold-adapted enzymes (2006) Annual Review of Biochemistry, 75, pp. 403-433. , DOI 10. 1146/annurev. biochem. 75. 103004. 142723 Miller, A. F., Superoxide dismutases: Ancient enzymes and new insights (2012) FEBS Lett., 586, pp. 585-595 Perry, J. J., Shin, D. S., Getzoff, E. D., Tainer, J. A., The structural biochemistry of the superoxide dismutases (2010) Biochim. Biophys. Acta, 1804, pp. 245-262 Parge, H. E., Getzoff, E. D., Scandella, C. S., Crystallographic characterization of recombinant human CuZn superoxide dismutase (1986) Journal of Biological Chemistry, 261 (34), pp. 16215-16218 McRee, D. E., Redford, S. M., Getzoff, E. D., Lepock, J. R., Hallewell, R. A., Tainer, J. A., Changes in crystallographic structure and thermostability of a Cu, Zn superoxide dismutase mutant resulting from the removal of a buried cysteine (1990) J. Biol. Chem., 265, pp. 14234-14241 Lah, M. S., Dixon, M. M., Pattridge, K. A., Stallings, W. C., Fee, J. A., Ludwig, M. L., Structure-function in Escherichia coli iron superoxide dismutase: Comparisons with the manganese enzyme from Thermus thermophilus (1995) Biochemistry, 34, pp. 1646-1660 Brunger, A. T., Adams, P. D., Clore, G. M., Delano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Warren, G. L., Crystallography & NMR system: A new software suite for macromolecular structure determination (1998) Acta Crystallogr. D Biol. Crystallogr., 54 (PART 5), pp. 905-921 Murshudov, G. N., Vagin, A. A., Dodson, E. J., Refinement of macromolecular structures by the maximum-likelihood method (1997) Acta Crystallographica Section D: Biological Crystallography, 53 (3), pp. 240-255. , DOI 10. 1107/S0907444996012255 Jones, T. A., Bergdoll, M., Kjeldgaard, M., O: A macromolecule modeling environment (1990) Crystallogr Model Methods Mol Des, [Pap Symp], pp. 189-199. , C. Bugg, S. Ealick, Springer-Verlag Press Laskowski, R. A., Macarthur, M. W., Moss, M. D., Thorton, J. M., PROCHECK: A program to check the stereochemical quality of protein structure (1993) J. Appl. Crystallogr., 26, pp. 283-291 McCord, J. M., Fridovich, I., Superoxide dismutase. An enzymic function for erythrocuprein (hemocuprein) (1969) J. Biol. Chem., 244, pp. 6049-6055 Tierney, D. L., Fee, J. A., Ludwig, M. L., Penner-Hahn, J. E., X-ray absorption spectroscopy of the iron site in Escherichia coli Fe (III) superoxide dismutase (1995) Biochemistry, 34, pp. 1661-1668 Pedersen, H. L., Willassen, N. P., Leiros, I., The first structure of a cold-adapted superoxide dismutase (SOD): Biochemical and structural characterization of iron SOD from Aliivibrio salmonicida (2009) Acta Crystallogr. Sect. F: Struct. Biol. Cryst. Commun., 65, pp. 84-92 Ludwig, M. L., Metzger, A. L., Pattridge, K. A., Stallings, W. C., Manganese superoxide dismutase from Thermus thermophilus. A structural model refined at 1. 8 A resolution (1991) J. Mol. Biol., 219, pp. 335-358 Vance, C. K., Miller, A. -F., Spectroscopic comparisons of the pH dependencies of Fe-substituted (Mn) superoxide dismutase and Fe-superoxide dismutase (1998) Biochemistry, 37 (16), pp. 5518-5527. , DOI 10. 1021/bi972580r Unsworth, L. D., Van Der Oost, J., Koutsopoulos, S., Hyperthermophilic enzymes - Stability, activity and implementation strategies for high temperature applications (2007) FEBS Journal, 274 (16), pp. 4044-4056. , DOI 10. 1111/j. 1742-4658. 2007. 05954. x Shin, D. S., Didonato, M., Barondeau, D. P., Hura, G. L., Hitomi, C., Berglund, J. A., Getzoff, E. D., Tainer, J. A., Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: Structures, stability, mechanism, and insights into amyotrophic lateral sclerosis (2009) J. Mol. Biol., 385, pp. 1534-1555 Myers, J. K., Pace, C. N., Scholtz, J. M., Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding (1995) Protein Sci., 4, pp. 2138-2148 O'Brien, E. P., Dima, R. I., Brooks, B., Thirumalai, D., Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism (2007) Journal of the American Chemical Society, 129 (23), pp. 7346-7353. , DOI 10. 1021/ja069232+}, document_type={Journal Article, }, affiliation={Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di Monte sant'Angelo, I-80126 Napoli, Italy Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via S. Pansini 5, I-80131 Napoli, Italy Istituto Nazionale di Biostrutture e Biosistemi, Consorzio Interuniversitario, Viale Medaglie d'Oro 305, I-00136 Roma, Italy}, ibbaffiliation={1}, } @article{IBB_ID_11456, author={Russo Krauss I, Parkinson GN, Merlino A, Mattia CA, Randazzo A, Novellino E, Mazzarella L, Sica F}, title={A regular thymine tetrad and a peculiar supramolecular assembly in the first crystal structure of an all-LNA G-quadruplex}, date={2014 Feb}, journal={Acta Crystallogr D Biol Crystallogr (ISSN: 0907-4449, 0907-4449linking)}, year={2014}, fullvolume={484}, volume={484}, pages={362--370}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84894210808&partnerID=40&md5=150ded0c90cbfe5575a524b3aefd43e1}, abstract={Locked nucleic acids (LNAs) are formed by bicyclic ribonucleotides where the O2' and C4' atoms are linked through a methylene bridge and the sugar is blocked in a 3'-endo conformation. They represent a promising tool for therapeutic and diagnostic applications and are characterized by higher thermal stability and nuclease resistance with respect to their natural counterparts. However, structural descriptions of LNA-containing quadruplexes are rather limited, since few NMR models have been reported in the literature. Here, the first crystallographically derived model of an all-LNA-substituted quadruplex-forming sequence 5'-TGGGT-3' is presented refined at 1.7 angstrom resolution. This high-resolution crystallographic analysis reveals a regular parallel G-quadruplex arrangement terminating in a well defined thymine tetrad at the 3'-end. The detailed picture of the hydration pattern reveals LNA-specific features in the solvent distribution. Interestingly, two closely packed quadruplexes are present in the asymmetric unit. They face one another with their 3'-ends giving rise to a compact higher-order structure. This new assembly suggests a possible way in which sequential quadruplexes can be disposed in the crowded cell environment. Furthermore, as the formation of ordered structures by molecular self-assembly is an effective strategy to obtain nanostructures, this study could open the way to the design of a new class of LNA-based building blocks for nanotechnology.}, keywords={G-Quadruplex, Locked Nucleic Acids, Thymine Tetrad, Guanine Quadruplex, Oligonucleotide, Article, Chemical Structure, Chemistry, Thermodynamics, X Ray Crystallography, X-Ray, Models, Molecular, }, references={Battye, T.G.G., Kontogiannis, L., Johnson, O., Powell, H.R., Leslie, A.G.W., (2011) Acta Cryst., D67, pp. 271-28 Beane, R., Gabillet, S., Montaillier, C., Arar, K., Corey, D.R., (2008) Biochemistry, 47, pp. 13147-13149 Beane, R.L., Ram, R., Gabillet, S., Arar, K., Monia, B.P., Corey, D.R., (2007) Biochemistry, 46, pp. 7572-7580 Blanchet, C., Pasi, M., Zakrzewska, K., Lavery, R., (2011) Nucleic Acids Res., 39, pp. W68-W73 Bondensgaard, K., Petersen, M., Singh, S.K., Rajwanshi, V.K., Kumar, R., Wengel, J., Jacobsen, J.P., (2000) Chemistry, 6, pp. 2687-2695 Bonifacio, L., Church, F.C., Jarstfer, M.B., (2008) Int. 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K., (2009) Nucleic Acids Res., 37, pp. W240-W246}, document_type={Journal Article, }, affiliation={Department of Chemical Sciences, University of Naples 'Federico II', Complesso Universitario di Monte sant'Angelo, Via Cinthia, I-80126 Napoli, Italy Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom Institute of Biostructure and Bioimages, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy National Institute Biostructures and Biosystems, Inter-University Consortium, Viale Medaglie d'Oro 305, I-00136 Rome, Italy}, ibbaffiliation={1}, } @article{IBB_ID_12434, author={Caterino M, Merlino A, Balsamo A, Russo Krauss I, Parisi S, Vergara A}, title={Reaction of Hg2+ Insertion into Cysteine Pairs Within Bovine Insulin Crystals Followed via Raman Spectroscopy}, date={2014 Feb}, journal={J Solution Chem (ISSN: 0095-9782)}, year={2014}, fullvolume={315}, volume={315}, pages={135--143}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84894429683&partnerID=40&md5=ff5bdb8fd6dd1e495720a24cbba8d8d2}, abstract={Chemical modifications of protein crystals may be achieved via soaking of reactants from their precipitating solution, through the solvent channel, into the protein matrix. We describe a Raman microscopy approach to follow mercury insertion into cysteine pairs within protein single crystals, via soaking in an aqueous Hg2+ solution. The method has been developed using bovine insulin as the model system. Applying an efficient mercuration protocol, consisting of a first step of disulphide bridge TCEP-induced reduction within the crystal, followed by overnight reaction with a HgCl2 solution, we obtained Hg-derivative crystals. Raman spectra collected on these derivative crystals, kept in the mother liquor, reveal a characteristic Raman band at 335 cm(-1), which has been assigned to a -S-Hg-S- bridge. The analysis provides Raman-based markers of mercury binding to cysteines, and thus of mercury intoxication.}, keywords={Disulfide Bridges, Insulin, Mercury Binding, Protein Crystallization, Raman Spectroscopy, }, references={Park, J.D., Zheng, W., Human exposure and health effects of inorganic and elemental mercury (2012) J. Prev. Med. 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H., The structure of T6 bovine insulin (2005) Acta Crystallogr. Sect. D, 61, pp. 1476-1482. , 10. 1107/S0907444905025771 During, J. R., Cox, A. W., Spectra and structure of organophosphorus compounds. XIV. Infrared and Raman spectra, vibrational assignment and the asymmetric potential function for ethylphosphine and ethylphosphine-d2 (1975) J. Chem. Phys., 63, pp. 2303-2310. , 10. 1063/1. 431681 Hoffmann, G. G., Brockner, W., Steinfatt, I., Bis (n-alkanethiolato) mercury (II) compounds, Hg (SC n H 2n+1) 2 (n = 1 to 10, 12): Preparation methods, vibrational spectra, GC/MS investigations, and exchange reactions with diorganyl disulfides (2001) Inorg. Chem., 40, pp. 977-985. , 1: CAS: 528: DC%2BD3MXnvVOmsw%3D%3D 10. 1021/ic000638b Fahey, R. C., Hunt, J. S., Windham, G. C., On the cysteine and cystine content of proteins. Differences between intracellular and extracellular proteins (1977) J. Mol. Evol., 10, pp. 155-160. , 1: CAS: 528: DyaE1cXjtlCmsQ%3D%3D 10. 1007/BF01751808 Hansen, R. E., Roth, D., Winther, J. R., Quantifying the global cellular thiol-disulfide status (2009) Proc. Natl. Acad. Sci. USA, 106, pp. 422-437. , 1: CAS: 528: DC%2BD1MXhtVelsb4%3D 10. 1073/pnas. 0812149106}, document_type={Journal Article, }, affiliation={Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte sant'Angelo, Via Cintia, 80126 Naples, Italy CNR, Institute of Biostructures and Bioimages, Naples, Italy Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy}, ibbaffiliation={1}, } @article{IBB_ID_12435, author={Messori L, Scaletti F, Massai L, Cinellu MA, Russo Krauss I, Di Martino G, Vergara A, Paduano L, Merlino A}, title={Interactions of gold-based drugs with proteins: crystal structure of the adduct formed between ribonuclease A and a cytotoxic gold(III) compound}, date={2014}, journal={Metallomics (ISSN: 1756-5901, 1756-591x)}, year={2014}, fullvolume={339}, volume={339}, pages={233--236}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84893276097&partnerID=40&md5=6ba50ce6078b2777e720fe9dcdca3ca6}, abstract={The reaction of Auoxo6, a dinuclear gold(III) complex, with the model protein bovine pancreatic ribonuclease is explored here by X-ray diffraction and ESI mass spectrometry. Data provide clues on the processes of adduct formation and of enzyme inhibition and, inductively, on the likely mode of action of this metallodrug.}, keywords={Adduct Formation, Bovine Pancreatic Ribonuclease, Cytotoxic, Dinuclear, Esi Mass Spectrometry, Mode Of Action, Model Proteins, X Ray Diffraction, Gold, Auoxo6, Auranofin, Gold Complex, Histidine, Ligand, Metallodrug, Peroxiredoxin, Prodrug, Thioredoxin Reductase, Unclassified Drug, Antineoplastic Activity, Cattle, Chemical Structure, Complex Formation, Conference Paper, Crystal Structure, Electrospray Mass Spectrometry, Enzyme Activity, Nonhuman, Priority Journal, Animals, Cell Death, Crystallography, X-Ray, Hydrolysis, Molecular, Saccharomyces Cerevisiae, Electrospray Ionization, }, references={Sun, R.W.-Y., Lok, C.-N., Fong, T.T.-H., Li, C.K.-L., Yang, Z.F., Zou, T., Siu, A.F.-M., Che, C.-M., (2013) Chem. Sci., 4, p. 197 Zhang, J.-J., Sun, R.W.-Y., Che, C.-M., (2012) Chem. Commun., 48, p. 3388 Zhang, J.-J., Lu, W., Sun, R.W.-Y., Che, C.-M., (2012) Angew. Chem., Int. Ed., 51, p. 4882 Yan, J.J., Chow, A.L.-F., Leung, C.H., Sun, R.W.-Y., Ma, D.L., Che, C.-M., (2010) Chem. Commun., 46, p. 3893 Li, C.K.-L., Sun, R.W.-Y., Kui, S.C.-F., Zhu, N., Che, C.-M., (2006) Chem.-Eur. J., 12, p. 5253 Nobili, S., Mini, E., Landini, I., Gabbiani, C., Casini, A., Messori, L., (2010) Med. Res. Rev., 30, p. 550 Barnes, K.R., Lippard, S.J., (2004) Metal Ions Biol. Syst., Cisplatin and Related Anticancer Drugs: Recent Advances and Insights, 42, pp. 43-77. , ed. A. Sigel and H. Sigel, Marcel Dekker Inc., New York Basel Netherlands Sun, R.W.-Y., Li, C.K.-L., Ma, D.-L., Yan, J.J., Lock, C.-N., Leung, C.-H., Zhu, N., Che, C.-M., (2010) Chem.-Eur. 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J., Mugesh, G., (2011) Dalton Trans., 40, p. 2099 Richards, F. M., Wyckoff, H. W., (1971) The Enzymes, 4, pp. 647-806. , ed. D. Boyer, Academic Press, San Diego Raines, R. T., (1998) Chem. Rev., 98, p. 1045 Marshal, G. R., Fengand, J. A., Kuster, D. J., (2008) Biopolymers, 90, p. 259 Isab, A. A., Sadler, P. J., (1977) Biochim. Biophys. Acta, 492, p. 322 Cinellu, M. A., Maiore, L., Manassero, M., Casini, A., Arca, M., Fiebig, H. -H., Kelter, G., Messori, L., (2010) ACS Med. Chem. Lett., 1, p. 336}, document_type={Journal Article, }, affiliation={Department of Chemistry Ugo Schiff, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy CNR Institute of Biostructures and Bioimages, Napoli, Italy}, ibbaffiliation={1}, } @article{IBB_ID_11636, author={Russo Krauss I, Messori L, Cinellu MA, Marasco D, Sirignano R, Merlino A}, title={Interactions of gold-based drugs with proteins: the structure and stability of the adduct formed in the reaction between lysozyme and the cytotoxic gold(III) compound Auoxo3}, date={2014}, journal={Dalton T (ISSN: 1477-9226, 1477-9234, 1477-9226linking)}, year={2014}, fullvolume={339}, volume={339}, pages={17483--17488}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84908638607&partnerID=40&md5=89f8874bd9754ddd31b46ec597f6df42}, abstract={The structure and stability of the adduct formed in the reaction between Auoxo3, a dinuclear gold(iii) compound, and the model protein hen egg white lysozyme (HEWL) are investigated by X-ray crystallography, UV-Vis absorption spectroscopy and circular dichroism (CD). It is found that Auoxo3 breaks down completely, undergoes reduction and produces reactive gold(i) species able to bind the protein and form stable derivatives. The behaviour of Auoxo3 is compared with that of two analogous gold(iii) complexes previously studied: a few significant differences are highlighted. The general implications of these new results for the mode of action of cytotoxic gold complexes are discussed.}, keywords={Cytotoxic, }, references={Bernard, P.J., Berners-Price, S.J., (2007) Coord. Chem. Rev., 251, p. 188 Nobili, S., Mini, E., Landini, I., Gabbiani, C., Casini, A., Messori, L., (2010) Med. Res. Rev., 30, p. 550 Barnes, K.R., Lippard, S.J., (2004) Metal Ions Biol. Syst., Cisplatin and Related Anticancer Drugs: Recent Advances and Insights, 42. , ed. A. Sigel and H. Sigel, Marcel Dekker Inc., New York, Basel, Netherlands, p. 43 Sun, R.W.-Y., Li, C.K.-L., Ma, D.-L., Yan, J.J., Lock, C.-N., Leung, C.-H., Zhu, N., Che, C.-M., (2010) Chem.-Eur. 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Crystallogr., 67, p. 355}, document_type={Journal Article, Research Support, Non-U. S. Gov'T, }, affiliation={Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte sant'Angelo, Via CintiaNapoli, Italy CNR Institute of Biostructures and BioimagesNapoli, Italy Department of Pharmacy, University of Naples Federico IINapoli, Italy}, ibbaffiliation={1}, } @article{IBB_ID_52074, author={Pica A, Russo Krauss I, Merlino A, Nagatoishi S, Sugimoto N, Sica F}, title={Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer}, date={2013 Dec}, journal={Febs Journal (ISSN: 1742-464x)}, year={2013}, fullvolume={387}, volume={387}, pages={6581--6588}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84889679159&partnerID=40&md5=1f45d2202a9a3ad23e2a5852b16dc0c8}, abstract={Thrombin plays a pivotal role in the coagulation cascade; therefore, it represents a primary target in the treatment of several blood diseases. The 15-mer DNA oligonucleotide 5-GGTTGGTGTGGTTGG-3, known as thrombin binding aptamer (TBA), is a highly potent inhibitor of the enzyme. TBA folds as an antiparallel chair-like G-quadruplex structure, with two G-tetrads surrounded by two TT loops on one side and a TGT loop on the opposite side. Previous crystallographic studies have shown that TBA binds thrombin exosite I by its TT loops, T3T4 and T12T13. In order to get a better understanding of the thrombin-TBA interaction, we have undertaken a crystallographic characterization of the complexes between thrombin and two TBA mutants, TBAT3 and TBAT12, which lack the nucleobase of T3 and T12, respectively. The structural details of the two complexes show that exosite I is actually split into two regions, which contribute differently to TBA recognition. These results provide the basis for a more rational design of new aptamers with improved therapeutic action.}, keywords={Biosensors, G-Quadruplex, Human Thrombin, Protein-Nucleic Acid Complex, Thrombin Binding Aptamer, Thrombosis, Guanine Quadruplex, Thrombin Binding Aptamer Delta T12, Thrombin Exosite I, Unclassified Drug, Article, Complex Formation, Crystallography, Molecular Mechanics, Molecular Recognition, Priority Journal, Protein Binding, Protein Folding, Protein Function, Protein Interaction, Protein Modification, Structure Analysis, Nucleotide, Circular Dichroism, Crystallization, Mutation, }, references={Janin, J., Rodier, F., Chakrabarti, P., Bahadur, R.P., Macromolecular recognition in the Protein Data Bank (2007) Acta Crystallogr D, 63, pp. 1- Hong, H., Goel, S., Zhang, Y., Cai, W., Molecular imaging with nucleic acid aptamers (2011) Curr Med Chem, 18, pp. 4195-4205 Keefe, A.D., Pai, S., Ellington, A., Aptamers as therapeutics (2010) Nat Rev Drug Discov, 9, pp. 537-550 Hermann, T., Patel, D.J., Adaptive recognition by nucleic acid aptamers (2000) Science, 287, pp. 820-825 Tan, W., Wang, H., Chen, Y., Zhang, X., Zhu, H., Yang, C., Yang, R., Liu, C., Molecular aptamers for drug delivery (2011) Trends Biotechnol, 29, pp. 634-640 Musumeci, D., Montesarchio, D., Polyvalent nucleic acid aptamers and modulation of their activity: A focus on the thrombin binding aptamer (2012) Pharmacol Ther, 136, pp. 202-215 Dhar, S., Gu, F.X., Langer, R., Farokhzad, O.C., Lippard, S.J., Targeted delivery of cisplatin to prostate cancer cells by aptamer functionalized Pt(IV) prodrug-PLGA-PEG nanoparticles (2008) Proc Natl Acad Sci USA, 105, pp. 17356-17361 Bunka, D.H., Platonova, O., Stockley, P.G., Development of aptamer therapeutics (2010) Curr Opin Pharmacol, 10, pp. 557-562 Bompiani, K.M., Woodruff, R.S., Becker, R.C., Nimjee, S.M., Sullenger, B.A., Antidote control of aptamer therapeutics: The road to a safer class of drug agents (2012) Curr Pharm Biotechnol, 13, pp. 1924-1934 Avino, A., Fabrega, C., Tintore, M., Eritja, R., Thrombin binding aptamer, more than a simple aptamer: Chemically modified derivatives and biomedical applications (2012) Curr Pharm des, 18, pp. 2036-2047 Huntington, J.A., Molecular recognition mechanisms of thrombin (2005) J Thromb Haemost, 3, pp. 1861-1872 Fenton II, J.W., Thrombin specificity (1981) Ann N y Acad Sci, 370, pp. 468-495 Adams, T.E., Huntington, J.A., Thrombin-cofactor interactions: Structural insights into regulatory mechanisms (2006) Arterioscler Thromb Vasc Biol, 26, pp. 1738-1745 Welsby, I.J., Monroe, D.M., Lawson, J.H., Hoffmann, M., Recombinant activated factor VII and the anaesthetist (2005) Anaesthesia, 60, pp. 1203-1212 Bock, L.C., Griffin, L.C., Latham, J.A., Vermaas, E.H., Toole, J.J., Selection of single-stranded DNA molecules that bind and inhibit human thrombin (1992) Nature, 355, pp. 564-566 Russo Krauss, I., Pica, A., Merlino, A., Mazzarella, L., Sica, F., Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer (2013) Acta Crystallogr D, 69. , doi: 10.1107/S0907444913022269 Russo Krauss, I., Merlino, A., Randazzo, A., Novellino, E., Mazzarella, L., Sica, F., High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity (2012) Nucleic Acids Res, 40, pp. 8119-8128 MacAya, R.F., Schultze, P., Smith, F.W., Roe, J.A., Feigon, J., Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution (1993) Proc Natl Acad Sci USA, 90, pp. 3745-3749 Burge, S., Parkinson, G.N., Hazel, P., Todd, A.K., Neidle, S., Quadruplex DNA: Sequence, topology and structure (2006) Nucleic Acids Res, 34, pp. 5402-5415 Borbone, N., Bucci, M., Oliviero, G., Morelli, E., Amato, J., D'Atri, V., D'Errico, S., Piccialli, G., Investigating the role of T7 and T12 residues on the biological properties of thrombin-binding aptamer: Enhancement of anticoagulant activity by a single nucleobase modification (2012) J Med Chem, 55, pp. 10716-10728 Sagi, J., G-quadruplexes incorporating modified constituents: A review (2013) J Biomol Struct Dyn, , in press. doi: 10.1080/07391102.2013.775074 Bunka, D.H., Stockley, P.G., Aptamers come of age - 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M., Becker, C. F., Giesel, G. M., Marques, A. F., Cargnelutti, M. T., De Oliveira Neto, M., Monteiro, R. Q., Polikarpov, I., Structural and thermodynamic analysis of thrombin: suramin interaction in solution and crystal phases (2009) Biochim Biophys Acta, 1794, pp. 873-881 Davis, J. T., G-quartets 40 years later: From 5 -GMP to molecular biology and supramolecular chemistry (2004) Angew Chem Int Ed Engl, 43, pp. 668-698 McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., Read, R. J., Phaser crystallographic software (2007) J Appl Crystallogr, 40, pp. 658-674 Brunger, A. T., Adams, P. D., Clore, G. M., Delano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Pannu, N. S., Crystallography and NMR system: A new software suite for macromolecular structure determination (1998) Acta Crystallogr D, 54, pp. 905-921 Vagin, A. A., Steiner, R. A., Lebedev, A. A., Potterton, L., McNicholas, S., Long, F., Murshudov, G. 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M., Main-chain bond lengths and bond angles in protein structures (1993) J Mol Biol, 231, pp. 1049-1067}, document_type={Journal Article, }, affiliation={Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy Institute of Biostructures and Bioimaging, CNR, Naples, Italy Medical Proteomics Laboratory, Institute of Medical Science, University of Tokyo, Japan Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Japan Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan Interuniversity Consortium of Structural and Systems Biology, Rome, Italy}, ibbaffiliation={1}, } @article{IBB_ID_52073, author={Russo Krauss I, Pica A, Merlino A, Mazzarella L, Sica F}, title={Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer}, date={2013 Dec}, journal={Acta Crystallogr D Biol Crystallogr (ISSN: 0907-4449, 0907-4449linking)}, year={2013}, fullvolume={384}, volume={384}, pages={2403--2411}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84889634850&partnerID=40&md5=8ea8ccc2fa482b88751ad6b0a6fb5aa6}, abstract={Potent second-generation thrombin aptamers adopt a duplex-quadruplex bimodular folding and recognize thrombin exosite II with very high affinity and specificity. A sound model of these oligonucleotides, either free or in complex with thrombin, is not yet available. Here, a structural study of one of these aptamers, HD22-27mer, is presented. The crystal structure of this aptamer in complex with thrombin displays a novel architecture in which the helical stem is enchained to a pseudo-G-quadruplex. The results also underline the role of the residues that join the duplex and quadruplex motifs and control their recruitment in thrombin binding. © 2013 International Union of Crystallography.}, keywords={Aptamers, Duplex-Quadruplex Motifs, Thrombin, Thrombin Aptamer, Article, Chemical Structure, Chemistry, Conformation, Human, Metabolism, Nucleotide Sequence, Protein Binding, X Ray Crystallography, Base Sequence, X-Ray, Models, Molecular, Nucleic Acid Conformation, Chemistry Metabolism, Duplex Quadruplex Motifs, }, references={Balasubramanian, S., Neidle, S., (2009) Curr. Opin. Chem. 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Struct., 23, pp. 703-730}, document_type={Journal Article, }, affiliation={Department of Chemical Sciences, University of Naples 'Federico II', Complesso Universitario di Monte Sant'Angelo, I-80126 Naples, Italy Institute of Biostructure and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Naples, Italy National Institute Biostructures and Biosystems, Inter-University Consortium, Viale Medaglie d'Oro 305, I-00136 Rome, Italy}, ibbaffiliation={1}, } @article{IBB_ID_52076, author={Sica F, Pica A, Merlino A, Russo Krauss I, Ercole C, Picone D}, title={The multiple forms of bovine seminal ribonuclease: Structure and stability of a C-terminal swapped dimer}, date={2013 Nov 29}, journal={Febs Lett (ISSN: 0014-5793, 0014-5793print, 1873-3468electronic)}, year={2013}, fullvolume={328}, volume={328}, pages={3755--3762}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84887989317&partnerID=40&md5=69ab07525e4c7e1b7cd5d22f32504202}, abstract={Bovine seminal ribonuclease (BS-RNase) acquires an interesting anti-tumor activity associated with the swapping on the N-terminal. The first direct experimental evidence on the formation of a C-terminal swapped dimer (C-dimer) obtained from the monomeric derivative of BS-RNase, although under non-native conditions, is here reported. The X-ray model of this dimer reveals a quaternary structure different from that of the C-dimer of RNase A, due to the presence of three mutations in the hinge peptide 111-116. The mutations increase the hinge peptide flexibility and decrease the stability of the C-dimer against dissociation. The biological implications of the structural data are also discussed. Structure summary of protein interactions: BS-RNase and BS-RNase bind by x-ray crystallography (View interaction) BS-RNase and BS-RNase bind by molecular sieving (1, 2) BS-RNase and BS-RNase bind by blue native page (View interaction) (C) 2013 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.}, keywords={Bovine Seminal Ribonuclease, C-Terminal 3d Domain Swapping, Cytotoxic Rnase, Hinge Peptide, Multiple Swapping, Dimer, Isoenzyme, Amino Acid Sequence, Article, Carboxy Terminal Sequence, Chemical Model, Controlled Study, Enzyme Stability, Enzyme Structure, Mutation, Nonhuman, Priority Journal, Protein Function, Protein Quaternary Structure, Seminal Plasma, X Ray, Artificial Dimer Of Bs-Rnase Obtained By Incubation In Acetic Acid Of Mbs And Lyophilisation, Artificial Dimer Of Staa-Bs-Rnase Obtained By Incubation In Acetic Acid Of Staa-Mbs And Lyophilisation, Bovine Pancreatic Ribonuclease (ec 3 1 2 27 5), Covalent Swapped Isomer Of Bs-Rnase, Covalent Unswapped Isomer Of Bs-Rnase, D(art)-Bs, D(art)-Staa-Bs, Dithiothreitol, G16s N17t P19a S20a Variant Of Bs-Rnase, G16s N17t P19a S20a Variant Of Mbs, Iodoacetamide, L28q Variant Of Mbs, L28q-Mbs, M×m, Monomeric Derivative Of Bs-Rnase With Cysteines 31 And 32 Either Linked To Glutathione Moieties Or Alkylated With Iodoacetamide, Ncd-Bs, Non-Covalent Swapped Dimer Of Bs-Rnase With Cysteines 31 And 32 Linked To Iodoacetamide, Obtained By Selective Reduction Of The Swapped Isoform And Iodoalkylation, P19a L28q Variant Of Bs-Rnase, P19a L28q Variant Of Mbs, Palq-Bs-Rnase, Palq-Mbs, R80s Variant Of Staa-Bs-Rnase, R80s Variant Of Staa-Mbs, R80s-Staa-Bs-Rnase, R80s-Staa-Mbs, Ribonuclease Inhibitor, Size-Exclusion Chromatography, Animals, Cattle, Crystallography, X-Ray, Endoribonucleases, Molecular Sequence Data, Protein Multimerization, Protein Structure, Tertiary, D (art)-Bs, D (art)-Staa-Bs, }, references={Liu, Y., Eisenberg, D., 3D domain swapping: As domains continue to swap (2002) Protein Sci., 11, pp. 1285-129 Vitagliano, L., Adinolfi, S., Sica, F., Merlino, A., Zagari, A., A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease (1999) J. 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Pymol, , http: //wwwpymolorg, Schrodinger, LLC}, document_type={Journal Article, }, affiliation={Department of Chemical Sciences, University of Naples 'Federico II', via Cintia, 80126 Naples, Italy Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Naples, Italy National Institute Biostructures and Biosystems, Inter-University Consortium, Viale Medaglie d'Oro 305, I-00136 Rome, Italy}, ibbaffiliation={1}, } @article{IBB_ID_12438, author={Vergara A, Russo Krauss I, Montesarchio D, Paduano L, Merlino A}, title={Investigating the Ruthenium Metalation of Proteins: X-ray Structure and Raman Microspectroscopy of the Complex between RNase A and AziRu}, date={2013 Oct 7}, journal={Inorg Chem (ISSN: 0020-1669, 1520-510x, 1520-510xelectronic)}, year={2013}, fullvolume={307}, volume={307}, pages={10714--10716}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84885157077&partnerID=40&md5=e4877193b33ab5d1ca7c09a9db438965}, abstract={A Raman-assisted crystallographic study on the adduct between AziRu, a Ru(III) complex with high antiproliferative activity, and RNase A is presented. The protein structure is not perturbed significantly by the Ru label. The metal coordinates to ND atoms of His105 or of His119 imidazole rings, losing all of its original ligands but retaining octahedral, although distorted, coordination geometry. The AziRu binding inactivates the enzyme, suggesting that its antitumor action can be exerted by a mechanism of competitive inhibition.}, keywords={Antineoplastic Agent, Coordination Compound, Pancreatic Ribonuclease, Protein, Ruthenium, Article, Chemical Structure, Chemistry, Raman Spectrometry, X Ray Crystallography, Coordination Complexes, X-Ray, Molecular Structure, Spectrum Analysis, Coordination Complexes Chemistry, Proteins Chemistry, Pancreatic Chemistry, Ruthenium Chemistry, }, references={Ang, W.H., Casini, A., Sava, G., Dyson, P.J., (2011) J. Org. Chem., 696, p. 98 Komeda, S., Casini, A., (2012) Curr. Top. Med. 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Chem., 122, p. 1705 Balakrishnan, A. R., Ramasubbu, N., Varughese, K. I., Parthasarathy, R., (1997) Proc. Natl. Acad. Sci. U. S. A., 94, p. 9620 George, G. N., Pickering, I. J., Pushie, M. J., Nienaber, K., Hackett, M. J., Ascone, I., Hedman, B., Lay, P. A., (2012) J. Synchrotron Radiat., 19, p. 875}, document_type={Journal Article, Research Support, Non-U. S. Gov'T, }, affiliation={Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy CNR Institute of Biostructures and Bioimages, Napoli, Italy CSGI (Consorzio per Lo Sviluppo Dei Sistemi A Grande Interfase), Florence, Italy}, ibbaffiliation={1}, } @article{IBB_ID_10754, author={Russo Krauss I, Merlino A, Vergara A, Sica F}, title={An overview of biological macromolecule crystallization}, date={2013 May 31}, journal={Int J Mol Sc (ISSN: 1422-0067, 1661-6596, 1422-0067electronic)}, year={2013}, fullvolume={1010}, volume={1010}, pages={11643--11691}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84879013039&partnerID=40&md5=17d40cda9df6f6067d1021ce8aa1886c}, abstract={The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality.}, keywords={Crystallization, Membrane, New Methodologies, Nucleic Acid, Protein, Antibody, Fv Antibody, Guanine Quadruplex, Immunoglobulin F(ab) Fragment, Membrane Protein, Unclassified Drug, Batch Process, Chemical Reaction Kinetics, Complex Formation, Crystallography, Density Gradient, Electric Field, Free Interface Diffusion, Gel Counter Diffusion, Gel Crystallization, Lipid Bilayer, Macromolecule, Magnetic Field, Microdialysis, Nucleic Acid Structure, Precipitation, Protein Nucleic Acid Interaction, Review, Temperature Sensitivity, Thermostability, Water Vapor, X Ray Diffraction, Immunoglobulin F (ab) Fragment, }, references={McPherson, A., Protein crystallization in the structural genomics era (2004) J. Struct. Funct. 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J., Polarization-resolved second-harmonic generation microsc}, document_type={Journal Article, }, affiliation={Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, Napoli I-80126, Italy Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy}, ibbaffiliation={1}, } @article{IBB_ID_51895, author={Pica A, Russo Krauss I, Castellano I, La Cara F, Graziano G, Sica F, Merlino A}, title={Effect Of Nacl On The Conformational Stability Of The Thermophilic Gamma-Glutamyltranspeptidase From Geobacillus Thermodenitrificans: Implication For Globular Protein Halotolerance}, date={2013 Jan}, journal={Bba-Gen Subjects (ISSN: 1570-9639, 0006-3002, 0925-4439)}, year={2013}, fullvolume={334}, volume={334}, pages={149--157}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84870170311&partnerID=40&md5=c5e8899857de733b34befc5883cc442c}, abstract={The transpeptidation activity of gamma-glutamyltranspeptidase from Geobacillus thermodenitrificans (GthGT) is negligible and the enzyme is highly thermostable. Here we have examined the effect of concentrated NaCl solutions on structure, stability, dynamics and enzymatic activity of GthGT. The protein exhibited hydrolytic activity over a broad range of NaCl concentrations. Even at 4. 0 M NaCl, GthGT retained more than 90% of the initial activity and showed unaltered fluorescence emission, secondary structure and acrylamide quenching on tryptophan fluorescence. Furthermore, at 2. 8 M and 4. 0 M NaCl the temperature-induced unfolding profiles are dramatically changed with large (>20 degrees C) positive shifts in the denaturation temperature. These features make GthGT an ideal system to be used in industrial processes that require high temperatures and high-salt environments. A general explanation of the NaCl effect by means of a statistical thermodynamic model is also provided, together with an analysis of residue distribution between protein surface and interior in 15 non-redundant families of halophilic and non-halophilic proteins. The results are in line with a comparative sequence and structural analysis between halophilic and non-halophilic gamma-glutamyltranspeptidases which revealed that a major role in halotolerance should be played by solvent exposed negatively charged residues. (C) 2012 Elsevier B. V. All rights reserved}, keywords={Circular Dichroism, Fluorescence, Gamma-Glutamyl Transferase, Gamma-Glutamyl Transpeptidase, Nacl, Protein Stabilization, Acrylamide, Gamma Glutamyltransferase, Globular Protein, Sodium Chloride, Solvent, Tryptophan, Amino Acid Sequence, Article, Conformation, Denaturation, Geobacillus, Nonhuman, Priority Journal, Protein Family, Protein Unfolding, Salt Tolerance, Temperature, Thermodynamics, Bacterial Proteins, Enzyme Stability, Gamma-Glutamyltransferase, Protein Structure, Secondary, Geobacillus Thermodenitrificans, }, references={Meister, A., On the enzymology of amino acid transport (1973) Science, 180, pp. 33-3 Meister, A., Anderson, M.E., Glutathione (1983) Annu. Rev. 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L., Biophysical characterization of Bacillus licheniformis and Escherichia coli -glutamyltranspeptidases: A comparative analysis (2011) Int. J. Biol. Macromol., 48, pp. 414-422 Bradford, M. M., A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding (1976) Anal. Biochem., 72, pp. 248-254 Eftink, M. R., Ghiron, C. A., Fluorescence quenching studies with proteins (1981) Anal. Biochem., 114, pp. 199-227 Tate, S. S., Meister, A., Interaction of -glutamyl transpeptidase with amino acids, dipeptides, and derivatives and analogs of glutathione (1974) J. Biol. Chem., 249, pp. 7593-7602 Wright, D. B., Banks, D. D., Lohman, J. R., Hilsenbeck, J. L., Gloss, L. M., The effect of salts on the activity and stability of Escherichia coli and Haloferax volcanii dihydrofolate reductases (2002) J. Mol. Biol., 323, pp. 327-344 Waldron, T. T., Schrift, G. L., Murphy, K. P., The salt-dependence of a protein-ligand interaction: Ion-protein binding energetics (2005) J. Mol. Biol., 346, pp. 895-905 Dragan, A. I., Li, Z., Makeyeva, E. N., Milgotina, E. I., Liu, Y., Crane-Robinson, C., Privalov, P. L., Forces driving the binding of homeodomains to DNA (2006) Biochemistry, 45, pp. 141-151 Ashbaugh, H. S., Pratt, L. R., Scaled-particle theory and the length scales of hydrophobicity (2006) Rev. Mod. Phys., 78, pp. 159-178 Rees, D. C., Robertson, A. D., Some thermodynamic implications for the thermostability of proteins (2001) Protein Sci., 10, pp. 1187-1194 Pace, C. N., Hebert, E. J., Shaw, K. L., Schell, D., Both, V., Krajcikova, D., Sevcik, J., Grimsley, G. R., Conformational stability and thermodynamics of folding of ribonucleases Sa, Sa2 and Sa3 (1998) J. Mol. Biol., 279, pp. 271-286 Nandi, P. K., Leclerc, E., Marc, D., Unusual property of prion protein unfolding in neutral salt solution (2002) Biochemistry, 41, pp. 11017-11024 Antal k, M., Fedunov, D., B gelov, J., Conformational transition of cytochrome c (2010) Open Macromol. J., 4, pp. 53-55}, document_type={Journal Article, }, affiliation={Department of Chemical Sciences, Università di Napoli Federico II, Complesso di Monte S. Angelo, Via Cinthia, I-80126 Napoli, Italy Institute of Protein Biochemistry, CNR, Naples, Italy Dipartimento di Scienze per la Biologia, la Geologia e l'Ambiente, Università Del Sannio, Benevento, Italy Istituto di Biostrutture e Bioimmagini, CNR, Naples, Italy}, ibbaffiliation={1}, } @article{IBB_ID_10761, author={Russo Krauss I, Pica A, Merlino A, Mazzarella L, Sica F}, title={Duplex-Quadruplex Motifs In A Novel Structural Organization Cooperatively Contribute To Thrombin Binding Of Hd22-27mer}, date={2013}, journal={Acta Crystallogr D Biol Crystallogr (ISSN: 0907-4449, 0907-4449linking)}, year={2013}, fullvolume={267}, volume={267}, pages={2403--2411}, url={}, abstract={}, keywords={, }, references={}, document_type={Journal Article, }, affiliation={}, ibbaffiliation={1}, } @article{IBB_ID_10760, author={Vergara A, Montesarchio D, Russo Krauss I, Paduano L, Merlino A}, title={Investigating The Ruthenium Metallation Of Proteins: X-Ray Structure And Raman Microspectroscopy Of The Complex Between Rnase A And Aziru}, date={2013}, journal={Inorg Chem (ISSN: 0020-1669, 1520-510xe, 1520-510xelectronic)}, year={2013}, fullvolume={293}, volume={293}, pages={10714--10716}, url={}, abstract={}, keywords={, }, references={}, document_type={Journal Article, }, affiliation={}, ibbaffiliation={1}, } @article{IBB_ID_52306, author={Russo Krauss I, Merlino A, Randazzo A, Novellino E, Mazzarella L, Sica F}, title={High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity}, date={2012 Sep}, journal={Nucleic Acids Res (ISSN: 0305-1048, 1362-4962, 1362-4962electronic)}, year={2012}, fullvolume={556}, volume={556}, pages={8119--8128}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84870535712&partnerID=40&md5=9d7b4dd51a4851550419d9da18feb223}, abstract={The G-quadruplex architecture is a peculiar structure adopted by guanine-rich oligonucleotidic sequences, and, in particular, by several aptamers, including the thrombin-binding aptamer (TBA) that has the highest inhibitory activity against human alpha-thrombin. A crucial role in determining structure, stability and biological properties of G-quadruplexes is played by ions. In the case of TBA, K(+) ions cause an enhancement of the aptamer clotting inhibitory activity. A detailed picture of the interactions of TBA with the protein and with the ions is still lacking, despite the importance of this aptamer in biomedical field for detection and inhibition of alpha-thrombin. Here, we fill this gap by presenting a high-resolution crystallographic structural characterization of the thrombin-TBA complex formed in the presence of Na(+) or K(+) and a circular dichroism study of the structural stability of the aptamer both free and complexed with alpha-thrombin, in the presence of the two ionic species. The results indicate that the different effects exerted by Na(+) and K(+) on the inhibitory activity of TBA are related to a subtle perturbation of a few key interactions at the protein-aptamer interface. The present data, in combination with those previously obtained on the complex between alpha-thrombin and a modified aptamer, may allow the design of new TBA variants with a pharmacological performance enhancement.}, keywords={Aptamer, Calcium Ion, Cation, Potassium Ion, Thrombin, Thrombin Binding Aptamer, Unclassified Drug, Article, Circular Dichroism, Crystallography, Human, Priority Journal, Protein Analysis, Protein Function, Protein Protein Interaction, Protein Stability, Protein Structure, Nucleotide, X-Ray, Models, Molecular, Sodium, }, references={Gellert, M., Lipsett, M.N., Davies, D.R., Helix formation by guanylic acid (1962) Proc. Natl. Acad. Sci. USA, 48, pp. 2013-201 Williamson, J.R., G-quartet structures in telomeric DNA (1994) Annu. Rev. Biophys. Biomol. 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Chem., 7, pp. 4677-4684}, document_type={Journal Article, }, affiliation={Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Via Cintia, I-80126 Napoli, Italy Istituto di Biostrutture e Bioimmagini, C.N.R., Via Mezzocannone 16, I-80134 Napoli, Italy Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli Federico II, Via D. Montesano 49, I-80131 Napoli, Italy}, ibbaffiliation={1}, } @article{IBB_ID_50395, author={Pica A, Russo Krauss I, Castellano I, Rossi M, La Cara F, Graziano G, Sica F, Merlino A}, title={Exploring The Unfolding Mechanism Of Gamma-Glutamyltranspeptidases: The Case Of The Thermophilic Enzyme From Geobacillus Thermodenitrificans}, date={2012 Apr}, journal={Bba-Gen Subjects (ISSN: 1570-9639, 0006-3002, 0925-4439)}, year={2012}, fullvolume={381}, volume={381}, pages={571--577}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84857350575&partnerID=40&md5=d5272471456f5ca8da76a33763b84090}, abstract={γ-glutamyltranspeptidases (γ-GTs) are ubiquitous enzymes that catalyze the hydrolysis of γ-glutamyl bonds in glutathione and glutamine and the transfer of the released γ-glutamyl group to amino acids or short peptides. These enzymes are generally synthesized as precursor proteins, which undergo an intra-molecular autocatalytic cleavage yielding a large and a small subunit. In this study, circular dichroism and intrinsic fluorescence measurements have been used to investigate the structural features and the temperature- and guanidinium hydrochloride (GdnHCl)-induced unfolding of the mature form of the γ-GT from Geobacillus thermodenitrificans (GthGT) and that of its T353A mutant, which represents a mimic of the precursor protein. Data indicate that a) the mutant and the mature GthGT have a different secondary structure content and a slightly different exposure of hydrophobic regions, b) the thermal unfolding processes of both GthGT forms occur through a three-state model, characterized by a stable intermediate species, whereas chemical denaturations proceed through a single transition, c) both GthGT forms exhibit remarkable stability against temperature, but they do not display a strong resistance to the denaturing action of GdnHCl. These findings suggest that electrostatic interactions significantly contribute to the protein stability and that both the precursor and the mature form of GthGT assume compact and stable conformations to resist to the extreme temperatures where G. thermodenidrificans lives. Owing to its thermostability and unique catalytic properties, GthGT is an excellent candidate to be used as a glutaminase in food industry. © 2012 Elsevier B.V. All rights reserved.}, keywords={γ-Glutamyltranspeptidases, Chemical Denaturation, Circular Dichroism, Intermediate State, Protein Stability, Thermal Unfolding, Gamma Glutamyltransferase, Guanidine, Article, Enzyme Stability, Enzyme Structure, Fluorescence, Geobacillus, Geobacillus Thermodenitrifican, Nonhuman, Priority Journal, Protein Unfolding, Spectroscopy, Temperature, Amino Acid Substitution, Anilino Naphthalenesulfonates, Bacterial Proteins, Fluorescent Dyes, Gamma-Glutamyltransferase, Hydrogen-Ion Concentration, Hydrophobic And Hydrophilic Interactions, Mutagenesis, Site-Directed, Protein Structure, Secondary, Spectrometry, Transition Temperature, Chemistry, Bacterial Proteins Chemistry, Genetics, Geobacillus Enzymology, Gamma-Glutamyltransferase Chemistry, Anilino Naphthalenesulfonates Chemistry, Bacterial Proteins Chemistry Genetics, Fluorescent Dyes Chemistry, Guanidine Chemistry, Gamma-Glutamyltransferase Chemistry Genetics, }, references={Tate, S.S., Meister, A., γ-glutamyltranspeptidase: Catalytic, structural and functional aspects (1981) Mol. 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M., Growth retardation and cysteine deficiency in - glutamyltranspeptidase-deficient mice (1996) Proc. Natl. Acad. Sci. U. S. A., 93, pp. 7923-7926 Lee, D. H., Jacobs, Jr. D. R., Gross, M., Kiefe, C. I., Roseman, J., Lewis, C. E., Steffes, M., -glutamyltransferase is a predictor of incident diabetes and hypertension: The Coronary Artery Risk Development in Young Adults (CARDIA) Study (2003) Clin. Chem., 49, pp. 1358-1366 Jean, J. C., Liu, Y., Brown, L. A., Marc, R. E., Klings, E., Joyce-Brady, M., -glutamyltransferase deficiency results in lung oxidant stress in normoxia (2002) Am. J. Physiol. Lung Cell. Mol. Physiol., 283, pp. 766-L776 Kinlough, C. L., Poland, P. A., Bruns, J. B., Hughey, R. P., -glutamyltranspeptidase: Disulfide bridges, propeptide cleavage, and activation in the endoplasmic reticulum (2005) Methods Enzymol., 401, pp. 426-449 Lyu, R. C., Hu, H. Y., Kuo, L. Y., Lo, H. F., Ong, P. L., Chang, H. P., Lin, L. L., Role of the conserved Thr399 and Thr417 residues of Bacillus licheniformis -glutamyltranspeptidase as evaluated by mutational analysis (2009) Curr. Microbiol., 59, pp. 101-106 Yang, J. C., Liang, W. C., Chen, Y. Y., Chi, M. C., Lo, H. F., Chen, H. L., Lin, L. L., Biophysical characterization of Bacillus licheniformis and Escherichia coli -glutamyltranspeptidases: A comparative analysis (2011) Int J Biol Macromol, 48, pp. 414-422 Ong, P. L., Yao, Y. F., Weng, Y. M., Hsu, W. H., Lin, L. L., Residues Arg114 and Arg337 are critical for the proper function of Escherichia coli -glutamyltranspeptidase (2008) Biochem. Biophys. Res. Commun., 366, pp. 294-300 Chang, H. P., Liang, W. C., Lyu, R. C., Chi, M. C., Wang, T. F., Su, K. L., Hung, H. C., Lin, L. L., Effects of C-terminal truncation on autocatalytic processing of Bacillus licheniformis -glutamyltranspeptidase (2010) Biochemistry (Mosc), 75, pp. 919-929 Hsu, W. H., Ong, P. L., Chen, S. C., Lin, L. L., Contribution of Ser463 residue to the enzymatic and autoprocessing activities of Escherichia coli -glutamyltranspeptidase (2009) Indian J. Biochem. Biophys., 46, pp. 281-288 Hung, C. P., Yang, J. C., Chen, J. H., Chi, M. C., Lin, L. L., Unfolding analysis of the mature and unprocessed forms of Bacillus licheniformis -glutamyltranspeptidase (2011) J. Biol. Phys., 37, pp. 463-475 Bradford, M. M., A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding (1976) Anal. Biochem., 72, pp. 248-254 Rumfeldt, J. A., Galvagnion, C., Vassall, K. A., Meiering, E. M., Conformational stability and folding mechanisms of dimeric proteins (2008) Prog. Biophys. Mol. Biol., 98, pp. 61-84 Mayo, S. L., Baldwin, R. L., Guanidinium chloride induction of partial unfolding in amide proton exchange in RNase A (1993) Science, 262, pp. 873-876 Nandi, P. K., Robinson, D. R., Effects of urea and guanidine hydrochloride on peptide and nonpolar groups (1984) Biochemistry, 23, pp. 6661-6668}, document_type={Journal Article, }, affiliation={Department of Chemical Sciences, University of Naples Federico II, Complesso di Monte S. Angelo, Via Cinthia, I-80126 Napoli, Italy Istituto di Biochimica Delle Proteine, CNR, Naples, Italy Dipartimento di Scienze Biologiche Ed Ambientali, Università Del Sannio, Benevento, Italy Istituto di Biostrutture e Bioimmagini, CNR, Naples, Italy}, ibbaffiliation={1}, } @article{IBB_ID_10742, author={Merlino A, Russo Krauss I, Rossi B, De Vendittis A, Marco S, De Vendittis E, Vergara A, Sica F}, title={Identification of an active dimeric intermediate populated during the unfolding process of the cambialistic superoxide dismutase from Streptococcus mutans}, date={2012 Mar}, journal={Biochimie (ISSN: 0300-9084, 1638-6183, 1638-6183electronic)}, year={2012}, fullvolume={342}, volume={342}, pages={768--775}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84857051056&partnerID=40&md5=08a1aee43a84b31a20c1136b81ec0b01}, abstract={Superoxide dismutases are enzymes that protect biological systems against oxidative damage caused by superoxide radicals. In this paper, a detailed characterization is presented on the stability of SmSOD, the dimeric cambialistic superoxide dismutase from the dental pathogenic microorganism Streptococcus mutans, towards temperature and guanidine hydrochloride. Thermal and chemical denaturations were investigated by means of circular dichroism, fourth-derivative UV spectroscopy and fluorescence measurements. Data indicate that SmSOD is endowed with a significant thermostability and that both its thermal and guanidine hydrochloride-induced unfolding processes occur through a three-state model, characterized by a catalytically active dimeric intermediate species. To our knowledge, SmSOD is the smallest known dimeric protein that populates a well-structured active dimeric rather than a monomeric intermediate during unfolding processes. (C) 2011 Elsevier Masson SAS. All rights reserved.}, keywords={Chemical Stability, Dimeric Intermediate, Superoxide Dismutase, Thermal Stability, Unfolding, Guanidine, Article, Circular Dichroism, Enzyme Active Site, Enzyme Activity, Enzyme Denaturation, Enzyme Stability, Enzyme Structure, Fluorescence Analysis, Molecular Model, Nonhuman, Protein Unfolding, Streptococcus Mutans, Structure Analysis, Thermostability, Ultraviolet Spectroscopy, Bacterial Proteins, Protein Folding, Chemistry Metabolism, Streptococcus Mutans Enzymology, }, references={Matthews, C.R., Pathway of protein folding (1993) Annu. Rev. Biochem., 62, pp. 653-68 Neet, K.E., Timm, D.E., Conformational stability of dimeric proteins: Quantitative studies by equilibrium denaturation (1994) Protein Sci., 3, pp. 2167-2174 Rumfeldt, J.A., Galvagnion, C., Vassall, K.A., Meiering, E.M., Conformational stability and folding mechanisms of dimeric proteins (2008) Prog. Biophys. Mol. 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Angelo, Via Cinthia, I-80126 Naples, Italy Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli Federico II, Via Pansini 5, I-80131 Napoli, Italy}, ibbaffiliation={1}, } @article{IBB_ID_10746, author={Russo Krauss I, Sica F, Mattia CA, Merlino A}, title={Increasing the X-ray diffraction power of protein crystals by dehydration: the case of bovine serum albumin and a survey of literature data}, date={2012 Mar}, journal={Int J Mol Sc (ISSN: 1422-0067, 1661-6596, 1422-0067electronic)}, year={2012}, fullvolume={457}, volume={457}, pages={3782--3800}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84858964808&partnerID=40&md5=09a3a8a6828305342d630265f6ff2de3}, abstract={Serum albumin is one of the most widely studied proteins. It is the most abundant protein in plasma with a typical concentration of 5 g/100 mL and the principal transporter of fatty acids in plasma. While the crystal structures of human serum albumin (HSA) free and in complex with fatty acids, hemin, and local anesthetics have been characterized, no crystallographic models are available on bovine serum albumin (BSA), presumably because of the poor diffraction power of existing hexagonal BSA crystals. Here, the crystallization and diffraction data of a new BSA crystal form, obtained by the hanging drop method using MPEG 5K as precipitating agent, are presented. The crystals belong to space group C2, with unit-cell parameters a = 216.45 A, b = 44.72 A, c = 140.18 A, beta = 114.5°. Dehydration was found to increase the diffraction limit of BSA crystals from ~8 A to 3.2 A, probably by improving the packing of protein molecules in the crystal lattice. These results, together with a survey of more than 60 successful cases of protein crystal dehydration, confirm that it can be a useful procedure to be used in initial screening as a method of improving the diffraction limits of existing crystals.}, keywords={Crystal Dehydration, Crystal Quality, Post-Crystallization Treatment, Protein Crystallization, Serum Albumin, X-Ray Crystallography, Apolipoprotein A4, Bovine Serum Albumin, Cytochrome C Oxidase, Dipeptidyl Peptidase, Fatty Acid, Fatty Acid Synthase, Fatty Acid Transporter, Ferredoxin, Ferredoxin Reductase, Glutaryl 7 Aminocephalosporanic Acid Acylase, Hemin, Human Serum Albumin, Lipase Foldase Complex, Local Anesthetic Agent, Maoc Like Dehydratase, Monoclinic Lysozyme, N Acetylglucosamine 1 Phosphate Uridyltransferase, Nectin 1 Ec Complex, Penicillin Amidase, Peptide Deformylase, Phosphoglycerate Kinase, Plasma Protein, Porphobilinogen Synthase, Pyruvate Dehydrogenase, Stat1 Protein, Tetragonal Lysozyme, Thioredoxin, Trehalose Phosphorylase, Tricom Interacting Factor F3, Unclassified Drug, Article, Complex Formation, Crystal Structure, Desiccation, Hanging Drop Vapor Diffusion Method, X Ray Diffraction, }, references={Carter, D.C., Ho, J.X., Structure of serum albumin (1994) Adv. 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K., Prakash, B., Structure of N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) from Mycobacterium tuberculosis in a cubic space group (2009) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun, 65, pp. 435-439 Yap, T. L., Chen, Y. L., Xu, T., Wen, D., Vasudevan, S. G., Lescar, J., A multi-step strategy to obtain crystals of the dengue virus RNA-dependent RNA polymerase that diffract to high resolution (2007) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun, 63, pp. 78-83 Wheeler, M. J., Russi, S., Bowler, M. G., Bowler, M. W., Measurement of the equilibrium relative humidity for common precipitant concentrations: Facilitating controlled dehydration experiments (2012) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun, 68, pp. 111-114 Matthews, B. W., Solvent content of protein crystals (1968) J. Mol. Biol, 33 (491-497), p. 93 Storoni, L. C., McCoy, A. J., Read, R. J., Likelihood-enhanced fast rotation functions (2004) Acta Crystallogr. D Biol. Crystallogr, 60 (432-438), p. 96}, document_type={Journal Article, }, affiliation={Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cinthia, Naples I-80126, Italy Institute of Biostructures and Bioimages, CNR, Via Mezzocannone, 16, Naples I-80134, Italy Department of Pharmaceutical, Biomedical Sciences, University of Salerno, Via Ponte Don Melillo, I-84084 Fisciano, Italy}, ibbaffiliation={1}, } @article{IBB_ID_9848, author={Merlino A, Russo Krauss I, Albino A, Pica A, Vergara A, Masullo M, De Vendittis E, Sica F}, title={Improving Protein Crystal Quality by the Without-Oil Microbatch Method: Crystallization and Preliminary X-ray Diffraction Analysis of Glutathione Synthetase from Pseudoalteromonas haloplanktis}, date={2011 Sep}, journal={Int J Mol Sc (ISSN: 1422-0067, 1661-6596, 1422-0067electronic)}, year={2011}, fullvolume={360}, volume={360}, pages={6312--6319}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80053206933&partnerID=40&md5=9ec9c40b3434ed0ebff0bd50fadccefe}, abstract={Glutathione synthetases catalyze the ATP-dependent synthesis of glutathione from L-gamma-glutamyl-L-cysteine and glycine. Although these enzymes have been sequenced and characterized from a variety of biological sources, their exact catalytic mechanism is not fully understood and nothing is known about their adaptation at extremophilic environments. Glutathione synthetase from the Antarctic eubacterium Pseudoalteromonas haloplanktis (PhGshB) has been expressed, purified and successfully crystallized. An overall improvement of the crystal quality has been obtained by adapting the crystal growth conditions found with vapor diffusion experiments to the without-oil microbatch method. The best crystals of PhGshB diffract to 2.34 angstrom resolution and belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 83.28 angstrom, b = 119.88 angstrom, c = 159.82 angstrom. Refinement of the model, obtained using phases derived from the structure of the same enzyme from Escherichia coli by molecular replacement, is in progress. The structural determination will provide the first structural characterization of a psychrophilic glutathione synthetase reported to date.}, keywords={Crystal Quality, Glutathione Synthetase, Psychrophile, Without-Oil Microbatch, X-Ray Crystallography, Glutathione Synthase, Article, Concentration (parameters), Controlled Study, Crystal Structure, Enzyme Purification, Escherichia Coli, Evaporation, Process Optimization, Protein Expression, Pseudoalteromonas, Pseudoalteromonas Haloplanktis, Psychrophilic Bacterium, Quality Control, Structure Analysis, Validation Process, X Ray Diffraction, }, references={Dalle-Donne, I., Rossi, R., Giustarini, D., Colombo, R., Milzani, A., S-glutathionylation in protein redox regulation (2007) Free Radic. Biol. Med, 43, pp. 883-89 Circu, M.L., Aw, T.Y., Glutathione and apoptosis (2008) Free Radic. Res, 42, pp. 689-706 Pallardo, F.V., Markovic, J., Garcia, J.L., Vina, J., Role of nuclear glutathione as a key regulator of cell proliferation (2009) Mol. Asp. Med, 30, pp. 77-85 Yamaguchi, H., Kato, H., Hata, Y., Nishioka, T., Kimura, A., Oda, J., Katsube, Y., Three-dimensional structure of the glutathione synthetase from Escherichia coli B at 2.0 Å resolution (1993) J. Mol. Biol, 229, pp. 1083-1100 Mooz, E.D., Meister, A., Tripeptide (glutathione) synthetase: Purification, properties and mechanism of action (1967) Biochemistry, 6, pp. 1722-1734 Gali, R.R., Board, P.G., Sequencing and expression of a cDNA for human glutathione synthetase (1995) Biochem. J, 310, pp. 353-358 Ota, T., Suzuki, Y., Nishikawa, T., Otsuki, T., Sugiyama, T., Irie, R., Wakamatsu, A., Nagai, K., Complete sequencing and characterization of 21,243 full-length human cDNAs (2004) Nat. Genet, 36, pp. 40-45 Huang, C.S., He, W., Meister, A., Anderson, M.E., Amino acid sequence of rat kidney glutathione synthetase (1995) Proc. Natl. Acad. Sci. USA, 92, pp. 1232-1236 Gushima, H., Yasuda, S., Soeda, E., Yokota, M., Kimura, A., Complete nucleotide sequence of the E. coli glutathione synthetase gsh-II (1984) Nucleic Acids Res, 12, pp. 9299-9307 Polekhina, G., Board, P.G., Gali, R.R., Rossjohn, J., Parker, M.W., Molecular basis of glutathione synthetase deficiency and a rare gene permutation event (1999) EMBO J, 18, pp. 3204-3213 Castellano, I., di Maro, A., Ruocco, M.R., Chambery, A., Parente, A., di Martino, M.T., Parlato, G., de Vendittis, E., Psychrophilic superoxide dismutase from Pseudoalteromonas haloplanktis: Biochemical characterization and identification of a highly reactive cysteine residue (2006) Biochimie, 88, pp. 1377-1389 Castellano, I., Ruocco, M.R., Cecere, F., di Maro, A., Chambery, A., Michniewicz, A., Parlato, G., de Vendittis, E., Glutathionylation of the iron superoxide dismutase from the psychrophilic eubacterium Pseudoalteromonas haloplanktis. Biochim. Biophys (2008) Acta Protein Proteonomics, 1784, pp. 816-826 Merlino, A., Russo Krauss, I., Castellano, I., de Vendittis, E., Rossi, B., Conte, M., Vergara, A., Sica, F., Structure and flexibility in cold-adapted iron superoxide dismutases: The case of the enzyme isolated from Pseudoalteromonas haloplanktis (2010) J. Struct. 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D, 62, pp. 72-82 Weiss, M.S., Global indicators of X-ray data quality (2001) J. Appl. Crystallogr, 34, pp. 130-135 Storoni, L.C., McCoy, A.J., Read, R.J., Likelihood-enhanced fast rotation functions (2004) Acta Crystallogr. D Biol. Crystallogr, 60, pp. 432-438 Circu, M. L., Aw, T. Y., Glutathione and apoptosis (2008) Free Radic. Res, 42, pp. 689-706 Pallardo, F. V., Markovic, J., Garcia, J. L., Vina, J., Role of nuclear glutathione as a key regulator of cell proliferation (2009) Mol. Asp. Med, 30, pp. 77-85 Mooz, E. D., Meister, A., Tripeptide (glutathione) synthetase: Purification, properties and mechanism of action (1967) Biochemistry, 6, pp. 1722-1734 Gali, R. R., Board, P. G., Sequencing and expression of a cDNA for human glutathione synthetase (1995) Biochem. J, 310, pp. 353-358 Huang, C. S., He, W., Meister, A., Anderson, M. E., Amino acid sequence of rat kidney glutathione synthetase (1995) Proc. Natl. Acad. Sci. USA, 92, pp. 1232-1236 Chayen, N. E., Shaw Stewart, P. D., Maeder, D. L., Blow, D. M., An automated system for micro-batch protein crystallization and screening (1990) J. Appl. Cryst, 23, pp. 297-302 Chayen, N. E., Recent advances in methodology for the crystallization of biological macromolecules (1999) J. Cryst. Growth, 199, pp. 649-655 Martins, P. M., Pessoa, J., Sarkany, Z., Rocha, F., Damas, A. M., Rationalizing protein crystallization Screenings through water equilibration theory and protein solubility data (2008) Cryst. Growth Des, 8, pp. 4233-4243 Matthews, B. W., Solvent content of protein crystals (1968) J. Mol. Biol, 33, pp. 491-497 Weiss, M. S., Global indicators of X-ray data quality (2001) J. Appl. Crystallogr, 34, pp. 130-135 Storoni, L. C., McCoy, A. J., Read, R. J., Likelihood-enhanced fast rotation functions (2004) Acta Crystallogr. D Biol. Crystallogr, 60, pp. 432-438}, document_type={Journal Article, }, affiliation={Dipartimento di Chimica Paolo Corradini, Università di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cinthia, Naples I-80126, Italy Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, Naples I-80134, Italy Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli Federico II, Via Pansini 5, Naples I-80131, Italy Dipartimento di Studi delle Istituzioni e dei Sistemi Territoriali, Università di Napoli Parthenope, Via Medina 40, Naples I-80133, Italy}, ibbaffiliation={1}, } @article{IBB_ID_12459, author={Troise F, Monti M, Merlino A, Cozzolino F, Fedele C, Russo Krauss I, Sica F, Pucci P, D'Alessio G, De Lorenzo C}, title={A novel ErbB2 epitope targeted by human antitumor immunoagents}, date={2011 Apr}, journal={Febs Journal (ISSN: 1742-464x)}, year={2011}, fullvolume={382}, volume={382}, pages={1156--1166}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79952857785&partnerID=40&md5=5e0ced118b1ef257c3ee6fba6b45067f}, abstract={Two novel human antitumor immunoconjugates, engineered by fusion of a single-chain antibody fragment against human ErbB2 receptor, termed Erbicin, with either a human RNase or the Fc region of a human IgG(1), are selectively cytotoxic for ErbB2-positive cancer cells in vitro and in vivo. These Erbicin-derived immunoagents (EDIAs) do not show the most negative properties of Herceptin, the only humanized mAb against ErbB2 used in the therapy of breast carcinoma: cardiotoxicity and the inability to act on resistant tumors. These differences are probably attributable to the different ErbB2 epitopes recognized by EDIAs and Herceptin, respectively, as we have previously reported that they induce different signaling mechanisms that control tumor and cardiac cell viability. Thus, to accurately identify the novel epitope recognized by EDIAs, three independent and complementary methodologies were used. They gave coherent results, which are reported here: EDIAs bind to a different ErbB2 epitope than Herceptin and the other human/humanized antibodies against ErbB2 reported so far. The epitope has been successfully located in region 122-195 of extracellular domain I. These findings could lead to the identification of novel epitopes on ErbB2 that could be used as potential therapeutic targets to mitigate anti-ErbB2-associated cardiotoxicity and eventually overcome resistance.}, keywords={Breast Cancer, Cardiotoxicity, Erbb2 Her2, Herceptin Trastuzumab, Immunotherapy, Antineoplastic Agent, Epidermal Growth Factor Receptor 2, Epidermal Growth Factor Receptor 2 Human Compact Antibody, Epitope, Erbicin, Erbicin Ribonuclease Fusion Protein, Pertuzumab, Unclassified Drug, Amino Acid Sequence, Article, Binding Assay, Controlled Study, Drug Receptor Binding, Drug Screening, Enzyme Linked Immunosorbent Assay, Epitope Mapping, Extracellular Space, Mass Spectrometry, Molecular Docking, Priority Journal, Protein Degradation, Animals, Antibodies, Monoclonal, Breast Neoplasms, Computer Simulation, Female, Immunoconjugates, Models, Molecular Sequence Data, Protein Binding, Protein Structure, Tertiary, Recombinant Fusion Proteins, Tumor Cells, Cultured, Immunology, Therapeutic Use, Humanized, Chemistry Immunology Therapeutic Use, Drug Therapy, Erbb-2 Immunology, }, references={Baselga, J., Albanell, J., Mechanism of action of anti-HER2 monoclonal antibodies (2001) Annals of Oncology, 12 (SUPPL. 1), pp. S35-S4 Slamon, D.J., Clark, G.M., Wong, S.G., Human breast cancer: Correlation of relapse and survival with amplification of the HER-2/neu oncogene (1987) Science, 235 (4785), pp. 177-182 Stebbing, J., Copson, E., O'Reilly, S., Herceptin (trastuzamab) in advanced breast cancer (2000) Cancer Treatment Reviews, 26 (4), pp. 287-290. , DOI 10.1053/ctrv.2000.0182 Sparano, J.A., Cardiac toxicity of trastuzumab (Herceptin): Implications for the design of adjuvant trials (2001) Semin Oncol, 28, pp. 20-27 Cardoso, F., Piccart, M.J., Durbecq, V., Di Leo, A., Resistance to trastuzumab: A necessary evil or a temporary challenge? 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M., Main-chain bond lengths and bond angles in protein structures (1993) Journal of Molecular Biology, 231 (4), pp. 1049-1067. , DOI 10. 1006/jmbi. 1993. 1351 Sippl, M. J., Recognition of errors in three-dimensional structures of proteins (1993) Proteins: Structure, Function and Genetics, 17 (4), pp. 355-362. , DOI 10. 1002/prot. 340170404 Van Dijk, A. D., Boelens, R., Bonvin, A. M., Data-driven docking for the study of biomolecular complexes (2005) FEBS J, 272, pp. 293-312 Gabb, H. A., Jackson, R. M., Sternberg, M. J. E., Modelling protein docking using shape complementarity, electrostatics and biochemical information (1997) Journal of Molecular Biology, 272 (1), pp. 106-120. , DOI 10. 1006/jmbi. 1997. 1203 McDonald, I. K., Thornton, J. M., Satisfying hydrogen bonding potential in proteins (1994) Journal of Molecular Biology, 238 (5), pp. 777-793. , DOI 10. 1006/jmbi. 1994. 1334 Lawrence, M. C., Colman, P. M., Shape complementarity at protein/protein interfaces (1993) Journal of Molecular Biology, 234 (4), pp. 946-950. , DOI 10. 1006/jmbi. 1993. 1648}, document_type={Journal Article, Research Support, Non-U. S. Gov'T, }, affiliation={Dipartimento di Biologia Strutturale e Funzionale, UniversitÀdi Napoli Federico II, via Cinthia, 80126 Napoli, Italy CEINGE Biotecnologie Avanzate, Napoli, Italy Dipartimento di Chimica Organica e Biochimica, UniversitÀ di Napoli Federico II, Italy Istituto di Biostrutture e Bioimmagini, CNR, Naples, Italy}, ibbaffiliation={1}, } @article{IBB_ID_8839, author={Pizzo E, Merlino A, Turano M, Russo Krauss I, Coscia F, Zanfardino A, Varcamonti M, Furia A, Giancola C, Mazzarella L, Sica F, D'Alessio G}, title={A new RNase sheds light on the RNase/angiogenin subfamily from zebrafish}, date={2011 Jan 15}, journal={Biochem J (ISSN: 1470-8728electronic, 0264-6021linking, 0264-6021print)}, year={2011}, fullvolume={766}, volume={766}, pages={345--355}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-78651266853&partnerID=40&md5=30a61a9b637299df0873584fb2dc55dc}, abstract={Recently, extracellular RNases of the RNase A superfamily, with the characteristic CKxxNTF sequence signature, have been identified in fish. This has led to the recognition that these RNases are present in the whole vertebrate subphylum. In fact, they comprise the only enzyme family unique to vertebrates. Four RNases from zebrafish (Danio rerio) have been previously reported and have a very low RNase activity; some of these are endowed, like human angiogenin, with powerful angiogenic and bactericidal activities. In the present paper, we report the three-dimensional structure, the thermodynamic behaviour and the biological properties of a novel zebrafish RNase, ZF-RNase-5. The investigation of its structural and functional properties, extended to all other subfamily members, provides an inclusive description of the whole zebrafish RNase subfamily. The Authors Journal compilation 2011 Biochemical Society}, keywords={Angiogenin, Bactericidal Activity, Rnase, Vertebrate, Zebrafish (zf) (danio Rerio), Enzyme, Ribonuclease, Unclassified Drug, Article, Biological Activity, Controlled Study, Drug Structure, Human, Nonhuman, Priority Journal, Thermodynamics, Zebra Fish, Amino Acid Sequence, Animals, Cells, Cultured, Gene Expression Regulation, Developmental, Enzymologic, Models, Molecular, Molecular Sequence Data, Protein Structure, Tertiary, Pancreatic, Sequence Alignment, Pancreatic Chemistry, Genetics, Metabolism, Ribonucleases Chemistry, Embryology, Genetics Metabolism, Pancreatic Chemistry Genetics Metabolism, Ribonucleases Chemistry Genetics Metabolism, Zebrafish Embryology Genetics Metabolism, }, references={Pizzo, E., D'Alessio, G., The success of the RNase scaffold in the advance of biosciences and in evolution (2007) Gene, 406, pp. 8-1 Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., FitzHugh, W., Initial sequencing and analysis of the human genome (2001) Nature, 409, pp. 860-921 Cho, S., Zhang, J., Zebrafish ribonucleases are bactericidal: Implications for the origin of the vertebrate RNase A superfamily (2007) Mol. 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Gov'T, }, affiliation={Dipartimento di Biologia Strutturale e Funzionale, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy Dipartimento di Chimica, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale Delle Ricerche (CNR), Via Mezzocannone 16, I-80134 Naples, Italy}, ibbaffiliation={1}, } @article{IBB_ID_52310, author={Russo Krauss I, Merlino A, Giancola C, Randazzo A, Mazzarella L, Sica F}, title={Thrombin-aptamer recognition: a revealed ambiguity}, date={2011}, journal={Nucleic Acids Res (ISSN: 0305-1048, 1362-4962, 1362-4962electronic)}, year={2011}, fullvolume={486}, volume={486}, pages={7858--7867}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80053183285&partnerID=40&md5=10458df8823d5431a24c26f060fdac93}, abstract={Aptamers are structured oligonucleotides that recognize molecular targets and can function as direct protein inhibitors. The best-known example is the thrombin-binding aptamer, TBA, a single-stranded 15-mer DNA that inhibits the activity of thrombin, the key enzyme of coagulation cascade. TBA folds as a G-quadruplex structure, as proved by its NMR structure. The X-ray structure of the complex between TBA and human alpha-thrombin was solved at 2.9-A resolution, but did not provide details of the aptamer conformation and the interactions with the protein molecule. TBA is rapidly processed by nucleases. To improve the properties of TBA, a number of modified analogs have been produced. In particular, a modified TBA containing a 5'-5' polarity inversion site, mTBA, has higher stability and higher affinity toward thrombin with respect to TBA, although it has a lower inhibitory activity. We present the crystal structure of the thrombin-mTBA complex at 2.15-A resolution; the resulting model eventually provides a clear picture of thrombin-aptamers interaction, and also highlights the structural bases of the different properties of TBA and mTBA. Our findings open the way for a rational design of modified aptamers with improved potency as anticoagulant drugs.}, keywords={Aptamer, Thrombin, Ambiguity, Article, Binding Affinity, Cell Polarity, Controlled Study, Crystal Structure, Crystallography, Molecular Recognition, Priority Journal, Protein Binding, Protein Dna Interaction, Protein Function, Protein Stability, Protein Structure, Structure Analysis, Nucleotide, X-Ray, Dna-Binding Proteins, Humans, Models, }, references={Bock, L.C., Griffin, L.C., Latham, J.A., Vermaas, E.H., Toole, J.J., Selection of single-stranded DNA molecules that bind and inhibit human thrombin (1992) Nature, 355, pp. 564-56 Burke, J.M., Berzal-Herranz, A., In vitro selection and evolution of RNA: Applications for catalytic RNA, molecular recognition, and drug discovery (1993) FASEB Journal, 7 (1), pp. 106-112 Lancellotti, S., De Cristofaro, R., Nucleotide-derived thrombin inhibitors: A new tool for an old issue (2009) Cardiovasc. Hematol. Agents Med. 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Montesano 49, I-8013 Napoli, Italy}, ibbaffiliation={1}, } @article{IBB_ID_8947, author={Merlino A, Russo Krauss I, Castellano I, De Vendittis E, Rossi B, Conte M, Vergara A, Sica F}, title={Structure and flexibility in cold-adapted iron superoxide dismutases: The case of the enzyme isolated from Pseudoalteromonas haloplanktis}, date={2010 Dec}, journal={J Struct Biol (ISSN: 1047-8477, 1047-8477linking)}, year={2010}, fullvolume={488}, volume={488}, pages={343--352}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77958176737&partnerID=40&md5=1b012c8e06d9b0760f4eb46c92ed9ff2}, abstract={Superoxide dismutases (SODs) are metalloenzymes catalysing the dismutation of superoxide anion radicals into molecular oxygen and hydrogen peroxide. Here, we present the crystal structure of a cold-adapted Fe-SOD from the Antarctic eubacterium Pseudoalteromonas haloplanktis (PhSOD), and that of its complex with sodium azide. The structures were compared with those of the corresponding homologues having a high sequence identity with PhSOD, such as the mesophilic SOD from Escherichia coli (EcSOD) or Pseudomonas ovalis, and the psychrophilic SOD from Aliivibrio salmonicida (AsSOD). These enzymes shared a large structural similarity, such as a conserved tertiary structure and arrangement of the two monomers, an almost identical total number of inter- and intramolecular hydrogen bonds and salt bridges. However, the two cold-adapted SODs showed an increased flexibility of the active site residues with respect to their mesophilic homologues. Structural information was combined with a characterisation of the chemical and thermal stability performed by CD and fluorescence measurements. Despite of its psychrophilic origin, the denaturation temperature of PhSOD was comparable with that of the mesophilic EcSOD, whereas AsSOD showed a lower denaturation temperature. On the contrary, the values of the denaturant concentration at the transition midpoint were in line with the psychrophilic/mesophilic origin of the proteins. These data provide additional support to the hypothesis that cold-adapted enzymes achieve efficient catalysis at low temperature, by increasing the flexibility of their active site; moreover, our results underline how fine structural modifications can alter enzyme flexibility and/or stability without compromising the overall structure of typical rigid enzymes, such as SODs. (C) 2010 Elsevier Inc. All rights reserved.}, keywords={Cold-Adapted Enzymes, Crystal Structure, Dynamics, Psychrophilic Proteins, Superoxide Dismutase, Thermal Stability, Bacterial Enzyme, Hydrogen, Iron Superoxide Dismutase, Monomer, Sodium Azide, Antarctica, Article, Catalysis, Chemical Bond, Cold Acclimatization, Controlled Study, Enzyme Active Site, Enzyme Isolation, Enzyme Stability, Enzyme Structure, Escherichia Coli, Eubacterium, Fluorescence, Hydrogen Bond, Low Temperature Procedures, Nonhuman, Priority Journal, Protein Denaturation, Pseudoalteromonas, Pseudoalteromonas Haloplanktis, Sequence Homology, Thermostability, Vibrio Salmonicida, Amino Acid Sequence, Bacterial Proteins, Catalytic Domain, Circular Dichroism, Molecular Sequence Data, Protein Folding, Protein Structure, Secondary, Pseudomonas Putida, }, references={Baldwin, R.L., Temperature dependence of the hydrophobic interaction in protein folding (1986) Proc. Natl. Acad. Sci. 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C., Collins, T., D'Amico, S., Feller, G., Gerday, C., Cold-adapted enzymes from marine Antarctic microorganisms (2007) Mar. Biotechnol. (NY), 9, pp. 293-304 Marx, J. C., Blaise, V., Collins, T., D'Amico, S., Delille, D., Gratia, E., Hoyoux, A., Gerday, C., A perspective on cold enzymes: current knowledge and frequently asked questions (2004) Cell Mol. Biol. (Noisy-le-grand), 50, pp. 643-655 Mccord, J. M., Fridovich, I., Superoxide dismutase. An enzymic function for erythrocuprein (hemocuprein) (1969) J. Biol. Chem., 244, pp. 6049-6055 Mcdonald, I. K., Thornton, J. M., Satisfying hydrogen bonding potential in proteins (1994) J. Mol. Biol., 238, pp. 777-793 Miller, A. F., Superoxide dismutases: active sites that save, but a protein that kills (2004) Curr. Opin. Chem. Biol., 8, pp. 162-168 Munoz, I. G., Moran, J. F., Becana, M., Montoya, G., The crystal structure of an eukaryotic iron superoxide dismutase suggests intersubunit cooperation during catalysis (2005) Protein Sci., 14, pp. 387-394 Pedersen, H. L., Willassen, N. P., Leiros, I., The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida (2009) Acta Crystallogr. Sect. F: Struct. Biol. Cryst. Commun., 65, pp. 84-92 Siddiqui, K. S., Cavicchioli, R., Cold-adapted enzymes (2006) Annu. Rev. Biochem., 75, pp. 403-433 Slykhouse, T. O., Fee, J. A., Physical and chemical studies on bacterial superoxide dismutases. Purification and some anion binding properties of the iron-containing protein of Escherichia coli B (1976) J. Biol. Chem., 251, pp. 5472-5477 Stallings, W. C., Pattridge, K. A., Strong, R. K., Ludwig, M. L., Manganese and iron superoxide dismutases are structural homologs (1984) J. Biol. Chem., 259, pp. 10695-10699 Stoddard, B. L., Ringe, D., Petsko, G. A., The structure of iron superoxide dismutase from Pseudomonas ovalis complexed with the inhibitor azide (1990) Protein Eng., 4, pp. 113-119}, document_type={Journal Article, }, affiliation={Dipartimento di Chimica, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli Federico II, Via Pansini 5, I-80131 Napoli, Italy}, ibbaffiliation={1}, } @article{IBB_ID_51017, author={Russo Krauss I, Merlino A, Randazzo A, Mazzarella L, Sica F}, title={Crystallization and preliminary X-ray analysis of the complex of human alpha-thrombin with a modified thrombin-binding aptamer}, date={2010 Aug 1}, journal={Nucleosides Nucleotides Nucleic Acids (ISSN: 1744-3091, 1744-4309, 1532-2335electronic)}, year={2010}, fullvolume={361}, volume={361}, pages={961--963}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77955446114&partnerID=40&md5=a4c2092a293437c2d79737ffbfa18074}, abstract={The thrombin-binding aptamer (TBA) is a consensus DNA 15-mer that binds specifically to human-thrombin at nanomolar concentrations and inhibits its procoagulant functions. Recently, a modified TBA (mTBA) containing a 5 -5 inversion-of-polarity site has been shown to be more stable and to possess a higher thrombin affinity than its unmodified counterpart. The structure of the thrombin-TBA complex has previously been determined at low resolution, but did not provide a detailed picture of the aptamer conformation or of the protein-DNA assembly, while that of the complex with mTBA is unknown. Crystallographic analysis of the thrombin-mTBA complex has been attempted. The crystals diffracted to 2. 15 resolution and belonged to space group I222. 2010 International Union of Crystallography All rights reserved}, keywords={Protein-Nucleic Acid Interactions, Quadruplexes, Thrombin, Thrombin-Binding Aptamers, Thrombin Aptamer, Article, Chemistry, Crystallization, Human, Metabolism, Protein Binding, Protein Multimerization, X Ray Crystallography, Nucleotide, X-Ray, Base Sequence, Biomimetic Materials, Chemical Synthesis, Chemistry Techniques, Synthetic, Catalytic, Genetics, 10-23, Chimeric Oligonucleotide, Dnazyme, Deoxyribozyme, Nucleic Acid Crystallization, }, references={Bock, L. C., Griffin, L. C., Latham, J. A., Vermaas, E. H., Toole, J. J., (1992) Nature (London), 355, pp. 564-56 Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S. R., Hofsteenge, J., (1989) EMBO J., 8, pp. 3467-3475 Kelly, J. A., Feigon, J., Yeates, T. O., (1996) J. Mol. Biol., 256, pp. 417-422 Lancellotti, S., De Cristofaro, R., (2009) Cardiovasc. Hematol. Agents Med. Chem., 7, pp. 19-28 MacAya, R. F., Schultze, P., Smith, F. W., Roe, J. A., Feigon, J., (1993) Proc. Natl Acad. Sci. USA, 90, pp. 3745-3749 Martino, L., Virno, A., Randazzo, A., Virgilio, A., Esposito, V., Giancola, C., Bucci, M., Mayol, L., (2006) Nucleic Acids Res., 34, pp. 6653-6662 Navaza, J., Saludjian, P., (1997) Methods Enzymol., 276, pp. 581-594 Otwinowski, Z., Minor, W., (1997) Methods Enzymol., 276, pp. 307-326 Padmanabhan, K., Padmanabhan, K. P., Ferrara, J. D., Sadler, J. E., Tulinsky, A., (1993) J. Biol. Chem., 268, pp. 17651-17654 Padmanabhan, K., Tulinsky, A., (1996) Acta Cryst., D52, pp. 272-282 Pagano, B., Martino, L., Randazzo, A., Giancola, C., (2007) Biophys. J., 94, pp. 562-569 Schultze, P., MacAya, R. F., Feigon, J., (1994) J. Mol. Biol., 235, pp. 1532-1547}, document_type={Journal Article, Abstract, Conference, }, affiliation={Dipartimento di Chimica, Universit di Napoli Federico II, Via Cintia, I-80126 Napoli, Italy Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy a Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Department of Bioorganic Chemistry , Lodz , Poland., }, ibbaffiliation={1}, } @article{IBB_ID_9112, author={Merlino A, Russo Krauss I, Perillo M, Mattia CA, Ercole C, Picone D, Vergara A, Sica F}, title={Toward an Antitumor Form of Bovine Pancreatic Ribonuclease: The Crystal Structure of Three Noncovalent Dimeric Mutants}, date={2009 Dec}, journal={Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print)}, year={2009}, fullvolume={384}, volume={384}, pages={1029--1037}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-71749105511&partnerID=40&md5=957f24d3be8ff257aa572a78597a8990}, abstract={The cytotoxic action of bovine seminal ribonuclease (BS-RNase) depends on its noncovalent swapped dimeric form (NCD-BS), which presents a compact structure that allows the molecule to escape ribonuclease inhibitor (RI). A Key role in the acquisition of this structure has been attributed to the concomitant presense of a proline in position 19 and a leucine in position 28. This introduction of Leu28, Cys31, and Cys32 and, in addition, of Pro19 in the sequence of bovine pancreatic ribonuclease (RNase A) has produced two dimeric variants LCC and PLCC, which do exhibit a cytotoxic activity, though at a much lower level than BS-RNase. The crystal structure analysis of the noncovalent swapped form (NCD) of LCC and PLCG complexed with the substrate analogue 2'-deoxycytidylyl(3',5')-2'-deoxyguanosine, has revealed that, differently from NCD-BS, the dimers adopt an opened quaternary structure, with the two Leu residues fully exposed to the solvent, that does not hinder the binding of RI. similar results have been obtained for a third mutant of the pancreatic enzyme, engineered with the hinge peptide sequence of the seminal enzyme (residues 16-22) and the two cysteines in position 31 and 31, but lacking the hydrophobic Leu residue in position. 28. The comparison of these three structures with those previously reported for other ribonuclease swapped dimers strongly suggests that, in addition to Pro19 and Leu28, the presence of a glycine at the N-terminal end of the hinge peptide is also important to push the swapped form of RNase A dimer into the compact quaternary organization observed for NCD-BS. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 1029-1037, 2009.}, keywords={3d-Domain Swapping, Antitumor Activity, Bovine Seminal Ribonuclease, Crystal Structure, Helix Exchange, Noncovalent Dimer, Protein Mutations And Evolution, Quaternary Structure Flexibility, Swapped Dimers, Anti-Tumor Activities, Amines, Amino Acids, Enzymes, Peptides, Three Dimensional, Cysteine, Glycine, Leucine, Pancreatic Ribonuclease, Proline, Deoxyguanosine, Ribonuclease Inhibitor, Solvent, Amino Acid Sequence, Amino Terminal Sequence, Antineoplastic Activity, Article, Complex Formation, Controlled Study, Drug Structure, Enzyme Engineering, Hinge Region, Protein Quaternary Structure, Amino Acid Composition, Cytotoxicity, Dimerization, Enzyme Substrate, Gel Permeation Chromatography, Protein Binding, Protein Engineering, Animals, Antineoplastic Agents, Catalytic Domain, Cattle, Crystallography, X-Ray, Endoribonucleases, Isoenzymes, Models, Molecular, Protein Multimerization, Protein Structure, Tertiary, Recombinant Proteins, Structure-Activity Relationship, }, references={Raines, R.T., (1998) Chem Rev, 98, pp. 1045-106 Leland, P.A., Raines, R.T., (2001) Chem Biol, 8, pp. 405-413 Youle, R.J., D'Alessio, G., (1996) Ribonuclease: Structures and Functions, pp. 491-514. , D'Alessio, G. 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T., (1998) Chem Rev, 98, pp. 1045-106 Leland, P. A., Raines, R. T., (2001) Chem Biol, 8, pp. 405-413 Youle, R. J., D'Alessio, G., (1996) Ribonuclease: Structures and Functions, pp. 491-514. , D'Alessio, G. Vogelzang, N. J., Aklilu, M., Stadler, W. M., Dumas, M. C., Mikulski, S. M., (2001) Invest New Drugs, 19, pp. 255-260 Makarov, A. A., Ilinskaya, O. N., (2003) FEBS Lett, 540, pp. 15-20 Kim, J. S., Soucek, J., Matousek, J., Raines, R. T., (1995) Biochem J, 308 (PART 2), pp. 547-550 Leland, P. A., Schultz, L. W., Kim, B. M., Raines, R. T., (1998) Proc Natl Acad Sci USA, 95, pp. 10407-10412 Bretscher, L. E., Abel, R. L., Raines, R. T., (2000) J Biol Chem, 275, pp. 9893-9896 Mastronicola, M. R., Piccoli, R., D'Alessio, G., (1995) Eur J Biochem, 230, pp. 242-249 Brunger, A. T., Adams, P. D., Clore, G. M., Delano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Warren, G. L., (1998) Acta Crystallogr D Biol Crystallogr, 54 (PART 5), pp. 905-921 Jones, T. A., Bergdoll, M., Kjeldgaard, M. O., (1990) Crystallography and Modelling Methods in Molecular Design, pp. 189-199. , Bugg, C. Laskowski, R. A., MacArthur, M. W., Moss, M. D., Thorton, J. M., (1993) J Appl Crystallogr, 26, pp. 283-291 Hooft, R. W., Vriend, G., Sander, C., Abola, E. E., (1996) Nature, 381, p. 272 Kraulis, P. J., (1991) J Appl Crystallogr, 24, pp. 946-950 Aguilar, C. F., Thomas, P. J., Mills, A., Moss, D. S., Palmer, R. A., (1992) J Mol Biol, 224, pp. 265-267 Liu, Y., Hart, P. J., Schlunegger, M. P., Eisenberg, D., (1998) Proc Natl Acad Sci USA, 95, pp. 3437-3442}, document_type={Journal Article, }, affiliation={Department of Chemistry, University of Naples Federico II Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy Department of Pharmaceutical Science, University of Salerno, via Ponte don Melillo, I-84084 Fisciano (SA), Italy}, ibbaffiliation={1}, } @article{IBB_ID_9152, author={Merlino A, Russo Krauss I, Castellano I, De Vendittis E, Vergara A, Sica F}, title={Crystallization and preliminary x-ray diffraction studies of a psychrophilic iron superoxide dismutase from Pseudoalteromonas haloplanktis}, date={2008}, journal={Protein Pept Lett (ISSN: 0929-8665, 1875-5305)}, year={2008}, fullvolume={354}, volume={354}, pages={415--418}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-43549114985&partnerID=40&md5=a1aa4174d75402a1c6ba02961449ec1b}, abstract={The Antarctic eubacterium Pseudoalteromonas haloplanktis (Ph) produces a cold-active iron superoxide dismutase (SOD). PhSOD is a homodimeric enzyme, that displays a high catalytic activity even at low temperature. Using hanging-drop vapour-diffusion technique, PhSOD has been successfully crystallized in two different crystal forms. Both crystal forms are monoclinic with space group P2(1) and diffract to 2.1 A resolution. Form I has unit-cell parameters a=45.49A b=103.63A c=50.37A beta=108.2 degrees and contains a homodimer in the asymmetric unit. Form II has unit-cell parameters a=50.48A b=103.78A c=90.25A beta=103.8 degrees and an asymmetric unit containing two PhSOD homodimers. Structure determination has been achieved using molecular replacement. The crystallographic study of this cold-adapted enzyme could contribute to the understanding of the molecular mechanisms of cold-adaptation and of the high catalytic efficiency at low temperature.}, keywords={Cold Adaptation, Crystallization, Iron Superoxide Dismutase, Pseudoalteromonas Haloplanktis, X-Ray, Article, Chemistry, Dimerization, Enzymology, Isolation And Purification, X Ray Crystallography, }, references={Jaenicke, R., Böhm, G., (1998) Curr. Opin. Struct. Biol, 8, pp. 738-74 Vogt, G., Woell, S., Argos, P., (1997) J. Mol. Biol, 269, pp. 631-643 Szilagyi, A., Zavodszky, P., (2000) Structure, 8, pp. 493-504 Zavodszki, P., Kardos, J., Svingor, A., Petsko, G.A., (1998) Proc. Natl. Acad. Sci. USA, 95, pp. 7406-7411 Feller, G., Narinx, E., Arpigny, J.L., Aittaleb, M., Baise, E., Genicot, S., Gerday, C., (1996) FEMS Microbiol. Rev, 18, pp. 189-202 Goldman, A., (1995) Structure, 3, pp. 1277-1279 Siddiqui, K.S., Cavicchioli, R., (2006) Annu. Rev. 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Acta, doi: 10.1016/j.bbapap.2008.02.003.?Minor, W., Tomchick, D., Otwinowski, Z., (2000) Structure, 8, pp. R105-R110 Navaza, J., Saludjian, P., (1997) Methods Enzymol, 276, pp. 581-594 Morris, R.J., Zwart, P.H., Cohen, S., Fernandez, F.J., Kakaris, M., Kirillova, O., Vonrhein, C., Lamzin, V.S., (2004) J. Synchrotron Radiat, 11, pp. 56-59 Jones, T.A., (2004) Acta Crystallogr. D Biol. Crystallogr, 60, pp. 2115-2125 Jaenicke, R., B hm, G., (1998) Curr. Opin. Struct. Biol, 8, pp. 738-74 Siddiqui, K. S., Cavicchioli, R., (2006) Annu. Rev. Biochem, 75, pp. 403-433 Lah, M. S., Dixon, M. M., Pattridge, K. A., Stallings, W. C., Fee, J. A., Ludwig, M. L., (1995) Biochemistry, 34, pp. 1646-1660 Morris, R. J., Zwart, P. H., Cohen, S., Fernandez, F. J., Kakaris, M., Kirillova, O., Vonrhein, C., Lamzin, V. S., (2004) J. Synchrotron Radiat, 11, pp. 56-59 Jones, T. A., (2004) Acta Crystallogr. D Biol. Crystallogr, 60, pp. 2115-2125}, document_type={Journal Article, }, affiliation={Dipartimento di Chimica, Università degli Studi di Napoli 'Federico II', Via Cintia, I-80126 Napoli, Italy Dipartimento di Biochimica e Biotecnologie Mediche, Università degli Studi di Napoli 'Federico II', Via Pansini 5, I-80131 Napoli, Italy Istituto di Biostrutture e Bioimmagini, C.N.R., via Mezzocannone 16, I-80134 Napoli, Italy Department of Chemistry, University of Naples 'Federico II', Via Cintia, I-80126 Napoli, Italy}, ibbaffiliation={1}, }