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Volumn 75, Issue 2, 2009, Pages 413-429

Satisfaction of hydrogen-bonding potential influences the conservation of polar sidechains

Author keywords

Buried residues; Hydrogen bonds; Polar sidechains; Protein stability; Protein structure

Indexed keywords

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; HYDROGEN BOND; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STABILITY; PROTEIN STRUCTURE; CHEMISTRY; ENTROPY; METABOLISM; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE;

EID: 66149139802     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22248     Document Type: Article
Times cited : (25)

References (41)
  • 1
    • 76549252207 scopus 로고
    • The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain
    • Pauling L, Corey RB, Branson HR. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 1951;37:205-211.
    • (1951) Proc Natl Acad Sci USA , vol.37 , pp. 205-211
    • Pauling, L.1    Corey, R.B.2    Branson, H.R.3
  • 2
    • 0000573263 scopus 로고
    • Configurations of polypeptide chains with favored orientations around single bonds: Two new pleated sheets
    • Pauling L, Corey RB. Configurations of polypeptide chains with favored orientations around single bonds: two new pleated sheets. Proc Natl Acad Sci USA 1951;37:729-740.
    • (1951) Proc Natl Acad Sci USA , vol.37 , pp. 729-740
    • Pauling, L.1    Corey, R.B.2
  • 4
    • 0027163998 scopus 로고
    • The sixth Datta lecture. Protein folding and stability: The pathway of folding ofbarnase
    • Fersht AR. The sixth Datta lecture. Protein folding and stability: the pathway of folding ofbarnase. FEBS Lett 1993;325(1/2):5-16.
    • (1993) FEBS Lett , vol.325 , Issue.1-2 , pp. 5-16
    • Fersht, A.R.1
  • 5
    • 0029132790 scopus 로고
    • Thermodynamics of partly folded intermediates in proteins
    • Freire E. Thermodynamics of partly folded intermediates in proteins. Annu Rev Biophys Biomol Struct 1995;24:141-165.
    • (1995) Annu Rev Biophys Biomol Struct , vol.24 , pp. 141-165
    • Freire, E.1
  • 6
  • 8
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J Mol Biol 1994;238:777-793.
    • (1994) J Mol Biol , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 9
    • 22244449669 scopus 로고    scopus 로고
    • Do all backbone polar groups in proteins form hydrogen bonds?
    • Fleming PJ, Rose GD. Do all backbone polar groups in proteins form hydrogen bonds? Protein Sci 2005;14:1911-1917.
    • (2005) Protein Sci , vol.14 , pp. 1911-1917
    • Fleming, P.J.1    Rose, G.D.2
  • 10
    • 0033061876 scopus 로고    scopus 로고
    • Secondary structures without backbone: An analysis of backbone mimicry by polar side chains in protein structures
    • Eswar N, Ramakrishnan C. Secondary structures without backbone: an analysis of backbone mimicry by polar side chains in protein structures. Protein Eng 1999;12:447-55.
    • (1999) Protein Eng , vol.12 , pp. 447-455
    • Eswar, N.1    Ramakrishnan, C.2
  • 11
    • 0034062925 scopus 로고    scopus 로고
    • Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures
    • Eswar N, Ramakrishnan C. Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures. Protein Eng 2000;13:227-238.
    • (2000) Protein Eng , vol.13 , pp. 227-238
    • Eswar, N.1    Ramakrishnan, C.2
  • 12
    • 0027204024 scopus 로고
    • Helix stop signals in proteins and peptides: The capping box
    • Harper ET, Rose GD. Helix stop signals in proteins and peptides: the capping box. Biochemistry 1993;32:7605-7609.
    • (1993) Biochemistry , vol.32 , pp. 7605-7609
    • Harper, E.T.1    Rose, G.D.2
  • 13
    • 33645315212 scopus 로고    scopus 로고
    • Hydrogen bonding increases packing density in the protein interior
    • Schell D, Tsai J, Scholtz JM, Pace CN. Hydrogen bonding increases packing density in the protein interior. Proteins 2006;63:278-282.
    • (2006) Proteins , vol.63 , pp. 278-282
    • Schell, D.1    Tsai, J.2    Scholtz, J.M.3    Pace, C.N.4
  • 14
    • 0027062943 scopus 로고
    • Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds
    • Overington J, Donnelly D, Johnson MS, Sali A, Blundell TL. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci 1992;1:216-226.
    • (1992) Protein Sci , vol.1 , pp. 216-226
    • Overington, J.1    Donnelly, D.2    Johnson, M.S.3    Sali, A.4    Blundell, T.L.5
  • 15
    • 0025104478 scopus 로고
    • Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction
    • Overington J, Johnson MS, Sali A, Blundell TL. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc Biol Sci 1990;241:132-145.
    • (1990) Proc Biol Sci , vol.241 , pp. 132-145
    • Overington, J.1    Johnson, M.S.2    Sali, A.3    Blundell, T.L.4
  • 16
    • 0035895356 scopus 로고    scopus 로고
    • Polar group burial contributes more to protein stability than nonpolar group burial
    • Pace CN. Polar group burial contributes more to protein stability than nonpolar group burial. Biochemistry 2001;40:310-313.
    • (2001) Biochemistry , vol.40 , pp. 310-313
    • Pace, C.N.1
  • 17
    • 0041856175 scopus 로고    scopus 로고
    • The contribution of polar group burial to protein stability is strongly context-dependent
    • Takano K, Scholtz JM, Sacchettini JC, Pace CN. The contribution of polar group burial to protein stability is strongly context-dependent. J Biol Chem 2003;278:31790-31795.
    • (2003) J Biol Chem , vol.278 , pp. 31790-31795
    • Takano, K.1    Scholtz, J.M.2    Sacchettini, J.C.3    Pace, C.N.4
  • 18
    • 0031766401 scopus 로고    scopus 로고
    • HOM-STRAD: A database of protein structure alignments for homologous families
    • Mizuguchi K, Deane CM, Blundell TL, Overington JP. HOM-STRAD: a database of protein structure alignments for homologous families. Protein Sci 1998;7:2469-2471.
    • (1998) Protein Sci , vol.7 , pp. 2469-2471
    • Mizuguchi, K.1    Deane, C.M.2    Blundell, T.L.3    Overington, J.P.4
  • 19
    • 0030945495 scopus 로고    scopus 로고
    • Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties
    • Alexov EG, Gunner MR. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. Bio-phys J 1997;72:2075-2093.
    • (1997) Bio-phys J , vol.72 , pp. 2075-2093
    • Alexov, E.G.1    Gunner, M.R.2
  • 20
    • 25144518398 scopus 로고    scopus 로고
    • PROVAT: A tool for Voronoi tessellation analysis of protein structures and complexes
    • Gore SP, Burke DF, Blundell TL. PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes. Bioinformatics 2005;21:3316-3317.
    • (2005) Bioinformatics , vol.21 , pp. 3316-3317
    • Gore, S.P.1    Burke, D.F.2    Blundell, T.L.3
  • 21
    • 0031853406 scopus 로고    scopus 로고
    • New scoring schemes for protein fold recognition based on Voronoi contacts
    • Zimmer R, Wohler M, Thiele R. New scoring schemes for protein fold recognition based on Voronoi contacts. Bioinformatics 1998;14:295-308.
    • (1998) Bioinformatics , vol.14 , pp. 295-308
    • Zimmer, R.1    Wohler, M.2    Thiele, R.3
  • 22
    • 33846041078 scopus 로고    scopus 로고
    • Consortium T. The universal protein resource (UniProt). Nucleic Acids Res 2007;35(Database Issue):D193-D197.
    • Consortium T. The universal protein resource (UniProt). Nucleic Acids Res 2007;35(Database Issue):D193-D197.
  • 23
    • 0026342532 scopus 로고
    • Information-theoretical entropy as a measure of sequence variability
    • Shenkin PS, Erman B, Mastrandrea LD. Information-theoretical entropy as a measure of sequence variability. Proteins 1991;11:297-313.
    • (1991) Proteins , vol.11 , pp. 297-313
    • Shenkin, P.S.1    Erman, B.2    Mastrandrea, L.D.3
  • 24
    • 0000390762 scopus 로고
    • Lost hydrogen bonds and buried surface area: Rationalising stability in globular proteins
    • Savage HJ, Elliott CJ, Freeman CM, Finney JL. Lost hydrogen bonds and buried surface area: rationalising stability in globular proteins. J Chem Soc Faraday Trans 1993;89:2609-2617.
    • (1993) J Chem Soc Faraday Trans , vol.89 , pp. 2609-2617
    • Savage, H.J.1    Elliott, C.J.2    Freeman, C.M.3    Finney, J.L.4
  • 26
    • 26444443482 scopus 로고    scopus 로고
    • An assessment of the accuracy of methods for predicting hydrogen positions in protein structures
    • Forrest LR, Honig B. An assessment of the accuracy of methods for predicting hydrogen positions in protein structures. Proteins 2005;61:296-309.
    • (2005) Proteins , vol.61 , pp. 296-309
    • Forrest, L.R.1    Honig, B.2
  • 29
    • 0028332007 scopus 로고
    • A role for surface hydrophobicity in protein-protein recognition
    • Young L, Jernigan RL, Covell DG. A role for surface hydrophobicity in protein-protein recognition. Protein Sci 1994;3:717-729.
    • (1994) Protein Sci , vol.3 , pp. 717-729
    • Young, L.1    Jernigan, R.L.2    Covell, D.G.3
  • 30
    • 0035178383 scopus 로고    scopus 로고
    • Protein-protein interfaces: Analysis of amino acid conservation in homodimers
    • Valdar WS, Thornton JM. Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 2001;42:108-124.
    • (2001) Proteins , vol.42 , pp. 108-124
    • Valdar, W.S.1    Thornton, J.M.2
  • 31
    • 0030052841 scopus 로고    scopus 로고
    • Surface hydrophobic residues of multiubiquitin chains essential for proteo-lytic targeting
    • Beal R, Deveraux Q, Xia G, Rechsteiner M, Pickart C. Surface hydrophobic residues of multiubiquitin chains essential for proteo-lytic targeting. Proc Natl Acad Sci USA 1996;93:861-866.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 861-866
    • Beal, R.1    Deveraux, Q.2    Xia, G.3    Rechsteiner, M.4    Pickart, C.5
  • 32
    • 0036201059 scopus 로고    scopus 로고
    • Cyclin A-and cyclin E-Cdk complexes shuttle between the nucleus and the cytoplasm
    • Jackman M, Kubota Y, den Elzen N, Hagting A, Pines J. Cyclin A-and cyclin E-Cdk complexes shuttle between the nucleus and the cytoplasm. Mol Biol Cell 2002;13:1030-1045.
    • (2002) Mol Biol Cell , vol.13 , pp. 1030-1045
    • Jackman, M.1    Kubota, Y.2    den Elzen, N.3    Hagting, A.4    Pines, J.5
  • 33
    • 0032167631 scopus 로고    scopus 로고
    • Substrate recruitment to cyclin-dependent kinase 2 by a multipurpose docking site on cyclin A
    • Schulman BA, Lindstrom DL, Harlow E. Substrate recruitment to cyclin-dependent kinase 2 by a multipurpose docking site on cyclin A. Proc Natl Acad Sci USA 1998;95:10453-10458.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 10453-10458
    • Schulman, B.A.1    Lindstrom, D.L.2    Harlow, E.3
  • 34
    • 0025759275 scopus 로고
    • The protein-folding problem: The native fold determines packing, but does packing determine the native fold?
    • Behe MJ, Lattman EE, Rose GD. The protein-folding problem: the native fold determines packing, but does packing determine the native fold? Proc Natl Acad Sci USA 1991;88:4195-4199.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 4195-4199
    • Behe, M.J.1    Lattman, E.E.2    Rose, G.D.3
  • 35
    • 0037314097 scopus 로고    scopus 로고
    • Matrix2png: A utility for visualizing matrix data
    • Pavlidis P, Noble WS. Matrix2png: a utility for visualizing matrix data. Bioinformatics 2003;19:295-296.
    • (2003) Bioinformatics , vol.19 , pp. 295-296
    • Pavlidis, P.1    Noble, W.S.2
  • 37
    • 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
  • 38
    • 0024290488 scopus 로고
    • Helix signals in proteins
    • Presta LG, Rose GD. Helix signals in proteins. Science 1988;240: 1632-1641.
    • (1988) Science , vol.240 , pp. 1632-1641
    • Presta, L.G.1    Rose, G.D.2
  • 39
    • 0033548705 scopus 로고    scopus 로고
    • A recurring two-hydrogen-bond motif incorporating a serine or threonine residue is found both at alpha-helical N termini and in other situations
    • Wan WY, Milner-White EJ. A recurring two-hydrogen-bond motif incorporating a serine or threonine residue is found both at alpha-helical N termini and in other situations. J Mol Biol 1999;286: 1651-1662.
    • (1999) J Mol Biol , vol.286 , pp. 1651-1662
    • Wan, W.Y.1    Milner-White, E.J.2
  • 40
    • 0033548459 scopus 로고    scopus 로고
    • A natural grouping of motifs with an aspartate or asparagine residue forming two hydrogen bonds to residues ahead in sequence: Their occurrence at alpha-helical N termini and in other situations
    • Wan WY, Milner-White EJ. A natural grouping of motifs with an aspartate or asparagine residue forming two hydrogen bonds to residues ahead in sequence: their occurrence at alpha-helical N termini and in other situations. J Mol Biol 1999;286:1633-1649.
    • (1999) J Mol Biol , vol.286 , pp. 1633-1649
    • Wan, W.Y.1    Milner-White, E.J.2
  • 41
    • 0345411975 scopus 로고    scopus 로고
    • Tolerance to the substitution of buried apolar residues by charged residues in the homologous protein structures
    • Balaji S, Aruna S, Srinivasan N. Tolerance to the substitution of buried apolar residues by charged residues in the homologous protein structures. Proteins 2003;53:783-791.
    • (2003) Proteins , vol.53 , pp. 783-791
    • Balaji, S.1    Aruna, S.2    Srinivasan, N.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.