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Volumn 30, Issue 1, 2013, Pages 79-87

Protein conformational diversity modulates sequence divergence

Author keywords

conformational diversity; native state; protein evolution; sequence divergence

Indexed keywords

PROTEIN;

EID: 84871839239     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss080     Document Type: Article
Times cited : (27)

References (81)
  • 1
    • 13444302764 scopus 로고    scopus 로고
    • FunShift: A database of function shift analysis on protein subfamilies
    • Abhiman S, Sonnhammer EL. 2005. FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res. 33:D197-D200.
    • (2005) Nucleic Acids Res , vol.33
    • Abhiman, S.1    Sonnhammer, E.L.2
  • 2
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr. 19:716-723.
    • (1974) IEEE Trans Automat Contr , vol.19 , pp. 716-723
    • Akaike, H.1
  • 3
    • 38549161051 scopus 로고    scopus 로고
    • PROCOGNATE: A cognate ligand domain mapping for enzymes
    • Bashton M, Nobeli I, Thornton JM. 2008. PROCOGNATE: a cognate ligand domain mapping for enzymes. Nucleic Acids Res. 36: D618-D622.
    • (2008) Nucleic Acids Res , vol.36
    • Bashton, M.1    Nobeli, I.2    Thornton, J.M.3
  • 4
    • 0033533517 scopus 로고    scopus 로고
    • Neutral evolution of model proteins: Diffusion in sequence space and overdispersion
    • Bastolla U, Roman HE, VendruscoloM. 1999. Neutral evolution of model proteins: diffusion in sequence space and overdispersion. J Theor Biol. 200:49-64.
    • (1999) J Theor Biol , vol.200 , pp. 49-64
    • Bastolla, U.1    Roman, H.E.2    Vendruscolo, M.3
  • 6
    • 0642340510 scopus 로고    scopus 로고
    • Amino acid empirical contact energy definitions for fold recognition in the space of contact maps
    • Berrera M, Molinari H, Fogolari F. 2003. Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. BMC Bioinformatics 4:8.
    • (2003) BMC Bioinformatics , vol.4 , pp. 8
    • Berrera, M.1    Molinari, H.2    Fogolari, F.3
  • 8
    • 33748143748 scopus 로고    scopus 로고
    • Structural determinants of the rate of protein evolution in yeast
    • Bloom JD, Drummond DA, Arnold FH, Wilke CO. 2006. Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol. 23: 1751-1761.
    • (2006) Mol Biol Evol , vol.23 , pp. 1751-1761
    • Bloom, J.D.1    Drummond, D.A.2    Arnold, F.H.3    Wilke, C.O.4
  • 9
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase catalysis
    • Boehr DD, McElheny D, Dyson HJ, Wright PE. 2006. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313: 1638-1642.
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 10
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: A synthesis
    • Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. 1995. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 21:167-195.
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 11
    • 0024733407 scopus 로고
    • Intermediates and barrier crossing in a random energy model (with applications to protein folding)
    • Bryngelson JD,Wolynes PG. 1989. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J Phys Chem. 93:6902-6915.
    • (1989) J Phys Chem , vol.93 , pp. 6902-6915
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 13
    • 67649795139 scopus 로고    scopus 로고
    • Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure
    • Burra PV, Zhang Y, Godzik A, Stec B. 2009. Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure. Proc Natl Acad Sci USA. 106:10505-10510.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 10505-10510
    • Burra, P.V.1    Zhang, Y.2    Godzik, A.3    Stec, B.4
  • 14
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C, Lesk AM. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:823-826.
    • (1986) EMBO J , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 15
    • 0035823119 scopus 로고    scopus 로고
    • Understanding hierarchical protein evolution from first principles
    • Dokholyan NV, Shakhnovich EI. 2001. Understanding hierarchical protein evolution from first principles. J Mol Biol. 312:289-307.
    • (2001) J Mol Biol , vol.312 , pp. 289-307
    • Dokholyan, N.V.1    Shakhnovich, E.I.2
  • 17
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    • Drummond DA, Wilke CO. 2008. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352.
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 18
    • 0027024416 scopus 로고
    • Three-dimensional profiles for analysing protein sequence-structure relationships
    • Eisenberg D, Bowie JU, Luthy R, Choe S. 1992. Three-dimensional profiles for analysing protein sequence-structure relationships. Faraday Discuss. 93:25-34.
    • (1992) Faraday Discuss , vol.93 , pp. 25-34
    • Eisenberg, D.1    Bowie, J.U.2    Luthy, R.3    Choe, S.4
  • 19
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17:368-376.
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 20
    • 0000122573 scopus 로고
    • PHYLIP-phylogeny inference package (version 3.2)
    • Felsenstein J. 1989. PHYLIP-phylogeny inference package (version 3.2). Cladistics 5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 21
    • 67650021210 scopus 로고    scopus 로고
    • Effective knowledge-based potentials
    • Ferrada E, Melo F. 2009. Effective knowledge-based potentials. Protein Sci. 18:1469-1485.
    • (2009) Protein Sci , vol.18 , pp. 1469-1485
    • Ferrada, E.1    Melo, F.2
  • 23
    • 84892166712 scopus 로고
    • Einfluss der Configuration auf die wirkung der Enzyme
    • Fischer E. 1894. Einfluss der Configuration auf die wirkung der Enzyme. Ber Dtsch Chem Ges. 27:2985-2993.
    • (1894) Ber Dtsch Chem Ges , vol.27 , pp. 2985-2993
    • Fischer, E.1
  • 24
    • 0027943261 scopus 로고
    • Conformational isomerism and the diversity of antibodies
    • Foote J, Milstein C. 1994. Conformational isomerism and the diversity of antibodies. Proc Natl Acad Sci USA. 91:10370-10374.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 10370-10374
    • Foote, J.1    Milstein, C.2
  • 25
    • 0036184351 scopus 로고    scopus 로고
    • Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations
    • Fornasari MS, Parisi G, Echave J. 2002. Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations. Mol Biol Evol. 19:352-356.
    • (2002) Mol Biol Evol , vol.19 , pp. 352-356
    • Fornasari, M.S.1    Parisi, G.2    Echave, J.3
  • 26
    • 33846850375 scopus 로고    scopus 로고
    • Quaternary structure constraints on evolutionary sequence divergence
    • Fornasari MS, Parisi G, Echave J. 2007. Quaternary structure constraints on evolutionary sequence divergence. Mol Biol Evol. 24:349-351.
    • (2007) Mol Biol Evol , vol.24 , pp. 349-351
    • Fornasari, M.S.1    Parisi, G.2    Echave, J.3
  • 27
    • 67049155677 scopus 로고    scopus 로고
    • A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family
    • Friedland GD, Lakomek NA, Griesinger C,Meiler J, Kortemme T. 2009. A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol. 5:e1000393.
    • (2009) PLoS Comput Biol , vol.5
    • Friedland, G.D.1    Lakomek, N.A.2    Griesinger Cmeiler, J.3    Kortemme, T.4
  • 28
    • 33846033844 scopus 로고    scopus 로고
    • The CATH domain structure database: New protocols and classification levels giveamore comprehensive resource for exploring evolution
    • 14 co-authors
    • Greene LH, Lewis TE, Addou S, et al. (14 co-authors). 2007. The CATH domain structure database: new protocols and classification levels giveamore comprehensive resource for exploring evolution. Nucleic Acids Res. 35:D291-D297.
    • (2007) Nucleic Acids Res , vol.35
    • Greene, L.H.1    Lewis, T.E.2    Addou, S.3
  • 29
    • 0023984770 scopus 로고
    • Profile scanning for three-dimensional structural patterns in protein sequences
    • Gribskov M, Homyak M, Edenfield J, Eisenberg D. 1988. Profile scanning for three-dimensional structural patterns in protein sequences. Comput Appl Biosci. 4:61-66.
    • (1988) Comput Appl Biosci , vol.4 , pp. 61-66
    • Gribskov, M.1    Homyak, M.2    Edenfield, J.3    Eisenberg, D.4
  • 31
    • 12344307441 scopus 로고    scopus 로고
    • Conformational changes observed in enzyme crystal structures upon substrate binding
    • Gutteridge A, Thornton J. 2005. Conformational changes observed in enzyme crystal structures upon substrate binding. J Mol Biol. 346: 21-28.
    • (2005) J Mol Biol , vol.346 , pp. 21-28
    • Gutteridge, A.1    Thornton, J.2
  • 32
    • 0013817874 scopus 로고
    • The influence of amino-acid sequence on protein structure
    • Guzzo AV. 1965. The influence of amino-acid sequence on protein structure. Biophys J. 5:809-822.
    • (1965) Biophys J. , vol.5 , pp. 809-822
    • Guzzo, A.V.1
  • 33
    • 0034644783 scopus 로고    scopus 로고
    • Analysis and prediction of functional sub-types from protein sequence alignments
    • Hannenhalli SS, Russell RB. 2000. Analysis and prediction of functional sub-types from protein sequence alignments. J Mol Biol. 303:61-76.
    • (2000) J Mol Biol , vol.303 , pp. 61-76
    • Hannenhalli, S.S.1    Russell, R.B.2
  • 34
    • 36849048228 scopus 로고    scopus 로고
    • Intrinsic motions along an enzymatic reaction trajectory
    • 12 co-authors
    • Henzler-Wildman KA, Thai V, Lei M, et al. (12 co-authors). 2007. Intrinsic motions along an enzymatic reaction trajectory. Nature 450: 838-844.
    • (2007) Nature , vol.450 , pp. 838-844
    • Henzler-Wildman, K.A.1    Thai, V.2    Lei, M.3
  • 35
    • 76249122268 scopus 로고    scopus 로고
    • Biochemistry. An ensemble view of allostery
    • Hilser VJ. 2010. Biochemistry. An ensemble view of allostery. Science 327: 653-654.
    • (2010) Science , vol.327 , pp. 653-654
    • Hilser, V.J.1
  • 36
    • 0038148710 scopus 로고    scopus 로고
    • Conformational diversity and protein evolution-A 60-year-old hypothesis revisited
    • James LC, Tawfik DS. 2003. Conformational diversity and protein evolution-a 60-year-old hypothesis revisited. Trends Biochem Sci. 28: 361-368.
    • (2003) Trends Biochem Sci , vol.28 , pp. 361-368
    • James, L.C.1    Tawfik, D.S.2
  • 37
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8: 275-282.
    • (1992) Comput Appl Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 38
    • 78651327630 scopus 로고    scopus 로고
    • PCDB: A database of proteins with conformational diversity
    • Juritz J, Fernandez-Alberti S, Parisi G. 2011. PCDB: a database of proteins with conformational diversity. Nucleic Acids Res. 39(1 suppl): D475-D479.
    • (2011) Nucleic Acids Res , vol.39 , Issue.1 SUPPL.
    • Juritz, J.1    Fernandez-Alberti, S.2    Parisi, G.3
  • 39
    • 0025058563 scopus 로고
    • Escherichia coli aspartate transcarbamoylase: The molecular basis for a concerted allosteric transition
    • Kantrowitz ER, Lipscomb WN. 1990. Escherichia coli aspartate transcarbamoylase: the molecular basis for a concerted allosteric transition. Trends Biochem Sci. 15:53-59.
    • (1990) Trends Biochem Sci , vol.15 , pp. 53-59
    • Kantrowitz, E.R.1    Lipscomb, W.N.2
  • 41
    • 18744371588 scopus 로고    scopus 로고
    • Molecular dynamics and protein function
    • Karplus M, Kuriyan J. 2005. Molecular dynamics and protein function. Proc Natl Acad Sci USA. 102:6679-6685.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6679-6685
    • Karplus, M.1    Kuriyan, J.2
  • 42
    • 0001443732 scopus 로고
    • Heterogeneity of the binding sites of bovine serum albumin
    • Karush F. 1950. Heterogeneity of the binding sites of bovine serum albumin. J Am Chem Soc. 72:2705-2713.
    • (1950) J Am Chem Soc , vol.72 , pp. 2705-2713
    • Karush, F.1
  • 43
    • 0034029144 scopus 로고    scopus 로고
    • Proteins with similar architecture exhibit similar large-scale dynamic behavior
    • Keskin O, Jernigan RL, Bahar I. 2000. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys J. 78:2093-2106.
    • (2000) Biophys J , vol.78 , pp. 2093-2106
    • Keskin, O.1    Jernigan, R.L.2    Bahar, I.3
  • 44
    • 77953771357 scopus 로고    scopus 로고
    • Statistical potentials for improved structurally constrained evolutionary models
    • Kleinman CL, Rodrigue N, Lartillot N, Philippe H. 2010. Statistical potentials for improved structurally constrained evolutionary models. Mol Biol Evol. 27:1546-1560.
    • (2010) Mol Biol Evol , vol.27 , pp. 1546-1560
    • Kleinman, C.L.1    Rodrigue, N.2    Lartillot, N.3    Philippe, H.4
  • 45
    • 37849031192 scopus 로고    scopus 로고
    • Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments
    • Kondrashov DA, Zhang W, Aranda R, Stec B, Phillips GN Jr. 2008. Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments. Proteins 70: 353-362.
    • (2008) Proteins , vol.70 , pp. 353-362
    • Kondrashov, D.A.1    Zhang, W.2    Aranda, R.3    Stec, B.4    Phillips Jr., G.N.5
  • 46
    • 0028808763 scopus 로고
    • Context-dependent optimal substitution matrices
    • Koshi JM, Goldstein RA. 1995. Context-dependent optimal substitution matrices. Protein Eng. 8:641-645.
    • (1995) Protein Eng , vol.8 , pp. 641-645
    • Koshi, J.M.1    Goldstein, R.A.2
  • 48
    • 0028181441 scopus 로고
    • Hidden Markov models in computational biology. Applications to protein modeling
    • Krogh A, Brown M, Mian IS, Sjolander K, Haussler D. 1994. Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol. 235:1501-1531.
    • (1994) J Mol Biol , vol.235 , pp. 1501-1531
    • Krogh, A.1    Brown, M.2    Mian, I.S.3    Sjolander, K.4    Haussler, D.5
  • 49
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: Dynamic landscapes and population shifts
    • Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R. 2000. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci. 9: 10-19.
    • (2000) Protein Sci , vol.9 , pp. 10-19
    • Kumar, S.1    Ma, B.2    Tsai, C.J.3    Sinha, N.4    Nussinov, R.5
  • 51
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25:1307-1320.
    • (2008) Mol Biol Evol , vol.25 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 52
    • 0019332167 scopus 로고
    • How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
    • Lesk AM, Chothia C. 1980. How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol. 136:225-270.
    • (1980) J Mol Biol , vol.136 , pp. 225-270
    • Lesk, A.M.1    Chothia, C.2
  • 53
    • 0018093765 scopus 로고
    • Conformational preferences of amino acids in globular proteins
    • Levitt M. 1978. Conformational preferences of amino acids in globular proteins. Biochemistry 17:4277-4285.
    • (1978) Biochemistry , vol.17 , pp. 4277-4285
    • Levitt, M.1
  • 54
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • Luthy R, Bowie JU, Eisenberg D. 1992. Assessment of protein models with three-dimensional profiles. Nature 356:83-85.
    • (1992) Nature , vol.356 , pp. 83-85
    • Luthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 55
    • 0025997601 scopus 로고
    • Secondary structure-based profiles: Use of structure-conserving scoring tables in searching protein sequence databases for structural similarities
    • Luthy R, McLachlan AD, Eisenberg D. 1991. Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins 10: 229-239.
    • (1991) Proteins , vol.10 , pp. 229-239
    • Luthy, R.1    McLachlan, A.D.2    Eisenberg, D.3
  • 56
    • 0036147568 scopus 로고    scopus 로고
    • Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
    • Ma B, Shatsky M,Wolfson HJ, Nussinov R. 2002. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 11:184-197.
    • (2002) Protein Sci , vol.11 , pp. 184-197
    • Ma, B.1    Shatsky Mwolfson, H.J.2    Nussinov, R.3
  • 57
    • 49049096095 scopus 로고    scopus 로고
    • Evolutionary conservation of protein vibrational dynamics
    • Maguid S, Fernandez-Alberti S, Echave J. 2008. Evolutionary conservation of protein vibrational dynamics. Gene 422:7-13.
    • (2008) Gene , vol.422 , pp. 7-13
    • Maguid, S.1    Fernandez-Alberti, S.2    Echave, J.3
  • 58
    • 23244450294 scopus 로고    scopus 로고
    • Exploring the common dynamics of homologous proteins. Application to the globin family
    • Maguid S, Fernandez-Alberti S, Ferrelli L, Echave J. 2005. Exploring the common dynamics of homologous proteins. Application to the globin family. Biophys J. 89:3-13.
    • (2005) Biophys J , vol.89 , pp. 3-13
    • Maguid, S.1    Fernandez-Alberti, S.2    Ferrelli, L.3    Echave, J.4
  • 59
  • 60
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: A plausible model
    • Monod J, Wyman J, Changeux JP. 1965. On the nature of allosteric transitions: a plausible model. J Mol Biol. 12:88-118.
    • (1965) J Mol Biol , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.P.3
  • 61
    • 34547631623 scopus 로고    scopus 로고
    • Prevention of amyloid-like aggregation as a driving force of protein evolution
    • Monsellier E, Chiti F. 2007. Prevention of amyloid-like aggregation as a driving force of protein evolution. EMBO Rep. 8:737-742.
    • (2007) EMBO Rep , vol.8 , pp. 737-742
    • Monsellier, E.1    Chiti, F.2
  • 63
    • 0036839162 scopus 로고    scopus 로고
    • MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison
    • Ortiz AR, Strauss CE, Olmea O. 2002. MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci. 11:2606-2621.
    • (2002) Protein Sci , vol.11 , pp. 2606-2621
    • Ortiz, A.R.1    Strauss, C.E.2    Olmea, O.3
  • 64
    • 0026474167 scopus 로고
    • Structural constraints on residue substitution
    • Overington J. 1992. Structural constraints on residue substitution. Genet Eng (N Y). 14:231-249.
    • (1992) Genet Eng (N y , vol.14 , pp. 231-249
    • Overington, J.1
  • 65
    • 0025104478 scopus 로고
    • Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction
    • Overington J, Johnson MS, Sali A, Blundell TL. 1990. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc R Soc B Biol Sci. 241: 132-145.
    • (1990) Proc R Soc B Biol Sci , vol.241 , pp. 132-145
    • Overington, J.1    Johnson, M.S.2    Sali, A.3    Blundell, T.L.4
  • 66
    • 0035028705 scopus 로고    scopus 로고
    • Structural constraints and emergence of sequence patterns in protein evolution
    • Parisi G, Echave J. 2001. Structural constraints and emergence of sequence patterns in protein evolution. Mol Biol Evol. 18:750-756.
    • (2001) Mol Biol Evol , vol.18 , pp. 750-756
    • Parisi, G.1    Echave, J.2
  • 67
    • 33845548778 scopus 로고    scopus 로고
    • The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily
    • Parisi G, Echave J. 2004. The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily. BMC Evol Biol. 4:41.
    • (2004) BMC Evol Biol , vol.4 , pp. 41
    • Parisi, G.1    Echave, J.2
  • 68
    • 13444305208 scopus 로고    scopus 로고
    • Generality of the structurally constrained protein evolution model: Assessment on representatives of the four main fold classes
    • Parisi G, Echave J. 2005. Generality of the structurally constrained protein evolution model: assessment on representatives of the four main fold classes. Gene 345:45-53.
    • (2005) Gene , vol.345 , pp. 45-53
    • Parisi, G.1    Echave, J.2
  • 69
    • 15844406550 scopus 로고    scopus 로고
    • HyPhy: Hypothesis testing using phylogenies
    • Pond SL, Frost SD, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676-679.
    • (2005) Bioinformatics , vol.21 , pp. 676-679
    • Pond, S.L.1    Frost, S.D.2    Muse, S.V.3
  • 70
    • 0027288463 scopus 로고
    • The HSSP database of protein structuresequence alignments
    • Sander C, Schneider R. 1993. The HSSP database of protein structuresequence alignments. Nucleic Acids Res. 21:3105-3109.
    • (1993) Nucleic Acids Res , vol.21 , pp. 3105-3109
    • Sander, C.1    Schneider, R.2
  • 72
    • 0035853126 scopus 로고    scopus 로고
    • Point mutations and sequence variability in proteins: Redistributions of preexisting populations
    • Sinha N, Nussinov R. 2001. Point mutations and sequence variability in proteins: redistributions of preexisting populations. Proc Natl Acad Sci USA. 98:3139-3144.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 3139-3144
    • Sinha, N.1    Nussinov, R.2
  • 73
    • 64849101493 scopus 로고    scopus 로고
    • Protein dynamism and evolvability
    • Tokuriki N, Tawfik DS. 2009. Protein dynamism and evolvability. Science 324:203-207.
    • (2009) Science , vol.324 , pp. 203-207
    • Tokuriki, N.1    Tawfik, D.S.2
  • 74
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • Tsai CJ, Kumar S, Ma B, Nussinov R. 1999. Folding funnels, binding funnels, and protein function. Protein Sci. 8:1181-1190.
    • (1999) Protein Sci , vol.8 , pp. 1181-1190
    • Tsai, C.J.1    Kumar, S.2    Ma, B.3    Nussinov, R.4
  • 75
    • 0033621104 scopus 로고    scopus 로고
    • Folding and binding cascades: Shifts in energy landscapes
    • Tsai CJ, Ma B, Nussinov R. 1999. Folding and binding cascades: shifts in energy landscapes. Proc Natl Acad Sci USA. 96:9970-9972.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 9970-9972
    • Tsai, C.J.1    Ma, B.2    Nussinov, R.3
  • 76
    • 34547399613 scopus 로고    scopus 로고
    • A solution NMR study showing that active site ligands and nucleotides directly perturb the allosteric equilibriumin aspartate transcarbamoylase
    • Velyvis A, Yang YR, Schachman HK, Kay LE. 2007. A solution NMR study showing that active site ligands and nucleotides directly perturb the allosteric equilibriumin aspartate transcarbamoylase. Proc Natl Acad Sci USA. 104:8815-8820.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 8815-8820
    • Velyvis, A.1    Yang, Y.R.2    Schachman, H.K.3    Kay, L.E.4
  • 77
    • 0035937443 scopus 로고    scopus 로고
    • Two-state allosteric behavior in a single-domain signaling protein
    • Volkman BF, Lipson D, Wemmer DE, Kern D. 2001. Two-state allosteric behavior in a single-domain signaling protein. Science 291: 2429-2433.
    • (2001) Science , vol.291 , pp. 2429-2433
    • Volkman, B.F.1    Lipson, D.2    Wemmer, D.E.3    Kern, D.4
  • 78
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 18:691-699.
    • (2001) Mol Biol Evol , vol.18 , pp. 691-699
    • Whelan, S.1    Goldman, N.2
  • 79
    • 77958476428 scopus 로고    scopus 로고
    • Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes
    • Wolf YI, Gopich IV, Lipman DJ, Koonin EV. 2010. Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes. Genome Biol Evol. 2:190-199.
    • (2010) Genome Biol Evol , vol.2 , pp. 190-199
    • Wolf, Y.I.1    Gopich, I.V.2    Lipman, D.J.3    Koonin, E.V.4
  • 80
    • 79951681020 scopus 로고    scopus 로고
    • Protein functional landscapes, dynamics, allostery: A tortuous path towards a universal theoretical framework
    • Zhuravlev PI, Papoian GA. 2010. Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework. Q Rev Biophys. 43:295-332.
    • (2010) Q Rev Biophys , vol.43 , pp. 295-332
    • Zhuravlev, P.I.1    Papoian, G.A.2
  • 81
    • 0036298514 scopus 로고    scopus 로고
    • Relation between sequence and structure of HIV-1 protease inhibitor complexes: A model system for the analysis of protein flexibility
    • Zoete V, Michielin O, Karplus M. 2002. Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility. J Mol Biol. 315:21-52.
    • (2002) J Mol Biol , vol.315 , pp. 21-52
    • Zoete, V.1    Michielin, O.2    Karplus, M.3


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