Analysis and design of turns in α-helical hairpins (471 views)
J Mol Biol (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 2005; 346(5): 1441-1454.
Export to BibTeX Export to EndNote
Paper type: Journal Article,
Impact factor: 5.229, 5-year impact factor: 3.795
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-13844276055&partnerID=40&md5=6e850486131c8d587b0424911a2abe04
Keywords: Diiron Proteins, Helical Hairpin, Protein Design, Turns, Df1 Protein, Hairpin Protein, Protein Derivative, Unclassified Drug, Alpha Helix, Article, Conformational Transition, Correlation Analysis, Cross Linking, Dimerization, Experimental Design, Molecular Biology, Molecular Interaction, Molecular Model, Nuclear Magnetic Resonance, Priority Journal, Protein Determination, Protein Stability, Sequence Analysis, Structure Analysis, X Ray Crystallography, Amino Acid Sequence, Computational Biology, Computer-Aided Design, X-Ray, Magnetic Resonance Spectroscopy, Metalloproteins, Molecular Sequence Data, Protein Structure, Secondary, Sequence Homology,
Affiliations:
*** IBB - CNR ***
Dept. of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, United States
Department of Chemistry, University of Naples 'Federico II', Via Cinthia, I-80126 Naples, Italy
Ctr. Excellence Biocrystallography, Department of Chemical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
Department of Protein Design, Centocor, Malvern, PA 19355, United States
Ist. di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
References:
Rose, G.D., Gierasch, L.M., Smith, J.A., Turns in peptides and proteins (1985) Advan. Protein Chem., 37, pp. 1-11
Wilmot, C.M., Thornton, J.M., Analysis and prediction of the different types of beta-turn in proteins (1988) J. Mol. Biol., 203, pp. 221-232
Sibanda, B.L., Thornton, J.M., Beta-hairpin families in globular proteins (1985) Nature, 316, pp. 170-174
Gunasekaran, K., Ramakrishnan, C., Balaram, P., Beta-hairpins in proteins revisited: Lessons for de novo design (1997) Protein Eng., 10, pp. 1131-1141
Ramirez-Alvarado, M., Blanco, F.J., Serrano, L., De novo design and structural analysis of a model beta-hairpin peptide system (1996) Nature Struct. Biol., 3, pp. 604-612
Chung, Y.J., Christianson, L.A., Stanger, H.E., Powell, D.R., Gellman, S.H., A beta-peptide reverse turn that promotes hairpin formation (1998) J. Am. Chem. Soc., 120, pp. 10555-10556
Krauthauser, S., Christianson, L.A., Powell, D.R., Gellman, S.H., Antiparallel sheet formation in beta-peptide foldamers: Effects of beta-amino acid substitution on conformational preference (1997) J. Am. Chem. Soc., 119, pp. 11719-11720
Brunet, A.P., Huang, E.S., Huffine, M.E., Loeb, J.E., Weltman, R.J., Hecht, M.H., The role of turns in the structure of an alpha-helical protein (1993) Nature, 364, pp. 355-358
Predki, P.F., Agrawal, V., Brunger, A.T., Regan, L., Amino-acid substitutions in a surface turn modulate protein stability (1996) Nature Struct. Biol., 3, pp. 54-58
Nagi, A.D., Anderson, K.S., Regan, L., Using loop length variants to dissect the folding pathway of a four-helix-bundle protein (1999) J. Mol. Biol., 286, pp. 257-265
Glykos, N.M., Cesareni, G., Kokkinidis, M., Protein plasticity to the extreme: Changing the topology of a 4-alpha-helical bundle with a single amino acid substitution (1999) Struct. Fold. Des., 7, pp. 597-603
Hill, R.B., Degrado, W.F., A polar, solvent-exposed residue can be essential for native protein structure (2000) Struct. Fold. Des., 8, pp. 471-479
Lombardi, A., Summa, C., Degrado, W.F., Retrostructural analysis of metalloproteins: De novo design of a model for diiron proteins (2000) Proc. Natl Acad. Sci., 97, pp. 6298-6305
Efimov, A.V., Patterns of loop regions in proteins (1993) Curr. Opin. Struct. Biol., 3, pp. 379-384
Di Costanzo, L., Wade, H., Geremia, S., Randaccio, L., Pavone, V., Degrado, W.F., Lombardi, A., Toward the de novo design of a catalytically active helix bundle: A substrate-accessible carboxylate-bridged dinuclear metal center (2001) J. Am. Chem. Soc., 123, pp. 12749-12757
Efimov, A.V., Structure of alpha-alpha-hairpins with short connections (1991) Protein Eng., 4, pp. 245-250
Gunasekaran, K., Nagarajaram, H.A., Ramakrishnan, C., Balaram, P., Stereochemical punctuation marks in protein structures: Glycine and proline containing helix stop signals (1998) J. Mol. Biol., 275, pp. 917-932
Parker, M.H., Hefford, M.A., A consensus residue analysis of loop and helix-capping residues in four-alpha-helical-bundle proteins (1997) Protein Eng., 10, pp. 487-496
Pal, D., Chakrabarti, P., On residues in the disallowed region of the Ramachandran map (2002) Biopolymers, 63, pp. 195-206
Schellman, C., The αl-conformation at the ends of helices (1980) Protein Folding, pp. 53-61. , P. Jaenicke Elsevier New York
Hovmoller, S., Zhou, T., Ohlson, T., Conformations of amino acids in proteins (2002) Acta Crystallog. Sect. D, 58, pp. 768-776
Aurora, R., Srinivasan, R., Rose, G.D., Rules for α-helix termination by glycine (1994) Science, 264, pp. 1126-1130
Milner-White, E.J., Situations of gamma-turns in proteins. Their relation to alpha-helices, beta-sheets and ligand binding sites (1990) J. Mol. Biol., 216, pp. 386-397
Madan Babu, M., Kumar Singh, S., Balaram, P., A C-H triple bond O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins (2002) J. Mol. Biol., 322, pp. 871-880
Sagermann, M., Martensson, L.G., Baase, W.A., Matthews, B.W., A test of proposed rules for helix capping: Implications for protein design (2002) Protein Sci., 11, pp. 516-521
Engel, D.E., Degrado, W.F., Amino acid propensities are position-dependent throughout the length of alpha-helices (2004) J. Mol. Biol., 337, pp. 1195-1205
Doig, A.J., Baldwin, R.L., N- and C-capping preferences for all 20 amino acids in alpha-helical peptides (1995) Protein Sci., 4, pp. 1325-1336
Pasternak, A., Kaplan, J., Lear, J.D., Degrado, W.F., Proton and metal ion-dependent assembly of a model diiron protein (2001) Protein Sci., 10, pp. 958-969
Serrano, L., Sancho, J., Hirshberg, M., Fersht, A.R., α-Helix stability in proteins I. Empirical correlations concerning substitution of side-chains at the N and C-caps and the replacement of alanine by glycine or serine at the solvent-exposed surfaces (1992) J. Mol. Biol., 227, pp. 544-559
Munoz, V., Serrano, L., Helix design, prediction and stability (1995) Curr. Opin. Biotechnol., 6, pp. 382-386
Dasgupta, S., Bell, J.A., Design of helix ends. Amino acid preferences, hydrogen bonding and electrostatic interactions (1993) Int. J. Pept. Protein Res., 41, pp. 499-511
Aurora, R., Rose, G.D., Helix capping (1998) Protein Sci., 7, pp. 21-38
Maglio, O., Nastri, F., Pavone, V., Lombardi, A., Degrado, W.F., Preorganization of molecular binding sites in designed diiron proteins (2003) Proc. Natl Acad. Sci. USA, 100, pp. 3772-3777
Richardson, J., The anatomy and taxonomy of protein structures (1981) Advan. Protein Chem., 34, pp. 168-340
Baker, E.N., Hubbard, R.E., Hydrogen bonding in globular proteins (1984) Prog. Biophys. Mol. Biol., 44, pp. 97-179
Veber, D.F., Freidinger, R.M., Perlow, D.S., Paleveda, W.J., Holly, F.W., Strachan, R.G., A potent cyclic hexapeptide analogue of somatostatin (1981) Nature, 292, p. 55
Hynes, T.R., Kautz, R.A., Goodman, M.A., Gill, J.F., Fox, R.O., Transfer of a beta-turn structure to a new protein context (1989) Nature, 339, pp. 73-76
Kuhlman, B., O'Neill, J.W., Kim, D.E., Zhang, K.Y., Baker, D., Accurate computer-based design of a new backbone conformation in the second turn of protein L (2002) J. Mol. Biol., 315, pp. 471-477
Hobohm, U., Sander, C., Enlarged representative set of protein structures (1994) Protein Sci., 3, pp. 522-524
Bansal, M., Kumar, S., Velavan, R., HELANAL: A program to characterize helix geometry in proteins (2000) J. Biomol. Struct. Dynam., 17, pp. 811-819
Kabsch, W., Sander, C., Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features (1983) Biopolymers, 22, pp. 2577-2637
Otwinowski, Z., Minor, W., Processing of X-ray diffraction data collected in oscillation mode (1997) Methods Enzymol., 276, pp. 307-326
Navaza, J., AMoRe: An automated molecular replacement program package (1994) Acta Crystallog. Sect. a, 50, pp. 157-163
Jones, T.A., Zou, J.-Y., Cowan, S.W., Kjeldgaard, M., Improved methods for building protein models in electron density maps and the location of errors in these models (1991) Acta Crystallog. Sect. a, 47, pp. 110-119
Brunger, A.T., Adams, P.D., Clore, G.M., Delao, W.L., Gros, P., Grosse-Kunstleve, R.W., Crystallography NMR system: A new software suite for macromolecular structure determination (1998) Acta Crystallog. Sect. D, 54, pp. 905-921
Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M., PROCHECK: A program to check the stereochemical quality of protein structures (1993) J. Appl. Crystallog., 26, pp. 283-291
Wüthrich, K., (1986) NMR of Proteins and Nucleic Acids, , Wiley New York
Kumar, A., Ernst, R.R., Wuthrich, K., A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules (1980) Biochem. Biophys. Res. Commun., 95, pp. 1-6
Jeneer, J., Meier, B.H., Bachmann, P., Ernst, R.R., Investigation of exchange process by two-dimensional NMR spectroscopy (1979) J. Chem. Phys., 71, pp. 4546-4553
Bax, A.D., Davis, D.G., MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy (1985) J. Magn. Reson., 65, pp. 355-360
Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A., NMRPipe: A multidimensional spectral processing system based on UNIX pipes (1995) J. Biomol. NMR, 6, pp. 277-293
Bartels, C., Xia, T.-H., Billeter, M., Güntert, P., Wüthrich, K., The program XEASY for computer-supported NMR spectral analysis of biological macromolecules (1995) J. Biomol. NMR, 5, pp. 1-10
Guntert, P., Mumenthaler, C., Wüthrich, K., Torsion angle dynamics for NMR structure calculation with the new program DYANA (1997) J. Mol. Biol., 273, pp. 283-298
Rose, G. D., Gierasch, L. M., Smith, J. A., Turns in peptides and proteins (1985) Advan. Protein Chem., 37, pp. 1-11
Wilmot, C. M., Thornton, J. M., Analysis and prediction of the different types of beta-turn in proteins (1988) J. Mol. Biol., 203, pp. 221-232
Sibanda, B. L., Thornton, J. M., Beta-hairpin families in globular proteins (1985) Nature, 316, pp. 170-174
Chung, Y. J., Christianson, L. A., Stanger, H. E., Powell, D. R., Gellman, S. H., A beta-peptide reverse turn that promotes hairpin formation (1998) J. Am. Chem. Soc., 120, pp. 10555-10556
Brunet, A. P., Huang, E. S., Huffine, M. E., Loeb, J. E., Weltman, R. J., Hecht, M. H., The role of turns in the structure of an alpha-helical protein (1993) Nature, 364, pp. 355-358
Predki, P. F., Agrawal, V., Brunger, A. T., Regan, L., Amino-acid substitutions in a surface turn modulate protein stability (1996) Nature Struct. Biol., 3, pp. 54-58
Nagi, A. D., Anderson, K. S., Regan, L., Using loop length variants to dissect the folding pathway of a four-helix-bundle protein (1999) J. Mol. Biol., 286, pp. 257-265
Glykos, N. M., Cesareni, G., Kokkinidis, M., Protein plasticity to the extreme: Changing the topology of a 4-alpha-helical bundle with a single amino acid substitution (1999) Struct. Fold. Des., 7, pp. 597-603
Hill, R. B., Degrado, W. F., A polar, solvent-exposed residue can be essential for native protein structure (2000) Struct. Fold. Des., 8, pp. 471-479
Efimov, A. V., Patterns of loop regions in proteins (1993) Curr. Opin. Struct. Biol., 3, pp. 379-384
Efimov, A. V., Structure of alpha-alpha-hairpins with short connections (1991) Protein Eng., 4, pp. 245-250
Parker, M. H., Hefford, M. A., A consensus residue analysis of loop and helix-capping residues in four-alpha-helical-bundle proteins (1997) Protein Eng., 10, pp. 487-496
Milner-White, E. J., Situations of gamma-turns in proteins. Their relation to alpha-helices, beta-sheets and ligand binding sites (1990) J. Mol. Biol., 216, pp. 386-397
Engel, D. E., Degrado, W. F., Amino acid propensities are position-dependent throughout the length of alpha-helices (2004) J. Mol. Biol., 337, pp. 1195-1205
Doig, A. J., Baldwin, R. L., N- and C-capping preferences for all 20 amino acids in alpha-helical peptides (1995) Protein Sci., 4, pp. 1325-1336
Baker, E. N., Hubbard, R. E., Hydrogen bonding in globular proteins (1984) Prog. Biophys. Mol. Biol., 44, pp. 97-179
Veber, D. F., Freidinger, R. M., Perlow, D. S., Paleveda, W. J., Holly, F. W., Strachan, R. G., A potent cyclic hexapeptide analogue of somatostatin (1981) Nature, 292, p. 55
Hynes, T. R., Kautz, R. A., Goodman, M. A., Gill, J. F., Fox, R. O., Transfer of a beta-turn structure to a new protein context (1989) Nature, 339, pp. 73-76
Jones, T. A., Zou, J. -Y., Cowan, S. W., Kjeldgaard, M., Improved methods for building protein models in electron density maps and the location of errors in these models (1991) Acta Crystallog. Sect. a, 47, pp. 110-119
Brunger, A. T., Adams, P. D., Clore, G. M., Delao, W. L., Gros, P., Grosse-Kunstleve, R. W., Crystallography NMR system: A new software suite for macromolecular structure determination (1998) Acta Crystallog. Sect. D, 54, pp. 905-921
Laskowski, R. A., MacArthur, M. W., Moss, D. S., Thornton, J. M., PROCHECK: A program to check the stereochemical quality of protein structures (1993) J. Appl. Crystallog., 26, pp. 283-291
W thrich, K., (1986) NMR of Proteins and Nucleic Acids, , Wiley New York
Bax, A. D., Davis, D. G., MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy (1985) J. Magn. Reson., 65, pp. 355-360
J Mol Biol (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 2005; 346(5): 1441-1454.
Export to BibTeX Export to EndNote
Paper type: Journal Article,
Impact factor: 5.229, 5-year impact factor: 3.795
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-13844276055&partnerID=40&md5=6e850486131c8d587b0424911a2abe04
Keywords: Diiron Proteins, Helical Hairpin, Protein Design, Turns, Df1 Protein, Hairpin Protein, Protein Derivative, Unclassified Drug, Alpha Helix, Article, Conformational Transition, Correlation Analysis, Cross Linking, Dimerization, Experimental Design, Molecular Biology, Molecular Interaction, Molecular Model, Nuclear Magnetic Resonance, Priority Journal, Protein Determination, Protein Stability, Sequence Analysis, Structure Analysis, X Ray Crystallography, Amino Acid Sequence, Computational Biology, Computer-Aided Design, X-Ray, Magnetic Resonance Spectroscopy, Metalloproteins, Molecular Sequence Data, Protein Structure, Secondary, Sequence Homology,
Affiliations:
*** IBB - CNR ***
Dept. of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, United States
Department of Chemistry, University of Naples 'Federico II', Via Cinthia, I-80126 Naples, Italy
Ctr. Excellence Biocrystallography, Department of Chemical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
Department of Protein Design, Centocor, Malvern, PA 19355, United States
Ist. di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
References:
Rose, G.D., Gierasch, L.M., Smith, J.A., Turns in peptides and proteins (1985) Advan. Protein Chem., 37, pp. 1-11
Wilmot, C.M., Thornton, J.M., Analysis and prediction of the different types of beta-turn in proteins (1988) J. Mol. Biol., 203, pp. 221-232
Sibanda, B.L., Thornton, J.M., Beta-hairpin families in globular proteins (1985) Nature, 316, pp. 170-174
Gunasekaran, K., Ramakrishnan, C., Balaram, P., Beta-hairpins in proteins revisited: Lessons for de novo design (1997) Protein Eng., 10, pp. 1131-1141
Ramirez-Alvarado, M., Blanco, F.J., Serrano, L., De novo design and structural analysis of a model beta-hairpin peptide system (1996) Nature Struct. Biol., 3, pp. 604-612
Chung, Y.J., Christianson, L.A., Stanger, H.E., Powell, D.R., Gellman, S.H., A beta-peptide reverse turn that promotes hairpin formation (1998) J. Am. Chem. Soc., 120, pp. 10555-10556
Krauthauser, S., Christianson, L.A., Powell, D.R., Gellman, S.H., Antiparallel sheet formation in beta-peptide foldamers: Effects of beta-amino acid substitution on conformational preference (1997) J. Am. Chem. Soc., 119, pp. 11719-11720
Brunet, A.P., Huang, E.S., Huffine, M.E., Loeb, J.E., Weltman, R.J., Hecht, M.H., The role of turns in the structure of an alpha-helical protein (1993) Nature, 364, pp. 355-358
Predki, P.F., Agrawal, V., Brunger, A.T., Regan, L., Amino-acid substitutions in a surface turn modulate protein stability (1996) Nature Struct. Biol., 3, pp. 54-58
Nagi, A.D., Anderson, K.S., Regan, L., Using loop length variants to dissect the folding pathway of a four-helix-bundle protein (1999) J. Mol. Biol., 286, pp. 257-265
Glykos, N.M., Cesareni, G., Kokkinidis, M., Protein plasticity to the extreme: Changing the topology of a 4-alpha-helical bundle with a single amino acid substitution (1999) Struct. Fold. Des., 7, pp. 597-603
Hill, R.B., Degrado, W.F., A polar, solvent-exposed residue can be essential for native protein structure (2000) Struct. Fold. Des., 8, pp. 471-479
Lombardi, A., Summa, C., Degrado, W.F., Retrostructural analysis of metalloproteins: De novo design of a model for diiron proteins (2000) Proc. Natl Acad. Sci., 97, pp. 6298-6305
Efimov, A.V., Patterns of loop regions in proteins (1993) Curr. Opin. Struct. Biol., 3, pp. 379-384
Di Costanzo, L., Wade, H., Geremia, S., Randaccio, L., Pavone, V., Degrado, W.F., Lombardi, A., Toward the de novo design of a catalytically active helix bundle: A substrate-accessible carboxylate-bridged dinuclear metal center (2001) J. Am. Chem. Soc., 123, pp. 12749-12757
Efimov, A.V., Structure of alpha-alpha-hairpins with short connections (1991) Protein Eng., 4, pp. 245-250
Gunasekaran, K., Nagarajaram, H.A., Ramakrishnan, C., Balaram, P., Stereochemical punctuation marks in protein structures: Glycine and proline containing helix stop signals (1998) J. Mol. Biol., 275, pp. 917-932
Parker, M.H., Hefford, M.A., A consensus residue analysis of loop and helix-capping residues in four-alpha-helical-bundle proteins (1997) Protein Eng., 10, pp. 487-496
Pal, D., Chakrabarti, P., On residues in the disallowed region of the Ramachandran map (2002) Biopolymers, 63, pp. 195-206
Schellman, C., The αl-conformation at the ends of helices (1980) Protein Folding, pp. 53-61. , P. Jaenicke Elsevier New York
Hovmoller, S., Zhou, T., Ohlson, T., Conformations of amino acids in proteins (2002) Acta Crystallog. Sect. D, 58, pp. 768-776
Aurora, R., Srinivasan, R., Rose, G.D., Rules for α-helix termination by glycine (1994) Science, 264, pp. 1126-1130
Milner-White, E.J., Situations of gamma-turns in proteins. Their relation to alpha-helices, beta-sheets and ligand binding sites (1990) J. Mol. Biol., 216, pp. 386-397
Madan Babu, M., Kumar Singh, S., Balaram, P., A C-H triple bond O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins (2002) J. Mol. Biol., 322, pp. 871-880
Sagermann, M., Martensson, L.G., Baase, W.A., Matthews, B.W., A test of proposed rules for helix capping: Implications for protein design (2002) Protein Sci., 11, pp. 516-521
Engel, D.E., Degrado, W.F., Amino acid propensities are position-dependent throughout the length of alpha-helices (2004) J. Mol. Biol., 337, pp. 1195-1205
Doig, A.J., Baldwin, R.L., N- and C-capping preferences for all 20 amino acids in alpha-helical peptides (1995) Protein Sci., 4, pp. 1325-1336
Pasternak, A., Kaplan, J., Lear, J.D., Degrado, W.F., Proton and metal ion-dependent assembly of a model diiron protein (2001) Protein Sci., 10, pp. 958-969
Serrano, L., Sancho, J., Hirshberg, M., Fersht, A.R., α-Helix stability in proteins I. Empirical correlations concerning substitution of side-chains at the N and C-caps and the replacement of alanine by glycine or serine at the solvent-exposed surfaces (1992) J. Mol. Biol., 227, pp. 544-559
Munoz, V., Serrano, L., Helix design, prediction and stability (1995) Curr. Opin. Biotechnol., 6, pp. 382-386
Dasgupta, S., Bell, J.A., Design of helix ends. Amino acid preferences, hydrogen bonding and electrostatic interactions (1993) Int. J. Pept. Protein Res., 41, pp. 499-511
Aurora, R., Rose, G.D., Helix capping (1998) Protein Sci., 7, pp. 21-38
Maglio, O., Nastri, F., Pavone, V., Lombardi, A., Degrado, W.F., Preorganization of molecular binding sites in designed diiron proteins (2003) Proc. Natl Acad. Sci. USA, 100, pp. 3772-3777
Richardson, J., The anatomy and taxonomy of protein structures (1981) Advan. Protein Chem., 34, pp. 168-340
Baker, E.N., Hubbard, R.E., Hydrogen bonding in globular proteins (1984) Prog. Biophys. Mol. Biol., 44, pp. 97-179
Veber, D.F., Freidinger, R.M., Perlow, D.S., Paleveda, W.J., Holly, F.W., Strachan, R.G., A potent cyclic hexapeptide analogue of somatostatin (1981) Nature, 292, p. 55
Hynes, T.R., Kautz, R.A., Goodman, M.A., Gill, J.F., Fox, R.O., Transfer of a beta-turn structure to a new protein context (1989) Nature, 339, pp. 73-76
Kuhlman, B., O'Neill, J.W., Kim, D.E., Zhang, K.Y., Baker, D., Accurate computer-based design of a new backbone conformation in the second turn of protein L (2002) J. Mol. Biol., 315, pp. 471-477
Hobohm, U., Sander, C., Enlarged representative set of protein structures (1994) Protein Sci., 3, pp. 522-524
Bansal, M., Kumar, S., Velavan, R., HELANAL: A program to characterize helix geometry in proteins (2000) J. Biomol. Struct. Dynam., 17, pp. 811-819
Kabsch, W., Sander, C., Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features (1983) Biopolymers, 22, pp. 2577-2637
Otwinowski, Z., Minor, W., Processing of X-ray diffraction data collected in oscillation mode (1997) Methods Enzymol., 276, pp. 307-326
Navaza, J., AMoRe: An automated molecular replacement program package (1994) Acta Crystallog. Sect. a, 50, pp. 157-163
Jones, T.A., Zou, J.-Y., Cowan, S.W., Kjeldgaard, M., Improved methods for building protein models in electron density maps and the location of errors in these models (1991) Acta Crystallog. Sect. a, 47, pp. 110-119
Brunger, A.T., Adams, P.D., Clore, G.M., Delao, W.L., Gros, P., Grosse-Kunstleve, R.W., Crystallography NMR system: A new software suite for macromolecular structure determination (1998) Acta Crystallog. Sect. D, 54, pp. 905-921
Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M., PROCHECK: A program to check the stereochemical quality of protein structures (1993) J. Appl. Crystallog., 26, pp. 283-291
Wüthrich, K., (1986) NMR of Proteins and Nucleic Acids, , Wiley New York
Kumar, A., Ernst, R.R., Wuthrich, K., A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules (1980) Biochem. Biophys. Res. Commun., 95, pp. 1-6
Jeneer, J., Meier, B.H., Bachmann, P., Ernst, R.R., Investigation of exchange process by two-dimensional NMR spectroscopy (1979) J. Chem. Phys., 71, pp. 4546-4553
Bax, A.D., Davis, D.G., MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy (1985) J. Magn. Reson., 65, pp. 355-360
Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A., NMRPipe: A multidimensional spectral processing system based on UNIX pipes (1995) J. Biomol. NMR, 6, pp. 277-293
Bartels, C., Xia, T.-H., Billeter, M., Güntert, P., Wüthrich, K., The program XEASY for computer-supported NMR spectral analysis of biological macromolecules (1995) J. Biomol. NMR, 5, pp. 1-10
Guntert, P., Mumenthaler, C., Wüthrich, K., Torsion angle dynamics for NMR structure calculation with the new program DYANA (1997) J. Mol. Biol., 273, pp. 283-298
Rose, G. D., Gierasch, L. M., Smith, J. A., Turns in peptides and proteins (1985) Advan. Protein Chem., 37, pp. 1-11
Wilmot, C. M., Thornton, J. M., Analysis and prediction of the different types of beta-turn in proteins (1988) J. Mol. Biol., 203, pp. 221-232
Sibanda, B. L., Thornton, J. M., Beta-hairpin families in globular proteins (1985) Nature, 316, pp. 170-174
Chung, Y. J., Christianson, L. A., Stanger, H. E., Powell, D. R., Gellman, S. H., A beta-peptide reverse turn that promotes hairpin formation (1998) J. Am. Chem. Soc., 120, pp. 10555-10556
Brunet, A. P., Huang, E. S., Huffine, M. E., Loeb, J. E., Weltman, R. J., Hecht, M. H., The role of turns in the structure of an alpha-helical protein (1993) Nature, 364, pp. 355-358
Predki, P. F., Agrawal, V., Brunger, A. T., Regan, L., Amino-acid substitutions in a surface turn modulate protein stability (1996) Nature Struct. Biol., 3, pp. 54-58
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Analysis and design of turns in α-helical hairpins
Although the analysis and design of turns that connect the strands in antiparallel β-hairpins has reached an advanced state, much less is known concerning turns between antiparallel helices in helical hairpins. We have conducted an analysis of the structures and sequence preferences of two types of interhelical turns, each of which connects the two helices by a two-residue linker in an αL-β conformation. Based on this analysis, it became apparent that the turn introduced into a designed four-helix bundle protein, DF1, did not occur within an optimal structural context. DF1 is a dimeric model for the diiron class of proteins. A longer loop with a β-αR-β conformation was inserted between two helices in the protein, and a sequence was chosen to stabilize its conformation. X-ray crystallography and NMR analysis of the protein showed the structure to be in excellent agreement with design. © 2004 Elsevier Ltd. All rights reserved.
Although the analysis and design of turns that connect the strands in antiparallel β-hairpins has reached an advanced state, much less is known concerning turns between antiparallel helices in helical hairpins. We have conducted an analysis of the structures and sequence preferences of two types of interhelical turns, each of which connects the two helices by a two-residue linker in an αL-β conformation. Based on this analysis, it became apparent that the turn introduced into a designed four-helix bundle protein, DF1, did not occur within an optimal structural context. DF1 is a dimeric model for the diiron class of proteins. A longer loop with a β-αR-β conformation was inserted between two helices in the protein, and a sequence was chosen to stabilize its conformation. X-ray crystallography and NMR analysis of the protein showed the structure to be in excellent agreement with design. © 2004 Elsevier Ltd. All rights reserved.
Analysis and design of turns in α-helical hairpins
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Analysis and design of turns in α-helical hairpins
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Chino M, Zhang SQ, Pirro F, Leone L, Maglio O, Lombardi A, Degrado WF
* Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster (315 views)
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Impact Factor: 2.572
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Chino M, Leone L, Zambrano G, Pirro F, D'Alonzo D, Firpo V, Aref D, Lista L, Maglio O, Nastri F, Lombardi A
* Oxidation catalysis by iron and manganese porphyrins within enzyme-like cages (241 views)
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Impact Factor: 2.572
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Caserta G, Chino M, Firpo V, Zambrano G, Leone L, D'Alonzo D, Nastri F, Maglio O, Pavone V, Lombardi A
* Enhancement of Peroxidase Activity in Artificial Mimochrome VI Catalysts through Rational Design (266 views)
Chembiochem, 2018; 19: 1823-1826.
Impact Factor: 2.774
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Chino M, Leone L, Maglio O, D'Alonzo D, Pirro F, Pavone V, Nastri F, Lombardi A
* A De Novo Heterodimeric Due Ferri Protein Minimizes the Release of Reactive Intermediates in Dioxygen-Dependent Oxidation (246 views) (PDF 169 views)
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Impact Factor: 12.102
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Chino M, Maglio O, Nastri F, Pavone V, Degrado WF, Lombardi A
* Artificial Diiron Enzymes with a de Novo Designed Four-Helix Bundle Structure (563 views)
Eur J Inorg Chem (ISSN: 1434-1948, 1099-0682e), 2015; 2015(21): 3371-3390.
Impact Factor: 2.686
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Faiella M, Maglio O, Nastri F, Lombardi A, Lista L, Hagen WR, Pavone V
* De Novo Design, Synthesis and Characterisation of MP3, A New Catalytic Four-Helix Bundle Hemeprotein (474 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2012 Dec 7; 18(50): 15960-15971.
Impact Factor: 5.831
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Maglio O, Nastri F, Lombardi A, Ciferri A, Perico A
* Structural and Functional Aspects of Metal Binding Sites in Natural and Designed Metalloproteins (535 views)
Ionic Interactions In Nat And Synthetic Macromolecules John Wiley And Sons (ISSN: 9780-4705), 2012; N/D: 361-450.
Impact Factor: 5.927
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Nastri F, Lista L, Ringhieri P, Vitale R, Faiella M, Andreozzi C, Travascio P, Maglio O, Lombardi A, Pavone V
* A Heme-Peptide Metalloenzyme Mimetic with Natural Peroxidase-Like Activity (435 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2011 Apr; 17(16): 4444-4453.
Impact Factor: 5.925
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Diana D, Ziaco B, Scarabelli G, Pedone C, Colombo G, D'Andrea LD, Fattorusso R
* Structural analysis of a helical peptide unfolding pathway (461 views)
Chemistry (ISSN: 1521-3765, 0947-6539, 1521-3765electronic), 2010 May 10; 16(18): 5400-5407.
Impact Factor: 5.476
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Calhoun JR, Nastri F, Maglio O, Pavone V, Lombardi A, Degrado WF
* Artificial diiron proteins: From structure to function (481 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2005; 80(2-3): 264-278.
Impact Factor: 2.545
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Di Costanzo L, Geremia S, Randaccio L, Nastri F, Maglio O, Lombardi A, Pavone V
* Miniaturized heme proteins: crystal structure of Co(III)-mimochrome IV (378 views)
J Biol Inorg Chem (ISSN: 0949-8257, 1432-1327electronic, 0949-8257print), 2004 Dec; 9(8): 1017-1027.
Impact Factor: 3.3
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Lombardi A, Nastri F, Marasco D, Maglio O, De Sanctis G, Sinibaldi F, Santucci R, Coletta M, Pavone V
* Design of a new mimochrome with unique topology (534 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2003 Nov 21; 9(22): 5643-5654.
Impact Factor: 4.353
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Maglio O, Nastri F, Pavone V, Lombardi A, Degrado WF
* Preorganization of molecular binding sites in designed diiron proteins (378 views)
P Natl Acad Sci Usa (ISSN: 0027-8424print, 0027-8424linking), 2003 Apr 1; 100(7): 3772-3777.
Impact Factor: 10.272
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Main ERG, Xiong Y, Cocco MJ, D'Andrea LD, Regan L
* Design of stable α-helical arrays from an idealized TPR motif (927 views)
Structure (ISSN: 0969-2126, 1878-4186, 0969-2126linking), 2003; 11(5): 497-508.
Impact Factor: 5.993
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* Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster (315 views)
Biopolymers (ISSN: 1097-0282electronic, 0006-3525linking, 0006-3525print), 2018 Sep 11; 109(10): e23339-e23339.
Impact Factor: 2.572
View Export to BibTeX Export to EndNote
Chino M, Leone L, Zambrano G, Pirro F, D'Alonzo D, Firpo V, Aref D, Lista L, Maglio O, Nastri F, Lombardi A
* Oxidation catalysis by iron and manganese porphyrins within enzyme-like cages (241 views)
Biopolymers (ISSN: 0006-3525linking, 0006-3525print, 1097-0282electronic), 2018 Aug; 109(10): e23107-e23107.
Impact Factor: 2.572
View Export to BibTeX Export to EndNote
Caserta G, Chino M, Firpo V, Zambrano G, Leone L, D'Alonzo D, Nastri F, Maglio O, Pavone V, Lombardi A
* Enhancement of Peroxidase Activity in Artificial Mimochrome VI Catalysts through Rational Design (266 views)
Chembiochem, 2018; 19: 1823-1826.
Impact Factor: 2.774
View Export to BibTeX Export to EndNote
Chino M, Leone L, Maglio O, D'Alonzo D, Pirro F, Pavone V, Nastri F, Lombardi A
* A De Novo Heterodimeric Due Ferri Protein Minimizes the Release of Reactive Intermediates in Dioxygen-Dependent Oxidation (246 views) (PDF 169 views)
Angew Chem Int Ed (ISSN: 1433-7851, 1521-3773electronic, 1433-7851linking), 2017 Dec 4; 56(49): 15580-15583.
Impact Factor: 12.102
View Export to BibTeX Export to EndNote
Chino M, Maglio O, Nastri F, Pavone V, Degrado WF, Lombardi A
* Artificial Diiron Enzymes with a de Novo Designed Four-Helix Bundle Structure (563 views)
Eur J Inorg Chem (ISSN: 1434-1948, 1099-0682e), 2015; 2015(21): 3371-3390.
Impact Factor: 2.686
View Export to BibTeX Export to EndNote
Faiella M, Maglio O, Nastri F, Lombardi A, Lista L, Hagen WR, Pavone V
* De Novo Design, Synthesis and Characterisation of MP3, A New Catalytic Four-Helix Bundle Hemeprotein (474 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2012 Dec 7; 18(50): 15960-15971.
Impact Factor: 5.831
View Export to BibTeX Export to EndNote
Maglio O, Nastri F, Lombardi A, Ciferri A, Perico A
* Structural and Functional Aspects of Metal Binding Sites in Natural and Designed Metalloproteins (535 views)
Ionic Interactions In Nat And Synthetic Macromolecules John Wiley And Sons (ISSN: 9780-4705), 2012; N/D: 361-450.
Impact Factor: 5.927
View Export to BibTeX Export to EndNote
Nastri F, Lista L, Ringhieri P, Vitale R, Faiella M, Andreozzi C, Travascio P, Maglio O, Lombardi A, Pavone V
* A Heme-Peptide Metalloenzyme Mimetic with Natural Peroxidase-Like Activity (435 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2011 Apr; 17(16): 4444-4453.
Impact Factor: 5.925
View Export to BibTeX Export to EndNote
Diana D, Ziaco B, Scarabelli G, Pedone C, Colombo G, D'Andrea LD, Fattorusso R
* Structural analysis of a helical peptide unfolding pathway (461 views)
Chemistry (ISSN: 1521-3765, 0947-6539, 1521-3765electronic), 2010 May 10; 16(18): 5400-5407.
Impact Factor: 5.476
View Export to BibTeX Export to EndNote
Calhoun JR, Nastri F, Maglio O, Pavone V, Lombardi A, Degrado WF
* Artificial diiron proteins: From structure to function (481 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2005; 80(2-3): 264-278.
Impact Factor: 2.545
View Export to BibTeX Export to EndNote
Di Costanzo L, Geremia S, Randaccio L, Nastri F, Maglio O, Lombardi A, Pavone V
* Miniaturized heme proteins: crystal structure of Co(III)-mimochrome IV (378 views)
J Biol Inorg Chem (ISSN: 0949-8257, 1432-1327electronic, 0949-8257print), 2004 Dec; 9(8): 1017-1027.
Impact Factor: 3.3
View Export to BibTeX Export to EndNote
Lombardi A, Nastri F, Marasco D, Maglio O, De Sanctis G, Sinibaldi F, Santucci R, Coletta M, Pavone V
* Design of a new mimochrome with unique topology (534 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2003 Nov 21; 9(22): 5643-5654.
Impact Factor: 4.353
View Export to BibTeX Export to EndNote
Maglio O, Nastri F, Pavone V, Lombardi A, Degrado WF
* Preorganization of molecular binding sites in designed diiron proteins (378 views)
P Natl Acad Sci Usa (ISSN: 0027-8424print, 0027-8424linking), 2003 Apr 1; 100(7): 3772-3777.
Impact Factor: 10.272
View Export to BibTeX Export to EndNote
Main ERG, Xiong Y, Cocco MJ, D'Andrea LD, Regan L
* Design of stable α-helical arrays from an idealized TPR motif (927 views)
Structure (ISSN: 0969-2126, 1878-4186, 0969-2126linking), 2003; 11(5): 497-508.
Impact Factor: 5.993
View Export to BibTeX Export to EndNote
14 Records (14 excluding Abstracts).
Total impact factor: 72.328 (72.328 excluding Abstracts).
Total 5 year impact factor: 70.848 (70.848 excluding Abstracts).
Total impact factor: 72.328 (72.328 excluding Abstracts).
Total 5 year impact factor: 70.848 (70.848 excluding Abstracts).
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