A Molecular Dynamics Study of Pilus Subunits: Insights into Pilus Biogenesis (513 views)
J Mol Biol (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 2007 Apr 6; 367(4): 935-941.
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Paper type: Journal Article, Research Support, Non-U. S. Gov'T,
Impact factor: 4.472, 5-year impact factor: 4.733
Url: Not available.
Keywords: Bioinformatics, Chaperone, Donor-Strand Exchange, Protein-Protein Interaction, Escherichia Coli Protein, Pilin, Protein Papd, Protein Subunit, Unclassified Drug, Amino Terminal Sequence, Article, Bacterium Pilus, Carboxy Terminal Sequence, Hydrogen Bond, Molecular Dynamics, Nonhuman, Priority Journal, Protein Analysis, Protein Conformation, Protein Domain, Protein Folding, Protein Polymerization, Protein Protein Interaction, Protein Stability, Protein Structure, Structure Activity Relation, Bacterial Proteins, Fimbriae Proteins, Membrane Proteins, Models, Molecular Chaperones, Morphogenesis, Periplasmic Proteins, Protein Binding, Tertiary, Proton-Translocating Atpases, Bacteria (microorganisms),
Affiliations:
*** IBB - CNR ***
Istituto di Biostrutture e Bioimmagini, C.N.R., I-80134 Napoli, Italy
Dipartimento delle Scienze Biologiche - Sezione di Biostrutture, Università degli Studi di Napoli Federico II, I-80134 Napoli, Italy
References:
Not available.
J Mol Biol (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 2007 Apr 6; 367(4): 935-941.
Export to BibTeX Export to EndNote
Paper type: Journal Article, Research Support, Non-U. S. Gov'T,
Impact factor: 4.472, 5-year impact factor: 4.733
Url: Not available.
Keywords: Bioinformatics, Chaperone, Donor-Strand Exchange, Protein-Protein Interaction, Escherichia Coli Protein, Pilin, Protein Papd, Protein Subunit, Unclassified Drug, Amino Terminal Sequence, Article, Bacterium Pilus, Carboxy Terminal Sequence, Hydrogen Bond, Molecular Dynamics, Nonhuman, Priority Journal, Protein Analysis, Protein Conformation, Protein Domain, Protein Folding, Protein Polymerization, Protein Protein Interaction, Protein Stability, Protein Structure, Structure Activity Relation, Bacterial Proteins, Fimbriae Proteins, Membrane Proteins, Models, Molecular Chaperones, Morphogenesis, Periplasmic Proteins, Protein Binding, Tertiary, Proton-Translocating Atpases, Bacteria (microorganisms),
Affiliations:
*** IBB - CNR ***
Istituto di Biostrutture e Bioimmagini, C.N.R., I-80134 Napoli, Italy
Dipartimento delle Scienze Biologiche - Sezione di Biostrutture, Università degli Studi di Napoli Federico II, I-80134 Napoli, Italy
References:
Not available.
A Molecular Dynamics Study of Pilus Subunits: Insights into Pilus Biogenesis
Biogenesis of pili in the uropathogenic Echerichia coli, essential to the bacterial pathogenicity, is a complex molecular process, which involves several protein components of the Pap gene cluster. A crucial role in the process is played by the chaperone PapD and by the PapE pilus subunit. Interestingly, PapE exhibits an Ig-like fold with a missing strand. The missing G strand is donated by the chaperone during pilin folding and by adjacent pilus subunits in the final fibre. In order to obtain a detailed picture at atomic level of the molecular events related to this process, we undertook molecular dynamics studies of the non-canonical imuno-globulin-like PapE in its unliganded state. These analyses were extended to the complexes of PapE with the complementary G1 strand of PapD and with the N-terminal extension of PapK. All three systems investigated were stable in the time interval considered (20 ns). However, significant differences in their local and overall flexibilities were detected. Notably, the equilibrated structure of unliganded PapE, which is difficult to characterise experimentally, displays unexpected features. Indeed, a significant rearrangement of the local structure of the groove, which hosts the complementary strands, is observed. This reorganisation, characterised by the formation of several new hydrogen bonds, leads to a closure of the groove that likely makes pilin polymerisation more difficult. These data suggest that chaperone release and pilin-pilin association must be concerted processes and that chaperone plays an important role in preventing pilin transitions towards states that are not prone to polymerise. © 2007 Elsevier Ltd. All rights reserved.
Biogenesis of pili in the uropathogenic Echerichia coli, essential to the bacterial pathogenicity, is a complex molecular process, which involves several protein components of the Pap gene cluster. A crucial role in the process is played by the chaperone PapD and by the PapE pilus subunit. Interestingly, PapE exhibits an Ig-like fold with a missing strand. The missing G strand is donated by the chaperone during pilin folding and by adjacent pilus subunits in the final fibre. In order to obtain a detailed picture at atomic level of the molecular events related to this process, we undertook molecular dynamics studies of the non-canonical imuno-globulin-like PapE in its unliganded state. These analyses were extended to the complexes of PapE with the complementary G1 strand of PapD and with the N-terminal extension of PapK. All three systems investigated were stable in the time interval considered (20 ns). However, significant differences in their local and overall flexibilities were detected. Notably, the equilibrated structure of unliganded PapE, which is difficult to characterise experimentally, displays unexpected features. Indeed, a significant rearrangement of the local structure of the groove, which hosts the complementary strands, is observed. This reorganisation, characterised by the formation of several new hydrogen bonds, leads to a closure of the groove that likely makes pilin polymerisation more difficult. These data suggest that chaperone release and pilin-pilin association must be concerted processes and that chaperone plays an important role in preventing pilin transitions towards states that are not prone to polymerise. © 2007 Elsevier Ltd. All rights reserved.
A Molecular Dynamics Study of Pilus Subunits: Insights into Pilus Biogenesis
A Molecular Dynamics Study of Pilus Subunits: Insights into Pilus Biogenesis
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Grund ME, Choi SJ, Mcnitt DH, Barbier M, Hu G, Lasala PR, Cote CK, Berisio R, Lukomski S
* Burkholderia collagen-like protein 8, Bucl8, is a unique outer membrane component of a putative tetrapartite efflux pump in Burkholderia pseudomallei and Burkholderia mallei (74 views)
Plosone (ISSN: 1932-6203linking, 1932-6203electronic), 2020 Nov 23; 15(11): e0242593-N/D.
Impact Factor: 2.74
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Mercurio FA, Di Natale C, Pirone L, Vincenzi M, Marasco D, De Luca S, Pedone EM, Leone M
* Exploring the ability of cyclic peptides to target SAM domains: a computational and experimental study (270 views)
Chembiochem (ISSN: 1439-4227linking, 1439-7633), 2020 Mar 2; 21(5): 702-711.
Impact Factor: 2.641
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Ala U, Manco M, Mandili G, Tolosano E, Novelli F, Provero P, Altruda F, Fagoonee S
* Proteomics-Based Evidence for a Pro-Oncogenic Role of ESRP1 in Human Colorectal Cancer Cells (128 views)
Int J Mol Sc (ISSN: 1422-0067linking, 1661-6596, 1422-0067electronic), 2020 Jan 16; 21 (2 ): N/D-N/D.
Impact Factor: 2.598
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Vincenzi M, Mercurio FA, Leone M
* Sam Domains in Multiple Diseases (243 views)
Curr Med Chem (ISSN: 0929-8673linking, 1875-533xelectronic), 2020; 27(3): 450-476.
Impact Factor: 3.469
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Rega C, Russo R, Foca A, Sandomenico A, Iaccarino E, Raimondo D, Milanetti E, Tornatore L, Franzoso G, Pedone PV, Ruvo M, Chambery A
* Probing the interaction interface of the GADD45beta/MKK7 and MKK7/DTP3 complexes by chemical cross-linking mass spectrometry (278 views)
Int J Biol Macromol (ISSN: 1879-0003electronic, 0141-8130linking), 2018 Jul 15; 114: 114-123.
Impact Factor: 1.427
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Fusco FA, Fiorentino G, Pedone E, Contursi P, Bartolucci S, Limauro D
* Biochemical characterization of a novel thermostable beta-glucosidase from Dictyoglomus turgidum (1396 views)
Int J Biol Macromol (ISSN: 1879-0003electronic, 0141-8130linking), 2018 Jul 1; 113: 783-791.
Impact Factor: 4.784
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Pirone L, Ripoll-rozada J, Leone M, Ronca R, Lombardo F, Fiorentino G, Andersen JF, Pereira PJB, Arcà B, Pedone E
* Functional analyses yield detailedinsight into the mechanism of thrombin inhibition by the antihemostatic salivary protein cE5 from Anopheles gambiae (371 views) (PDF 192 views)
Jbc Papers (ISSN: 0021-9258linking, 1083-351x), 2017 Jul 28; 292(30): 12632-12642.
Impact Factor: 4.125
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Sacchi S, Cappelletti P, Pirone L, Smaldone G, Pedone E, Pollegioni L
* Elucidating the role of the pLG72 R30K substitution in schizophrenia susceptibility (378 views)
Febs Lett (ISSN: 1873-3468, 0014-5793, 0014-5793print), 2017 Feb; 591(4): 646-655.
Impact Factor: 2.999
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Lanza V, Travaglia A, Malgieri G, Fattorusso R, GrassoG, Di Natale G, Zito V, Arena G, Milardi D, Rizzarelli E
* Ubiquitin Associates with the N-Terminal Domain of Nerve Growth Factor: The Role of Copper(II) Ions (284 views) (PDF 175 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2016 Dec 05; 22(49): 17767-17775.
Impact Factor: 5.317
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Pirone L, Smaldone G, Esposito C, Balasco N, Petoukhov MV, Spilotros A, Svergun DI, Di Gaetano S, Vitagliano L, Pedone E
* Proteins involved in sleep homeostasis: Biophysical characterization of INC and its partners (328 views) (PDF 194 views)
Biochimie (ISSN: 0300-9084, 1638-6183, 0300-9084linking), 2016 Sep 24; 131: 106-114.
Impact Factor: 3.112
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Birolo L, Sacchi S, Smaldone G, Molla G, Leo G, Caldinelli L, Pirone L, Eliometri P, Di Gaetano S, Orefice I, Pedone E, Pucci P, Pollegioni L
* Regulating levels of the neuromodulator d-serine in human brain: structural insight into pLG72 and d-amino acid oxidase interaction (269 views) (PDF 209 views)
Febs J (ISSN: 1742-464x), 2016 Sep; 283(18): 3353-3370.
Impact Factor: 3.902
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Ruvo M, Doti N, Lorenzo V, Vitagliano L, Mascanzoni F
* The Interacting Domains of PREP1 and p160 are Endowed with a Remarkable Structural Stability (284 views)
Mol Biotechnol (ISSN: 1073-6085, 1559-0305electronic, 1073-6085linking), 2016 May; 58(5): 328-339.
Impact Factor: 1.634
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Santoro AM, Cunsolo A, D'Urso A, Sbardella D, Tundo GR, Ciaccio C, Coletta M, Diana D, Fattorusso R, Persico M, Di Dato A, Fattorusso C, Milardi D, Purrello R
* Cationic porphyrins are tunable gatekeepers of the 20S proteasome (681 views) (PDF 233 views)
Chem Sci (ISSN: 2041-6520, 2041-6520linking, 2041-6520print), 2016; 7(2): 1286-1297.
Impact Factor: 8.668
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Bottini A, Wu B, Barile E, De SK, Leone M, Pellecchia M
* High-Throughput Screening (HTS) by NMR Guided Identification of Novel Agents Targeting the Protein Docking Domain of YopH (426 views)
Chemmedchem (ISSN: 1860-7179, 1860-7187, 1860-7179linking), 2015 Nov 23; 11(8): 919-927.
Impact Factor: 2.98
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Guardiani C, Scorciapino MA, Amodeo GF, Grdadolnik J, Pappalardo G, De Pinto V, Ceccarelli M, Casu M
* The N-Terminal Peptides of the Three Human Isoforms of the Mitochondrial Voltage-Dependent Anion Channel Have Different Helical Propensities (524 views)
Biochemistry (ISSN: 0006-2960, 1520-4995), 2015 Sep 15; 54(36): 5646-5656.
Impact Factor: 2.876
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Correale S, de Paola I, Morgillo CM, Federico A, Zaccaro L, Pallante P, Galeone A, Fusco A, Pedone E, Luque FJ, Catalanotti B
* Structural Model of the hUbA1-UbcH10 Quaternary Complex: In Silico and Experimental Analysis of the Protein-Protein Interactions between E1, E2 and Ubiquitin (468 views)
Plosone (ISSN: 1932-6203, 1932-6203electronic, 1932-6203linking), 2014 Nov 6; 9(11): e112082-e112082.
Impact Factor: 3.234
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Balasco N, Pirone L, Smaldone G, Di Gaetano S, Esposito L, Pedone E, Vitagliano L
* Molecular recognition of Cullin3 by KCTDs: Insights from experimental and computational investigations (393 views)
Bba-Gen Subjects (ISSN: 0925-4439, 0006-3002, 1570-9639), 2014 Jul; 1844(7): 1289-1298.
Impact Factor: 4.882
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Diana D, Smaldone G, De Antonellis P, Pirone L, Carotenuto M, Alonzi A, Di Gaetano S, Zollo M, Pedone E, Fattorusso R
* Mapping Functional Interaction Sites of Human Prune C-Terminal Domain by NMR Spectroscopy in Human Cell Lysates (395 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2013 Sep 9; 19(37): 12217-12220.
Impact Factor: 5.696
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Farina B, Doti N, Pirone L, Malgieri G, Pedone E, Ruvo M, Fattorusso R
* Molecular basis of the PED/PEA15 interaction with the C-terminal fragment of phospholipase D1 revealed by NMR spectroscopy (513 views)
Bba-Gen Subjects (ISSN: 1570-9639, 0006-3002, 0925-4439), 2013 Sep; 1834(8): 1572-1580.
Impact Factor: 3.191
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Attanasio F, Convertino M, Magno A, Caflisch A, Corazza A, Haridas H, Esposito G, Cataldo S, Pignataro B, Milardi D, Rizzarelli E
* Carnosine Inhibits Abeta(42) Aggregation By Perturbing The H-Bond Network In And Around The Central Hydrophobic Cluster (883 views)
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2013 Mar 18; 14(5): 583-592.
Impact Factor: 3.06
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Grasso G, Spoto G
* Plasmonics for the study of metal ion-protein interactions (478 views)
Anal Bioanal Chem (ISSN: 1618-2642), 2013 Feb; 405(6): 1833-1843.
Impact Factor: 3.578
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Mercurio FA, Marasco D, Pirone L, Scognamiglio PL, Pedone E, Pellecchia M, Leone M
* Heterotypic Sam-Sam Association Between Odin-Sam1 And Arap3-Sam: Binding Affinity And Structural Insights (411 views)
Chembiochem (ISSN: 1439-4227, 1439-9422, 1439-7633), 2013 Jan 2; 14(1): 100-106.
Impact Factor: 2.92
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Poletto M, Vascotto C, Scognamiglio PL, Lirussi L, Marasco D, Tell G
* Role Of The Unstructured N-Terminal Domain Of The Human Apurinic/Apyrimidinic Endonuclease 1 (hape1) In The Modulation Of Its Interaction With Nucleic Acids And Nucleophosmin (npm1) (504 views)
Biochem J (ISSN: 0264-6021, 1470-8728electronic, 0264-6021linking), 2013; 452(3): 545-557.
Impact Factor: 4.779
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Ruggiero A, Smaldone G, Squeglia F, Berisio R
* Enhanced crystallizability by protein engineering approaches: A general overview (2106 views)
Protein Pept Lett (ISSN: 0929-8665, 1875-5305), 2012 Jul; 19(7): 732-742.
Impact Factor: 1.994
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Viparelli F, Doti N, Sandomenico A, Marasco D, Dathan NA, Miele C, Beguinot F, Monti SM, Ruvo M
* GSM48878: CD8 IL2-D2 (396 views)
Gene Expression Omnibus, 2011 Dec 2; 59(2): 302-308.
Impact Factor: 2.082
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Ruvo M, Sandomenico A, Tudisco L, De Falco S
* Branched peptides for the modulation of protein-protein interactions: More arms are better than one? (540 views)
Curr Med Chem (ISSN: 0929-8673, 1875-533x, 1875-533xelectronic), 2011 Jun; 18(16): 2429-2437.
Impact Factor: 4.859
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Correale S, Pirone L, Di Marcotullio L, De Smaele E, Greco A, Mazzà D, Moretti M, Alterio V, Vitagliano L, Di Gaetano S, Gulino A, Pedone E
* Molecular organization of the cullin E3 ligase adaptor KCTD11 (587 views)
Biochimie (ISSN: 0300-9084, 1638-6183, 1638-6183electronic), 2011 Apr; 93(4): 715-724.
Impact Factor: 3.022
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Farina B, Pirone L, Russo L, Viparelli F, Doti N, Pedone C, Pedone E, Fattorusso R
* NMR backbone dynamics studies of human PED/PEA-15 outline protein functional sites (739 views)
Febs J (ISSN: 1742-4658, 1742-464x, 1742-4658electronic), 2010 Oct; 277(20): 4229-4240.
Impact Factor: 3.129
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Sandomenico A, Monti SM, Sabatella M, De Capua A, Tornatore L, Doti N, Viparelli F, Dathan NA, Pedone C, Ruvo M, Marasco D
* Protein-protein interactions: a simple strategy to identify binding sites and peptide antagonists (663 views)
Chem Biol Drug Des (ISSN: 1747-0285, 1747-0277), 2009 May; 73(5): 483-493.
Impact Factor: 2.473
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Vitagliano L, Ruggiero A, Pedone C, Berisio R
* Molecular dynamics studies of the P pilus rod subunit PapA (582 views)
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2009 Mar; 15(3): 192-199.
Impact Factor: 1.807
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Merlino A, Varriale S, Coscia MR, Mazzarella L, Oreste U
* Structure and dimerization of the teleost transmembrane immunoglobulin region (420 views)
Journal Of Molecular Graphics & Modelling (ISSN: 1093-3263), 2008 Oct; 27(3): 401-407.
Impact Factor: 2.347
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Vitagliano L, Ruggiero A, Pedone C, Berisio R
* Conformational states and association mechanism of Yersinia pestis Caf1 subunits (330 views)
Biochem Biophys Res Commun (ISSN: 0006-291x, 1090-2104, 1090-2104electronic), 2008 Sep 8; 372(4): 804-810.
Impact Factor: 2.648
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Ruvo M, Marasco D, Viparelli F, Tornatore L, Sandomenico A, Doti N, Pedone C, Benedetti E, Monti SM
* Peptide antagonists of protein-protein interactions identified by screening protein fragments derived by enzyme degradation (349 views)
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2008 Sep; 14(8): N/D-N/D.
Impact Factor: 1.654
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Galdiero S, Vitiello M, Falanga A, D'Isanto M, Cantisani M, Kampanaraki A, Benedetti E, Browne H, Galdiero M
* Peptides containing membrane-interacting motifs inhibit herpes simplex virus type 1 infectivity (481 views)
Peptides (ISSN: 0196-9781, 1873-5169electronic, 0196-9781linking), 2008 Sep; 29(9): 1461-1471.
Impact Factor: 2.565
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Viparelli F, Doti N, Sandomenico A, Marasco D, Dathan NA, Miele C, Beguinot F, Monti SM, Ruvo M
* Expression and purification of the D4 region of PLD1 and characterization of its interaction with PED-PEA15 (481 views)
Protein Expr Purif (ISSN: 1046-5928), 2008 Jun; 59(2): 302-308.
Impact Factor: 1.621
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Limauro D, Pedone E, Galdi I, Bartolucci S
* Peroxiredoxins as cellular guardians in Sulfolobus solfataricus - characterization of Bcp1, Bcp3 and Bcp4 (399 views)
Febs Journal (ISSN: 1742-464x), 2008 May; 275(9): 2067-2077.
Impact Factor: 3.139
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Tornatore L, Marasco D, Dathan N, Vitale RM, Benedetti E, Papa S, Franzoso G, Ruvo M, Monti SM
* Gadd45 beta forms a homodimeric complex that binds tightly to MKK7 (532 views)
J Mol Biol (ISSN: 0022-2836, 0022-2283, 1089-8638), 2008 Apr 18; 378(1): 97-111.
Impact Factor: 5.673
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Bischof Delaloye A, Carrio I, Cuocolo A, Knapp W, Gourtsoyiannis N, Mccall I, Reiser M, Silberman B
* White paper of the European Association of Nuclear Medicine (EANM) and the European Society of Radiology (ESR) on multimodality imaging (407 views)
Eur J Nucl Med (ISSN: 1619-7070, 1619-7089, 0340-6997), 2007 Sep; 34(8): 1147-1151.
Impact Factor: 4.101
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D'Auria S, Varriale A, Gonnelli M, Saviano M, Staiano M, Rossi M, Strambini GB
* Tryptophan phosphorescence studies of the D-galactose/ D-glucose-binding protein from Escherichia coli provide a molecular portrait with structural and dynamics features of the protein (703 views)
J Proteome Res (ISSN: 1535-3893), 2007; 6(4): 1306-1312.
Impact Factor: 5.675
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Galdiero S, Vitiello M, Amodeo P, D'Isanto M, Cantisani M, Pedone C, Galdiero M
* Structural requirements for proinflammatory activity of porin P2 loop 7 from Haemophilus influenzae (594 views)
Biochemistry (ISSN: 0006-2960, 1520-4995, 1520-4995electronic), 2006 Apr 11; 45(14): 4491-4501.
Impact Factor: 3.633
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Mannini R, Rivieccio V, D'Auria S, Tanfani F, Ausili A, Pedone C, Grimaldi G, Facchiano A
* Erratum: Structure/function of KRAB repression domains: Structural properties of KRAB modules inferred from hydrodynamic, circular dichroism, and FTIR spectroscopic analyses (Proteins: Structure, Function and Bioinformatics (2006) 62 (604-616)) (241 views)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006; 65(2): 524-524.
Impact Factor: 3.73
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Berisio R, Loguercio S, De Simone A, Zagari A, Vitagliano L
* Polyproline helices in protein structures: A statistical survey (339 views)
Protein Pept Lett (ISSN: 0929-8665, 1875-5305), 2006; 13(8): 847-854.
Impact Factor: 1.13
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Sorrentino N, De Simone G, Menchise V, Mandrich L, Rossi M, Manco G, Pedone C
* Crystallization and preliminary X-ray diffraction studies of Aes acetyl-esterase from Escherichia coli (359 views)
Acta Crystallogr D Biol Crystallogr (ISSN: 0907-4449, 0907-4449linking), 2003 Oct; 59(10): 1846-1848.
Impact Factor: 2.208
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48 Records (44 excluding Abstracts).
Total impact factor: 163.473 (149.182 excluding Abstracts).
Total 5 year impact factor: 174.827 (161.646 excluding Abstracts).
Total impact factor: 163.473 (149.182 excluding Abstracts).
Total 5 year impact factor: 174.827 (161.646 excluding Abstracts).
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