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Volumn 61, Issue 2, 2005, Pages 310-317

Cooperative effects in hydrogen-bonding of protein secondary structure elements: A systematic analysis of crystal data using secbase

Author keywords

helix; sheet; 310 helix; Cooperative effects; H bond length; Secondary structure elements; Systematic analysis of crystal data

Indexed keywords

AMIDE; CARBONYL DERIVATIVE; LIGAND; PROTEIN;

EID: 26444561843     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20613     Document Type: Article
Times cited : (42)

References (31)
  • 1
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 3
    • 0024290472 scopus 로고
    • Amino acid preferences for specific locations at the ends of alpha helices
    • Richardson JS, Richardson DC. Amino acid preferences for specific locations at the ends of alpha helices. Science 1988;240:1648-1652.
    • (1988) Science , vol.240 , pp. 1648-1652
    • Richardson, J.S.1    Richardson, D.C.2
  • 4
    • 0034994293 scopus 로고    scopus 로고
    • The interrelationships of side-chain and main-chain conformations in proteins
    • Chakrabarti P, Pal D. The interrelationships of side-chain and main-chain conformations in proteins. Prog Biophys Mol Biol 2001;76:1-102.
    • (2001) Prog Biophys Mol Biol , vol.76 , pp. 1-102
    • Chakrabarti, P.1    Pal, D.2
  • 5
    • 1842523274 scopus 로고    scopus 로고
    • Amino acid propensities are position-dependent throughout the length of alpha helices
    • Engel DE, DeGrado WF. Amino acid propensities are position-dependent throughout the length of alpha helices. J Mol Biol 2004;337:1195-1205.
    • (2004) J Mol Biol , vol.337 , pp. 1195-1205
    • Engel, D.E.1    DeGrado, W.F.2
  • 6
    • 0019776488 scopus 로고
    • Dipoles of the alpha helix and beta sheet: Their role in protein folding
    • Hol WG, Halie LM, Sander C. Dipoles of the alpha helix and beta sheet: their role in protein folding. Nature 1981;294:532-536.
    • (1981) Nature , vol.294 , pp. 532-536
    • Hol, W.G.1    Halie, L.M.2    Sander, C.3
  • 8
    • 0034826730 scopus 로고    scopus 로고
    • Alpha- and 3(10) helix interconversion: A quantum-chemical study on polyalanine systems in the gas phase and in aqueous solvent
    • Topol IA, Burt SK, Deretey E, Tang TH, Perczel A, Rashin A, Csizmadia IG. alpha- and 3(10) helix interconversion: a quantum-chemical study on polyalanine systems in the gas phase and in aqueous solvent. J Am Chem Soc 2001;123:6054-6060.
    • (2001) J Am Chem Soc , vol.123 , pp. 6054-6060
    • Topol, I.A.1    Burt, S.K.2    Deretey, E.3    Tang, T.H.4    Perczel, A.5    Rashin, A.6    Csizmadia, I.G.7
  • 9
    • 0034806675 scopus 로고    scopus 로고
    • A theoretical study on the origin of cooperativity in the formation of 3(10)- and alpha helices
    • Wu YD, Zhao YL. A theoretical study on the origin of cooperativity in the formation of 3(10)- and alpha helices. J Am Chem Soc 2001;123:5313-5319.
    • (2001) J Am Chem Soc , vol.123 , pp. 5313-5319
    • Wu, Y.D.1    Zhao, Y.L.2
  • 10
    • 2342487975 scopus 로고    scopus 로고
    • Structure, spectra and the effects of twisting of beta sheet peptides. A density functional theory study
    • Bour P, Keiderling T. Structure, spectra and the effects of twisting of beta sheet peptides. A density functional theory study. J Mol Struct-Theochem 2004;675:95-105.
    • (2004) J Mol Struct-Theochem , vol.675 , pp. 95-105
    • Bour, P.1    Keiderling, T.2
  • 11
    • 0001731266 scopus 로고    scopus 로고
    • Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects
    • Bergner A, Günther J, Hendlich M, Klebe G, Verdenk M. Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects. Biopolymers 2001;61:99-110.
    • (2001) Biopolymers , vol.61 , pp. 99-110
    • Bergner, A.1    Günther, J.2    Hendlich, M.3    Klebe, G.4    Verdenk, M.5
  • 12
    • 0037436339 scopus 로고    scopus 로고
    • Relibase: Design and development of a database for comprehensive analysis of protein-ligand interactions
    • Hendlich M, Bergner A, Günther J, Klebe G. Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. J Mol Biol 2003;326:607-620.
    • (2003) J Mol Biol , vol.326 , pp. 607-620
    • Hendlich, M.1    Bergner, A.2    Günther, J.3    Klebe, G.4
  • 15
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994;3:522-524.
    • (1994) Protein Sci , vol.3 , pp. 522-524
    • Hobohm, U.1    Sander, C.2
  • 16
    • 0035314041 scopus 로고    scopus 로고
    • Pex, analytical tools for PDB files. II. H-Pex: Noncanonical H-bonds in alpha helices
    • Thomas A, Benhabiles N, Meurisse R, Ngwabije R, Brasseur R. Pex, analytical tools for PDB files. II. H-Pex: Noncanonical H-bonds in alpha helices. Proteins 2001;43:37-44.
    • (2001) Proteins , vol.43 , pp. 37-44
    • Thomas, A.1    Benhabiles, N.2    Meurisse, R.3    Ngwabije, R.4    Brasseur, R.5
  • 17
    • 0142104233 scopus 로고    scopus 로고
    • Atomic resolution density maps reveal secondary structure dependent differences in electronic distribution
    • Lario PI, Vrielink A. Atomic resolution density maps reveal secondary structure dependent differences in electronic distribution. J Am Chem Soc 2003;125:12787-12794.
    • (2003) J Am Chem Soc , vol.125 , pp. 12787-12794
    • Lario, P.I.1    Vrielink, A.2
  • 18
    • 0037434686 scopus 로고    scopus 로고
    • Density functional theory study of the cooperativity of hydrogen bonds in finite and infinite alphahelices
    • Ireta J, Neugebauer J, Scheffler M, Rojo A, Galvan M. Density functional theory study of the cooperativity of hydrogen bonds in finite and infinite alphahelices. J Phys Chem B 2003;107:1432-1437.
    • (2003) J Phys Chem B , vol.107 , pp. 1432-1437
    • Ireta, J.1    Neugebauer, J.2    Scheffler, M.3    Rojo, A.4    Galvan, M.5
  • 19
    • 0034829669 scopus 로고    scopus 로고
    • Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly-alpha-aminoisobutyric acid in vacuo
    • Improta R, Barone V, Kudin K, Scuseria G. Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly-alpha-aminoisobutyric acid in vacuo. J Am Chem Soc 2001;123:3311-3322.
    • (2001) J Am Chem Soc , vol.123 , pp. 3311-3322
    • Improta, R.1    Barone, V.2    Kudin, K.3    Scuseria, G.4
  • 20
    • 0347578256 scopus 로고    scopus 로고
    • Cooperativity in amide hydrogen bonding chains. Relation between energy, position, and H-bond chain length in peptide and protein folding models
    • Kobko N, Dannenberg J. Cooperativity in amide hydrogen bonding chains. Relation between energy, position, and H-bond chain length in peptide and protein folding models. J Phys Chem A 2003;107:10389-10395.
    • (2003) J Phys Chem A , vol.107 , pp. 10389-10395
    • Kobko, N.1    Dannenberg, J.2
  • 21
    • 0035063642 scopus 로고    scopus 로고
    • Observation of the closing of individual hydrogen bonds during TFE-induced helix formation in a peptide
    • Jaravine V, Alexandrescu A, Grzesiek S. Observation of the closing of individual hydrogen bonds during TFE-induced helix formation in a peptide. Protein Sci 2001;10:943-950.
    • (2001) Protein Sci , vol.10 , pp. 943-950
    • Jaravine, V.1    Alexandrescu, A.2    Grzesiek, S.3
  • 22
    • 0035138648 scopus 로고    scopus 로고
    • A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method
    • Cui Q, Elstner M, Kaxiras E, Frauenheim T, Karplus M. A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method. J Phys Chem B 2001;105:569-585.
    • (2001) J Phys Chem B , vol.105 , pp. 569-585
    • Cui, Q.1    Elstner, M.2    Kaxiras, E.3    Frauenheim, T.4    Karplus, M.5
  • 23
    • 0034656826 scopus 로고    scopus 로고
    • DFT studies on helix formation in N-acetyl-(L-alanyl)(n)-N′- methylamide for n = 1-20
    • Elstner M, Jalkanen K, Knapp-Mohammady M, Frauenheim T, Suhai S. DFT studies on helix formation in N-acetyl-(L-alanyl)(n)-N′-methylamide for n = 1-20. Chem Phys 2000;256:15-27.
    • (2000) Chem Phys , vol.256 , pp. 15-27
    • Elstner, M.1    Jalkanen, K.2    Knapp-Mohammady, M.3    Frauenheim, T.4    Suhai, S.5
  • 24
    • 77949975511 scopus 로고    scopus 로고
    • Potentials and algorithms for incorporating polarizability in computer simulations
    • Rick S, Stuart S. Potentials and algorithms for incorporating polarizability in computer simulations. Rev Comp Ch 2002:89-146.
    • (2002) Rev Comp Ch , pp. 89-146
    • Rick, S.1    Stuart, S.2
  • 25
    • 0036296028 scopus 로고    scopus 로고
    • Twist and shear in beta sheets and beta-ribbons
    • Ho B, Curmi P. Twist and shear in beta sheets and beta-ribbons. J Mol Biol 2002;317:291-308.
    • (2002) J Mol Biol , vol.317 , pp. 291-308
    • Ho, B.1    Curmi, P.2
  • 26
    • 0021978310 scopus 로고
    • The role of the alpha helix dipole in protein function and structure
    • Hol WG. The role of the alpha helix dipole in protein function and structure. Prog Biophys Mol Biol 1985;45:149-195.
    • (1985) Prog Biophys Mol Biol , vol.45 , pp. 149-195
    • Hol, W.G.1
  • 27
    • 4444306767 scopus 로고    scopus 로고
    • Crystal structure of phenylalanine ammonia lyase: Multiple helix dipoles implicated in catalysis
    • Calabrese JC, Jordan DB, Boodhoo A, Sariaslani S, Vannelli T. Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis. Biochemistry 2004;43:11403-11416.
    • (2004) Biochemistry , vol.43 , pp. 11403-11416
    • Calabrese, J.C.1    Jordan, D.B.2    Boodhoo, A.3    Sariaslani, S.4    Vannelli, T.5
  • 29
    • 0037122805 scopus 로고    scopus 로고
    • X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity
    • Dutzler R, Campbell EB, Cadene M, Chait BT, MacKinnon R. X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity. Nature 2002;415:287-294.
    • (2002) Nature , vol.415 , pp. 287-294
    • Dutzler, R.1    Campbell, E.B.2    Cadene, M.3    Chait, B.T.4    MacKinnon, R.5
  • 31
    • 26444593637 scopus 로고    scopus 로고
    • St. Louis, MI: Tripos Inc
    • Tripos. SYBYL 7.0. St. Louis, MI: Tripos Inc.
    • SYBYL 7.0


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.