메뉴 건너뛰기




Volumn 32, Issue 8, 2015, Pages 2195-2207

Maximum-likelihood phylogenetic inference with selection on protein folding stability

Author keywords

Folding stability; Maximum likelihood estimate; Misfolded state; Structurally constrained substitution models

Indexed keywords

AMINO ACID; GLOBULAR PROTEIN; PROTEIN;

EID: 84965107636     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msv085     Document Type: Article
Times cited : (40)

References (61)
  • 1
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automatic Control. 19:716-723.
    • (1974) IEEE Trans Automatic Control. , vol.19 , pp. 716-723
    • Akaike, H.1
  • 2
    • 84890067204 scopus 로고    scopus 로고
    • Protein evolution along phylogenetic histories under structurally constrained substitution models
    • Arenas M, Dos Santos HG, Posada D, Bastolla U. 2013. Protein evolution along phylogenetic histories under structurally constrained substitution models. Bioinformatics 29:3020-3028.
    • (2013) Bioinformatics , vol.29 , pp. 3020-3028
    • Arenas, M.1    Dos Santos, H.G.2    Posada, D.3    Bastolla, U.4
  • 3
    • 0030625954 scopus 로고    scopus 로고
    • Neutral networks in protein space: A computational study based on knowledge-based potentials of mean force
    • Babajide A, Hofacker IL, Sippl MJ, Stadler PF. 1997. Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force. Fold Des. 2:261-269.
    • (1997) Fold Des. , vol.2 , pp. 261-269
    • Babajide, A.1    Hofacker, I.L.2    Sippl, M.J.3    Stadler, P.F.4
  • 4
    • 0035427382 scopus 로고    scopus 로고
    • How to guarantee optimal stability for most representative structures in the Protein Data Bank
    • Bastolla U, Farwer J, Knapp EW, VendruscoloM. 2001. How to guarantee optimal stability for most representative structures in the Protein Data Bank. Proteins 44:79-96.
    • (2001) Proteins , vol.44 , pp. 79-96
    • Bastolla, U.1    Farwer, J.2    Knapp, E.W.3    Vendruscolo, M.4
  • 5
    • 6344282274 scopus 로고    scopus 로고
    • Genomic determinants of protein folding thermodynamics in prokaryotic organisms
    • Bastolla U, Moya A, Viguera E, van Ham RC. 2004. Genomic determinants of protein folding thermodynamics in prokaryotic organisms. J Mol Biol. 343:1451-1466.
    • (2004) J Mol Biol. , vol.343 , pp. 1451-1466
    • Bastolla, U.1    Moya, A.2    Viguera, E.3    Van Ham, R.C.4
  • 6
    • 58149292218 scopus 로고    scopus 로고
    • Effective connectivity profile: A structural representation that evidences the relationship between protein structures and sequences
    • Bastolla U, Ortiz AR, Porto M, Teichert F. 2008. Effective connectivity profile: a structural representation that evidences the relationship between protein structures and sequences. Proteins 73:872-888.
    • (2008) Proteins , vol.73 , pp. 872-888
    • Bastolla, U.1    Ortiz, A.R.2    Porto, M.3    Teichert, F.4
  • 8
    • 10844225367 scopus 로고    scopus 로고
    • Principal eigenvector of contact matrices and hydrophobicity profiles in proteins
    • Bastolla U, Porto M, Roman HE, Vendruscolo M. 2005. Principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins 58:22-30.
    • (2005) Proteins , vol.58 , pp. 22-30
    • Bastolla, U.1    Porto, M.2    Roman, H.E.3    Vendruscolo, M.4
  • 9
    • 33748925566 scopus 로고    scopus 로고
    • A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank
    • Bastolla U, Porto M, Roman HE, Vendruscolo M. 2006. A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank. BMC Evol Biol. 6:43.
    • (2006) BMC Evol Biol. , vol.6 , pp. 43
    • Bastolla, U.1    Porto, M.2    Roman, H.E.3    Vendruscolo, M.4
  • 10
    • 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
  • 11
    • 33845503073 scopus 로고    scopus 로고
    • Adaptive evolution of transcription factor binding sites
    • Berg J, Willmann S, Lässig M. 2004. Adaptive evolution of transcription factor binding sites. BMC Evol Biol. 4:42.
    • (2004) BMC Evol Biol. , vol.4 , pp. 42
    • Berg, J.1    Willmann, S.2    Lässig, M.3
  • 13
    • 84895752277 scopus 로고    scopus 로고
    • A new formulation of protein evolutionary models that account for structural constraints
    • Bordner AJ, Mittelmann HD. 2014. A new formulation of protein evolutionary models that account for structural constraints. Mol Biol Evol. 31:736-749.
    • (2014) Mol Biol Evol. , vol.31 , pp. 736-749
    • Bordner, A.J.1    Mittelmann, H.D.2
  • 14
    • 13044269058 scopus 로고    scopus 로고
    • Modeling evolutionary landscapes: Mutational stability, topology, and superfunnels in sequence space
    • Bornberg-Bauer E, Chan HS. 1999. Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space. Proc Natl Acad Sci U S A. 96:10689-10694.
    • (1999) Proc Natl Acad Sci U S A. , vol.96 , pp. 10689-10694
    • Bornberg-Bauer, E.1    Chan, H.S.2
  • 15
    • 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
  • 17
    • 79953747234 scopus 로고    scopus 로고
    • Cooperativity, localnonlocal coupling, and nonnative interactions: Principles of protein folding from coarse-grained models
    • Chan HS, Zhang Z, Wallin S, Liu Z. 2011. Cooperativity, localnonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models. Annu Rev Phys Chem. 62: 301-326.
    • (2011) Annu Rev Phys Chem. , vol.62 , pp. 301-326
    • Chan, H.S.1    Zhang, Z.2    Wallin, S.3    Liu, Z.4
  • 18
    • 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. 6:678-687.
    • (2005) Nat Rev Genet. , vol.6 , pp. 678-687
    • DePristo, M.A.1    Weinreich, D.M.2    Hartl, D.L.3
  • 19
    • 4243861085 scopus 로고
    • Random energy model: An exactly solvable model of disordered systems
    • Derrida B. 1981. Random energy model: an exactly solvable model of disordered systems. Phys Rev B. 24:2613-2626.
    • (1981) Phys Rev B. , vol.24 , pp. 2613-2626
    • Derrida, B.1
  • 20
    • 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
  • 21
    • 84959848780 scopus 로고
    • Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters
    • Felsenstein J. 1973. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst Zool. 22:240-249.
    • (1973) Syst Zool. , vol.22 , pp. 240-249
    • Felsenstein, J.1
  • 23
    • 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
  • 24
    • 70349911882 scopus 로고    scopus 로고
    • Structural determinants of protein evolution are context-sensitive at the residue level
    • Franzosa EA, Xia Y. 2009. Structural determinants of protein evolution are context-sensitive at the residue level. Mol Biol Evol. 26: 2387-2395.
    • (2009) Mol Biol Evol. , vol.26 , pp. 2387-2395
    • Franzosa, E.A.1    Xia, Y.2
  • 25
    • 84956127383 scopus 로고
    • Mean-field model for protein folding
    • Garel T, Orland H. 1988. Mean-field model for protein folding. Europhys Lett. 6:307-310.
    • (1988) Europhys Lett. , vol.6 , pp. 307-310
    • Garel, T.1    Orland, H.2
  • 26
    • 79954542203 scopus 로고    scopus 로고
    • The evolution and evolutionary consequences of marginal thermostability in proteins
    • Goldstein RA. 2011. The evolution and evolutionary consequences of marginal thermostability in proteins. Proteins 79:1396-1407.
    • (2011) Proteins , vol.79 , pp. 1396-1407
    • Goldstein, R.A.1
  • 27
    • 0030691734 scopus 로고    scopus 로고
    • Evolution of model proteins on a foldability landscape
    • Govindarajan S, Goldstein RA. 1997. Evolution of model proteins on a foldability landscape. Proteins 29:461-466.
    • (1997) Proteins , vol.29 , pp. 461-466
    • Govindarajan, S.1    Goldstein, R.A.2
  • 28
    • 83455238341 scopus 로고    scopus 로고
    • Biophysical and structural considerations for protein sequence evolution
    • Grahnen JA, Nandakumar P, Kubelka J, Liberles DA. 2011. Biophysical and structural considerations for protein sequence evolution. BMC Evol Biol. 11:361.
    • (2011) BMC Evol Biol. , vol.11 , pp. 361
    • Grahnen, J.A.1    Nandakumar, P.2    Kubelka, J.3    Liberles, D.A.4
  • 30
    • 0031875569 scopus 로고    scopus 로고
    • Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies
    • Halpern AL, Bruno WJ. 1998. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Mol Biol Evol. 15:910-917.
    • (1998) Mol Biol Evol. , vol.15 , pp. 910-917
    • Halpern, A.L.1    Bruno, W.J.2
  • 31
    • 84899480289 scopus 로고    scopus 로고
    • A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility
    • Huang TT, del Valle Marcos ML, Hwang JK, Echave J. 2014. A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility. BMC Evol Biol. 14:78.
    • (2014) BMC Evol Biol. , vol.14 , pp. 78
    • Huang, T.T.1    Del Valle Marcos, M.L.2    Hwang, J.K.3    Echave, J.4
  • 32
    • 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
  • 33
    • 0023475026 scopus 로고
    • Configurational entropy of native proteins
    • Karplus M, Ichiye T, Pettitt BM. 1987. Configurational entropy of native proteins. Biophys J. 52:1083-1085.
    • (1987) Biophys J. , vol.52 , pp. 1083-1085
    • Karplus, M.1    Ichiye, T.2    Pettitt, B.M.3
  • 34
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
    • Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30:772-780.
    • (2013) Mol Biol Evol. , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 35
    • 0032529584 scopus 로고    scopus 로고
    • Models of natural mutations including site heterogeneity
    • Koshi JM, Goldstein RA. 1998. Models of natural mutations including site heterogeneity. Proteins 32:289-295.
    • (1998) Proteins , vol.32 , pp. 289-295
    • Koshi, J.M.1    Goldstein, R.A.2
  • 36
    • 0035221408 scopus 로고    scopus 로고
    • Analyzing site heterogeneity during protein evolution
    • Koshi JM, Goldstein RA. 2001. Analyzing site heterogeneity during protein evolution. Pac Symp Biocomput. 191-202.
    • (2001) Pac Symp Biocomput. , pp. 191-202
    • Koshi, J.M.1    Goldstein, R.A.2
  • 37
    • 0033026624 scopus 로고    scopus 로고
    • Using physical-chemistrybased substitution models in phylogenetic analyses of HIV-1 subtypes
    • Koshi JM, Mindell DP, Goldstein RA. 1999. Using physical-chemistrybased substitution models in phylogenetic analyses of HIV-1 subtypes. Mol Biol Evol. 16:173-179.
    • (1999) Mol Biol Evol. , vol.16 , pp. 173-179
    • Koshi, J.M.1    Mindell, D.P.2    Goldstein, R.A.3
  • 38
    • 2442691520 scopus 로고    scopus 로고
    • A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
    • Lartillot N, Philippe H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 21:1095-1109.
    • (2004) Mol Biol Evol. , vol.21 , pp. 1095-1109
    • Lartillot, N.1    Philippe, H.2
  • 40
    • 77955013698 scopus 로고    scopus 로고
    • Mutation bias favors protein folding stability in the evolution of small populations
    • Mendez R, Fritsche M, Porto M, Bastolla U. 2010. Mutation bias favors protein folding stability in the evolution of small populations. PLoS Comput Biol. 6:e1000767.
    • (2010) PLoS Comput Biol. , vol.6
    • Mendez, R.1    Fritsche, M.2    Porto, M.3    Bastolla, U.4
  • 41
    • 84879410603 scopus 로고    scopus 로고
    • Detecting selection for negative design in proteins through an improved model of the misfolded state
    • Minning J, Porto M, Bastolla U. 2013. Detecting selection for negative design in proteins through an improved model of the misfolded state. Proteins 81:1102-1112.
    • (2013) Proteins , vol.81 , pp. 1102-1112
    • Minning, J.1    Porto, M.2    Bastolla, U.3
  • 43
    • 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
  • 44
    • 0036706015 scopus 로고    scopus 로고
    • Understanding protein folding with energy landscape theory. Part II: Quantitative aspects
    • Plotkin SS, Onuchic JN. 2002. Understanding protein folding with energy landscape theory. Part II: quantitative aspects. Q Rev Biophys. 35: 205-286.
    • (2002) Q Rev Biophys. , vol.35 , pp. 205-286
    • Plotkin, S.S.1    Onuchic, J.N.2
  • 45
    • 14544272929 scopus 로고    scopus 로고
    • Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences
    • Porto M, Roman HE, Vendruscolo M, Bastolla U. 2005. Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences. Mol Biol Evol. 22: 630-638.
    • (2005) Mol Biol Evol. , vol.22 , pp. 630-638
    • Porto, M.1    Roman, H.E.2    Vendruscolo, M.3    Bastolla, U.4
  • 48
    • 15544374861 scopus 로고    scopus 로고
    • Site interdependence attributed to tertiary structure in amino acid sequence evolution
    • Rodrigue N, Lartillot N, Bryant D, Philippe H. 2005. Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene 347:207-217.
    • (2005) Gene , vol.347 , pp. 207-217
    • Rodrigue, N.1    Lartillot, N.2    Bryant, D.3    Philippe, H.4
  • 49
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
    • (1987) Mol Biol Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 50
    • 22144437325 scopus 로고    scopus 로고
    • The application of statistical physics to evolutionary biology
    • Sella G, Hirsh AE. 2005. The application of statistical physics to evolutionary biology. Proc Natl Acad Sci U S A. 102:9541-9546.
    • (2005) Proc Natl Acad Sci U S A. , vol.102 , pp. 9541-9546
    • Sella, G.1    Hirsh, A.E.2
  • 51
    • 33646931471 scopus 로고    scopus 로고
    • Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
    • Shakhnovich E. 2006. Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. Chem Rev. 106: 1559-1588.
    • (2006) Chem Rev. , vol.106 , pp. 1559-1588
    • Shakhnovich, E.1
  • 52
    • 0024357911 scopus 로고
    • Formation of unique structure in polypeptide chains
    • Shakhnovich EI, Gutin AM. 1989. Formation of unique structure in polypeptide chains. Biophys Chem. 34:187-199.
    • (1989) Biophys Chem. , vol.34 , pp. 187-199
    • Shakhnovich, E.I.1    Gutin, A.M.2
  • 53
    • 0036139093 scopus 로고    scopus 로고
    • Why are proteins marginally stable?
    • Taverna DM, Goldstein RA. 2002. Why are proteins marginally stable? Proteins 46:105-109.
    • (2002) Proteins , vol.46 , pp. 105-109
    • Taverna, D.M.1    Goldstein, R.A.2
  • 56
    • 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
  • 57
    • 0035339920 scopus 로고    scopus 로고
    • Molecular phylogenetics: Stateof-the-art methods for looking into the past
    • Whelan S, Li ó P, Goldman N. 2001. Molecular phylogenetics: stateof-the-art methods for looking into the past. Trends Genet. 17: 262-272.
    • (2001) Trends Genet. , vol.17 , pp. 262-272
    • Whelan, S.1    Li Ó, P.2    Goldman, N.3
  • 58
    • 84864029746 scopus 로고    scopus 로고
    • Bringing molecules back into molecular evolution
    • Wilke CO. 2012. Bringing molecules back into molecular evolution. PLoS Comput Biol. 8:e1002572.
    • (2012) PLoS Comput Biol. , vol.8
    • Wilke, C.O.1
  • 59
    • 0027132974 scopus 로고
    • Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • Yang Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.Mol Biol Evol. 10: 1396-1401.
    • (1993) Mol Biol Evol. , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 60
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
    • (2007) Mol Biol Evol. , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 61
    • 0031792828 scopus 로고    scopus 로고
    • Models of amino acid substitution and applications to mitochondrial protein evolution
    • Yang Z, Nielsen R, Masami H. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution.Mol Biol Evol. 15:1600-1611.
    • (1998) Mol Biol Evol. , vol.15 , pp. 1600-1611
    • Yang, Z.1    Nielsen, R.2    Masami, H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.