메뉴 건너뛰기




Volumn 112, Issue 6, 2015, Pages 1797-1802

Protein folding and binding can emerge as evolutionary spandrels through structural coupling

Author keywords

Evolutionary spandrels; Fitness landscapes; Folding stability; Protein evolution; Protein interactions

Indexed keywords

AMINO ACID; LIGAND; PROTEIN; PROTEIN BINDING;

EID: 84922642514     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1415895112     Document Type: Article
Times cited : (49)

References (47)
  • 2
    • 0037062424 scopus 로고    scopus 로고
    • A monomeric red fluorescent protein
    • Campbell RE, et al. (2002) A monomeric red fluorescent protein. Proc Natl Acad Sci USA 99(12):7877-7882.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.12 , pp. 7877-7882
    • Campbell, R.E.1
  • 3
    • 67650287695 scopus 로고    scopus 로고
    • In the light of directed evolution: Pathways of adaptive protein evolution
    • Suppl 1
    • Bloom JD, Arnold FH (2009) In the light of directed evolution: Pathways of adaptive protein evolution. Proc Natl Acad Sci USA 106(Suppl 1):9995-10000.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 9995-10000
    • Bloom, J.D.1    Arnold, F.H.2
  • 4
    • 0037041420 scopus 로고    scopus 로고
    • Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases
    • Bucciantini M, et al. (2002) Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature 416(6880):507-511.
    • (2002) Nature , vol.416 , Issue.6880 , pp. 507-511
    • Bucciantini, M.1
  • 5
    • 0042467550 scopus 로고    scopus 로고
    • Rationalization of the effects of mutations on peptide and protein aggregation rates
    • Chiti F, Stefani M, Taddei N, Ramponi G, Dobson CM (2003) Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature 424(6950): 805-808.
    • (2003) Nature , vol.424 , Issue.6950 , pp. 805-808
    • Chiti, F.1    Stefani, M.2    Taddei, N.3    Ramponi, G.4    Dobson, C.M.5
  • 6
    • 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(2):341-352.
    • (2008) Cell , vol.134 , Issue.2 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 7
    • 79551674254 scopus 로고    scopus 로고
    • Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast
    • Geiler-Samerotte KA, et al. (2011) Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast. Proc Natl Acad Sci USA 108(2):680-685.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.2 , pp. 680-685
    • Geiler-Samerotte, K.A.1
  • 8
    • 34248674895 scopus 로고    scopus 로고
    • The stability effects of protein mutations appear to be universally distributed
    • Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawfik DS (2007) The stability effects of protein mutations appear to be universally distributed. J Mol Biol 369(5):1318-1332.
    • (2007) J Mol Biol , vol.369 , Issue.5 , pp. 1318-1332
    • Tokuriki, N.1    Stricher, F.2    Schymkowitz, J.3    Serrano, L.4    Tawfik, D.S.5
  • 10
    • 0036295508 scopus 로고    scopus 로고
    • Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs
    • Wang X, Minasov G, Shoichet BK (2002) Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol 320(1):85-95.
    • (2002) J Mol Biol , vol.320 , Issue.1 , pp. 85-95
    • Wang, X.1    Minasov, G.2    Shoichet, B.K.3
  • 11
    • 84880000622 scopus 로고    scopus 로고
    • Mutational analysis of 48G7 reveals that somatic hypermutation affects both antibody stability and binding affinity
    • Sun SB, et al. (2013) Mutational analysis of 48G7 reveals that somatic hypermutation affects both antibody stability and binding affinity. J Am Chem Soc 135(27):9980-9983.
    • (2013) J Am Chem Soc , vol.135 , Issue.27 , pp. 9980-9983
    • Sun, S.B.1
  • 12
    • 0036139093 scopus 로고    scopus 로고
    • Why are proteins marginally stable?
    • Taverna DM, Goldstein RA (2002) Why are proteins marginally stable? Proteins 46(1): 105-109.
    • (2002) Proteins , vol.46 , Issue.1 , pp. 105-109
    • Taverna, D.M.1    Goldstein, R.A.2
  • 13
    • 36049027813 scopus 로고    scopus 로고
    • Protein stability imposes limits on organism complexity and speed of molecular evolution
    • Zeldovich KB, Chen P, Shakhnovich EI (2007) Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci USA 104(41): 16152-16157.
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.41 , pp. 16152-16157
    • Zeldovich, K.B.1    Chen, P.2    Shakhnovich, E.I.3
  • 15
    • 23944490117 scopus 로고    scopus 로고
    • Missense meanderings in sequence space: A biophysical view of protein evolution
    • DePristo MA, Weinreich DM, Hartl DL (2005) Missense meanderings in sequence space: A biophysical view of protein evolution. Nat Rev Genet 6(9):678-687.
    • (2005) Nat Rev Genet , vol.6 , Issue.9 , pp. 678-687
    • DePristo, M.A.1    Weinreich, D.M.2    Hartl, D.L.3
  • 17
    • 84865730325 scopus 로고    scopus 로고
    • Protein biophysics explains why highly abundant proteins evolve slowly
    • Serohijos AWR, Rimas Z, Shakhnovich EI (2012) Protein biophysics explains why highly abundant proteins evolve slowly. Cell Reports 2(2):249-256.
    • (2012) Cell Reports , vol.2 , Issue.2 , pp. 249-256
    • Serohijos, A.W.R.1    Rimas, Z.2    Shakhnovich, E.I.3
  • 18
    • 79551667508 scopus 로고    scopus 로고
    • Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks
    • Johnson ME, Hummer G (2011) Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks. Proc Natl Acad Sci USA 108(2):603-608.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.2 , pp. 603-608
    • Johnson, M.E.1    Hummer, G.2
  • 19
    • 79952744659 scopus 로고    scopus 로고
    • Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions
    • Heo M, Maslov S, Shakhnovich E (2011) Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions. Proc Natl Acad Sci USA 108(10):4258-4263.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.10 , pp. 4258-4263
    • Heo, M.1    Maslov, S.2    Shakhnovich, E.3
  • 20
    • 0018692402 scopus 로고
    • The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme
    • Gould SJ, Lewontin RC (1979) The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme. Proc R Soc Lond B Biol Sci 205(1161): 581-598.
    • (1979) Proc R Soc Lond B Biol Sci , vol.205 , Issue.1161 , pp. 581-598
    • Gould, S.J.1    Lewontin, R.C.2
  • 21
    • 0034144568 scopus 로고    scopus 로고
    • The fall and rise of Dr Pangloss: Adaptationism and the Spandrels paper 20 years later
    • Pigliucci I, Kaplan I (2000) The fall and rise of Dr Pangloss: Adaptationism and the Spandrels paper 20 years later. Trends Ecol Evol 15(2):66-70.
    • (2000) Trends Ecol Evol , vol.15 , Issue.2 , pp. 66-70
    • Pigliucci, I.1    Kaplan, I.2
  • 22
    • 0037154126 scopus 로고    scopus 로고
    • Protein structure and the spandrels of San Marco: Insulin's receptor-binding surface is buttressed by an invariant leucine essential for its stability
    • Weiss MA, et al. (2002) Protein structure and the spandrels of San Marco: Insulin's receptor-binding surface is buttressed by an invariant leucine essential for its stability. Biochemistry 41(3):809-819.
    • (2002) Biochemistry , vol.41 , Issue.3 , pp. 809-819
    • Weiss, M.A.1
  • 23
    • 80054759105 scopus 로고    scopus 로고
    • Molecular spandrels: Tests of adaptation at the genetic level
    • Barrett RDH, Hoekstra HE (2011) Molecular spandrels: Tests of adaptation at the genetic level. Nat Rev Genet 12(11):767-780.
    • (2011) Nat Rev Genet , vol.12 , Issue.11 , pp. 767-780
    • Barrett, R.D.H.1    Hoekstra, H.E.2
  • 24
    • 33645666942 scopus 로고    scopus 로고
    • Darwinian evolution can follow only very few mutational paths to fitter proteins
    • Weinreich DM, Delaney NF, Depristo MA, Hartl DL (2006) Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312(5770):111-114.
    • (2006) Science , vol.312 , Issue.5770 , pp. 111-114
    • Weinreich, D.M.1    Delaney, N.F.2    Depristo, M.A.3    Hartl, D.L.4
  • 25
    • 79957958115 scopus 로고    scopus 로고
    • Diminishing returns epistasis among beneficial mutations decelerates adaptation
    • Chou HH, Chiu HC, Delaney NF, Segrè D, Marx CJ (2011) Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 332(6034):1190-1192.
    • (2011) Science , vol.332 , Issue.6034 , pp. 1190-1192
    • Chou, H.H.1    Chiu, H.C.2    Delaney, N.F.3    Segrè, D.4    Marx, C.J.5
  • 26
    • 84883140639 scopus 로고    scopus 로고
    • Path-based approach to random walks on networks characterizes how proteins evolve new functions
    • Manhart M, Morozov AV (2013) Path-based approach to random walks on networks characterizes how proteins evolve new functions. Phys Rev Lett 111(8):088102.
    • (2013) Phys Rev Lett , vol.111 , Issue.8 , pp. 088102
    • Manhart, M.1    Morozov, A.V.2
  • 29
    • 84903957091 scopus 로고    scopus 로고
    • Introducing protein intrinsic disorder
    • Habchi J, Tompa P, Longhi S, Uversky VN (2014) Introducing protein intrinsic disorder. Chem Rev 114(13):6561-6588.
    • (2014) Chem Rev , vol.114 , Issue.13 , pp. 6561-6588
    • Habchi, J.1    Tompa, P.2    Longhi, S.3    Uversky, V.N.4
  • 30
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson T, Wells JA (1995) A hot spot of binding energy in a hormone-receptor interface. Science 267(5196):383-386.
    • (1995) Science , vol.267 , Issue.5196 , pp. 383-386
    • Clackson, T.1    Wells, J.A.2
  • 31
    • 34548779127 scopus 로고    scopus 로고
    • Hot spots-A review of the proteinprotein interface determinant amino-acid residues
    • Moreira IS, Fernandes PA, Ramos MJ (2007) Hot spots-a review of the proteinprotein interface determinant amino-acid residues. Proteins 68(4):803-812.
    • (2007) Proteins , vol.68 , Issue.4 , pp. 803-812
    • Moreira, I.S.1    Fernandes, P.A.2    Ramos, M.J.3
  • 32
    • 0025082684 scopus 로고
    • Additivity of mutational effects in proteins
    • Wells JA (1990) Additivity of mutational effects in proteins. Biochemistry 29(37): 8509-8517.
    • (1990) Biochemistry , vol.29 , Issue.37 , pp. 8509-8517
    • Wells, J.A.1
  • 33
    • 33745758856 scopus 로고    scopus 로고
    • A microscopic interpretation for adaptive dynamics trait substitution sequence models
    • Champagnat N (2006) A microscopic interpretation for adaptive dynamics trait substitution sequence models. Stoch Proc Appl 116(8):1127-1160.
    • (2006) Stoch Proc Appl , vol.116 , Issue.8 , pp. 1127-1160
    • Champagnat, N.1
  • 35
    • 60349093708 scopus 로고    scopus 로고
    • Fundamental concepts in genetics: Effective population size and patterns of molecular evolution and variation
    • Charlesworth B (2009) Fundamental concepts in genetics: Effective population size and patterns of molecular evolution and variation. Nat Rev Genet 10(3):195-205.
    • (2009) Nat Rev Genet , vol.10 , Issue.3 , pp. 195-205
    • Charlesworth, B.1
  • 36
    • 84861663597 scopus 로고    scopus 로고
    • Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space
    • Shoval O, et al. (2012) Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space. Science 336(6085):1157-1160.
    • (2012) Science , vol.336 , Issue.6085 , pp. 1157-1160
    • Shoval, O.1
  • 37
    • 34548724489 scopus 로고    scopus 로고
    • The evolution of genetic networks by non-adaptive processes
    • Lynch M(2007) The evolution of genetic networks by non-adaptive processes. Nat Rev Genet 8(10):803-813.
    • (2007) Nat Rev Genet , vol.8 , Issue.10 , pp. 803-813
    • Lynch, M.1
  • 38
    • 84874923658 scopus 로고    scopus 로고
    • Cofactors and metabolites as protein folding helpers in metabolic diseases
    • Rodrigues JV, Henriques BJ, Lucas TG, Gomes CM (2012) Cofactors and metabolites as protein folding helpers in metabolic diseases. Curr Top Med Chem 12(22):2546-2559.
    • (2012) Curr Top Med Chem , vol.12 , Issue.22 , pp. 2546-2559
    • Rodrigues, J.V.1    Henriques, B.J.2    Lucas, T.G.3    Gomes, C.M.4
  • 39
    • 33644873184 scopus 로고    scopus 로고
    • BioGRID: A general repository for interaction datasets
    • Stark C, et al. (2006) BioGRID: A general repository for interaction datasets. Nucleic Acids Res 34(Database issue):D535-D539.
    • (2006) Nucleic Acids Res , vol.34 , pp. D535-D539
    • Stark, C.1
  • 40
    • 84859473329 scopus 로고    scopus 로고
    • Protein misinteraction avoidance causes highly expressed proteins to evolve slowly
    • Yang JR, Liao BY, Zhuang SM, Zhang J (2012) Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. Proc Natl Acad Sci USA 109(14):E831-E840.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.14 , pp. E831-E840
    • Yang, J.R.1    Liao, B.Y.2    Zhuang, S.M.3    Zhang, J.4
  • 41
    • 84876896201 scopus 로고    scopus 로고
    • Evolutionary capacitance and control of protein stability in protein-protein interaction networks
    • Dixit PD, Maslov S (2013) Evolutionary capacitance and control of protein stability in protein-protein interaction networks. PLOS Comput Biol 9(4):e1003023.
    • (2013) PLOS Comput Biol , vol.9 , Issue.4 , pp. e1003023
    • Dixit, P.D.1    Maslov, S.2
  • 42
    • 79960652801 scopus 로고    scopus 로고
    • Molecular chaperones in protein folding and proteostasis
    • Hartl FU, Bracher A, Hayer-Hartl M (2011) Molecular chaperones in protein folding and proteostasis. Nature 475(7356):324-332.
    • (2011) Nature , vol.475 , Issue.7356 , pp. 324-332
    • Hartl, F.U.1    Bracher, A.2    Hayer-Hartl, M.3
  • 43
    • 33846551980 scopus 로고    scopus 로고
    • Empirical fitness landscapes reveal accessible evolutionary paths
    • Poelwijk FJ, Kiviet DJ, Weinreich DM, Tans SJ (2007) Empirical fitness landscapes reveal accessible evolutionary paths. Nature 445(7126):383-386.
    • (2007) Nature , vol.445 , Issue.7126 , pp. 383-386
    • Poelwijk, F.J.1    Kiviet, D.J.2    Weinreich, D.M.3    Tans, S.J.4
  • 46
    • 84876090839 scopus 로고    scopus 로고
    • Replaying the tape of life: Quantification of the predictability of evolution
    • Lobkovsky AE, Koonin EV (2012) Replaying the tape of life: Quantification of the predictability of evolution. Front Genet 3:246.
    • (2012) Front Genet , vol.3 , pp. 246
    • Lobkovsky, A.E.1    Koonin, E.V.2
  • 47
    • 0035066602 scopus 로고    scopus 로고
    • ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions
    • Thorn KS, Bogan AA (2001) ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 17(3):284-285.
    • (2001) Bioinformatics , vol.17 , Issue.3 , pp. 284-285
    • Thorn, K.S.1    Bogan, A.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.