메뉴 건너뛰기




Volumn , Issue , 2016, Pages 1332-1340

Evolutionary dynamics of viral escape under antibodies stress: A biophysical model

Author keywords

folding stability; neutralizing antibodies; optimal mutation rate; viral evolution

Indexed keywords

ANTIBODY; VIRUS PROTEIN;

EID: 84976530836     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2915     Document Type: Article
Times cited : (12)

References (52)
  • 1
    • 0036888857 scopus 로고    scopus 로고
    • Fighting change with change: adaptive variation in an uncertain world
    • Meyers LA, Bull JJ (2002) Fighting change with change: adaptive variation in an uncertain world. Trends Ecol E 17:551–557.
    • (2002) Trends Ecol E , vol.17 , pp. 551-557
    • Meyers, L.A.1    Bull, J.J.2
  • 2
    • 84893777917 scopus 로고    scopus 로고
    • Variation in RNA virus mutation rates across host cells
    • Combe M, Sanjuan R (2014) Variation in RNA virus mutation rates across host cells. PLoS Pathog 10:e1003855.
    • (2014) PLoS Pathog , vol.10
    • Combe, M.1    Sanjuan, R.2
  • 3
    • 84975263995 scopus 로고    scopus 로고
    • Viral evolution under the pressure of an adaptive immune system: optimal mutation rates for viral escape
    • Kamp C, Wilke CO, Adami C, Bornholdt S (2002) Viral evolution under the pressure of an adaptive immune system: optimal mutation rates for viral escape. Complexity 8:28–33.
    • (2002) Complexity , vol.8 , pp. 28-33
    • Kamp, C.1    Wilke, C.O.2    Adami, C.3    Bornholdt, S.4
  • 4
    • 33847247125 scopus 로고    scopus 로고
    • Theory of lethal mutagenesis for viruses
    • Bull JJ, Sanjuan R, Wilke CO (2007) Theory of lethal mutagenesis for viruses. J Virol 81:2930–2939.
    • (2007) J Virol , vol.81 , pp. 2930-2939
    • Bull, J.J.1    Sanjuan, R.2    Wilke, C.O.3
  • 5
    • 70649097086 scopus 로고    scopus 로고
    • Lethal mutagenesis in viruses and bacteria
    • Chen P, Shakhnovich EI (2009) Lethal mutagenesis in viruses and bacteria. Genetics 183:639–650.
    • (2009) Genetics , vol.183 , pp. 639-650
    • Chen, P.1    Shakhnovich, E.I.2
  • 6
    • 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 104:16152–16157.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 16152-16157
    • Zeldovich, K.B.1    Chen, P.2    Shakhnovich, E.I.3
  • 8
    • 0036849786 scopus 로고    scopus 로고
    • Implications of high RNA virus mutation rates: lethal mutagenesis and the antiviral drug ribavirin
    • Crotty S, Andino R (2002) Implications of high RNA virus mutation rates: lethal mutagenesis and the antiviral drug ribavirin. Microbes Infect 4:1301–1307.
    • (2002) Microbes Infect , vol.4 , pp. 1301-1307
    • Crotty, S.1    Andino, R.2
  • 9
    • 0034685940 scopus 로고    scopus 로고
    • High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection
    • Oliver A, Canton R, Campo P, Baquero F, Blazquez J (2000) High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. Science 288:1251–1254.
    • (2000) Science , vol.288 , pp. 1251-1254
    • Oliver, A.1    Canton, R.2    Campo, P.3    Baquero, F.4    Blazquez, J.5
  • 11
    • 22544478419 scopus 로고    scopus 로고
    • The cost of replication fidelity in an RNA virus
    • Furio V, Moya A, Sanjuan R (2005) The cost of replication fidelity in an RNA virus. Proc Natl Acad Sci USA 102:10233–10237.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 10233-10237
    • Furio, V.1    Moya, A.2    Sanjuan, R.3
  • 12
    • 0035856499 scopus 로고    scopus 로고
    • Evolution: constantly avoiding mutation
    • Sniegowski P (2001) Evolution: constantly avoiding mutation. Curr Biol 11:R929–R931.
    • (2001) Curr Biol , vol.11 , pp. R929-R931
    • Sniegowski, P.1
  • 13
    • 84869854859 scopus 로고    scopus 로고
    • Viral mutation rates: modelling the roles of within-host viral dynamics and the trade-off between replication fidelity and speed
    • Regoes RR, Hamblin S, Tanaka MM (2013) Viral mutation rates: modelling the roles of within-host viral dynamics and the trade-off between replication fidelity and speed. Proc R Soc B Biol Sci 280:2012–2047.
    • (2013) Proc R Soc B Biol Sci , vol.280 , pp. 2012-2047
    • Regoes, R.R.1    Hamblin, S.2    Tanaka, M.M.3
  • 14
    • 0034542564 scopus 로고    scopus 로고
    • The evolution of mutation rates: separating causes from consequences
    • Sniegowski PD, Gerrish PJ, Johnson T, Shaver A (2000) The evolution of mutation rates: separating causes from consequences. Bioessays 22:1057–1066.
    • (2000) Bioessays , vol.22 , pp. 1057-1066
    • Sniegowski, P.D.1    Gerrish, P.J.2    Johnson, T.3    Shaver, A.4
  • 15
    • 85027949831 scopus 로고    scopus 로고
    • Experimental evolution and the dynamics of genomic mutation rate modifiers
    • Raynes Y, Sniegowski PD (2014) Experimental evolution and the dynamics of genomic mutation rate modifiers. Heredity 113:375–380.
    • (2014) Heredity , vol.113 , pp. 375-380
    • Raynes, Y.1    Sniegowski, P.D.2
  • 16
    • 34247349509 scopus 로고    scopus 로고
    • Understanding the evolutionary fate of finite populations: the dynamics of mutational effects
    • Silander OK, Tenaillon O, Chao L (2007) Understanding the evolutionary fate of finite populations: the dynamics of mutational effects. PLoS Biol 5:e94.
    • (2007) PLoS Biol , vol.5
    • Silander, O.K.1    Tenaillon, O.2    Chao, L.3
  • 17
    • 84891814272 scopus 로고    scopus 로고
    • Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions
    • Serohijos AW, Shakhnovich EI (2014) Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions. Mol Biol E 31:165–176.
    • (2014) Mol Biol E , vol.31 , pp. 165-176
    • Serohijos, A.W.1    Shakhnovich, E.I.2
  • 18
    • 77950833498 scopus 로고    scopus 로고
    • Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response
    • Heo M, Shakhnovich EI (2010) Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response. PLoS Comput Biol 6:e1000710.
    • (2010) PLoS Comput Biol , vol.6
    • Heo, M.1    Shakhnovich, E.I.2
  • 19
    • 61349112079 scopus 로고    scopus 로고
    • From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation
    • Mustonen V, Lassig M (2009) From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation. Trends Genet 25:111–119.
    • (2009) Trends Genet , vol.25 , pp. 111-119
    • Mustonen, V.1    Lassig, M.2
  • 20
    • 84879064073 scopus 로고    scopus 로고
    • Stability-mediated epistasis constrains the evolution of an influenza protein
    • Gong LI, Suchard MA, Bloom JD (2013) Stability-mediated epistasis constrains the evolution of an influenza protein. eLife 2:e00631.
    • (2013) eLife , vol.2
    • Gong, L.I.1    Suchard, M.A.2    Bloom, J.D.3
  • 21
    • 79959992592 scopus 로고    scopus 로고
    • A biophysical protein folding model accounts for most mutational fitness effects in viruses
    • Wylie CS, Shakhnovich EI (2011) A biophysical protein folding model accounts for most mutational fitness effects in viruses. Proc Natl Acad Sci USA 108:9916–9921.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 9916-9921
    • Wylie, C.S.1    Shakhnovich, E.I.2
  • 22
    • 60549115416 scopus 로고    scopus 로고
    • Emergence of species in evolutionary “simulated annealing
    • Heo M, Kang L, Shakhnovich EI (2009) Emergence of species in evolutionary “simulated annealing”. Proc Natl Acad Sci USA 106:1869–1874.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 1869-1874
    • Heo, M.1    Kang, L.2    Shakhnovich, E.I.3
  • 23
    • 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 369:1318–1332.
    • (2007) J Mol Biol , vol.369 , pp. 1318-1332
    • Tokuriki, N.1    Stricher, F.2    Schymkowitz, J.3    Serrano, L.4    Tawfik, D.S.5
  • 24
    • 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
  • 25
    • 33846515095 scopus 로고    scopus 로고
    • Thermodynamics of neutral protein evolution
    • Bloom JD, Raval A, Wilke CO (2007) Thermodynamics of neutral protein evolution. Genetics 175:255–266.
    • (2007) Genetics , vol.175 , pp. 255-266
    • Bloom, J.D.1    Raval, A.2    Wilke, C.O.3
  • 26
    • 84866267075 scopus 로고    scopus 로고
    • Escape from adaptive conflict follows from weak functional trade-offs and mutational robustness
    • Sikosek T, Chan HS, Bornberg-Bauer E (2012) Escape from adaptive conflict follows from weak functional trade-offs and mutational robustness. Proc Natl Acad Sci USA 109:14888–14893.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 14888-14893
    • Sikosek, T.1    Chan, H.S.2    Bornberg-Bauer, E.3
  • 28
    • 0013953942 scopus 로고
    • Air sampling for respiratory disease agents in army recruits
    • Artenstein MS, Miller WS (1966) Air sampling for respiratory disease agents in army recruits. Bacteriol Rev 30:571–572.
    • (1966) Bacteriol Rev , vol.30 , pp. 571-572
    • Artenstein, M.S.1    Miller, W.S.2
  • 30
    • 0023340209 scopus 로고
    • Bacterial colonization and infection resulting from multiplication of a single organism
    • Rubin LG (1987) Bacterial colonization and infection resulting from multiplication of a single organism. Rev Infect Dis 9:488–493.
    • (1987) Rev Infect Dis , vol.9 , pp. 488-493
    • Rubin, L.G.1
  • 32
    • 33646718792 scopus 로고    scopus 로고
    • Murine norovirus: a model system to study norovirus biology and pathogenesis
    • Wobus CE, Thackray LB, Virgin HWT (2006) Murine norovirus: a model system to study norovirus biology and pathogenesis. J Virol 80:5104–5112.
    • (2006) J Virol , vol.80 , pp. 5104-5112
    • Wobus, C.E.1    Thackray, L.B.2    Virgin, H.W.T.3
  • 33
    • 0018588511 scopus 로고
    • Stability of proteins: small globular proteins
    • Privalov PL (1979) Stability of proteins: small globular proteins. Adv Prot Chem 33:167–241.
    • (1979) Adv Prot Chem , vol.33 , pp. 167-241
    • Privalov, P.L.1
  • 35
    • 84902507257 scopus 로고    scopus 로고
    • Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics
    • Serohijos AW, Shakhnovich EI (2014) Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics. Curr Opin Struct Biol 26:84–91.
    • (2014) Curr Opin Struct Biol , vol.26 , pp. 84-91
    • Serohijos, A.W.1    Shakhnovich, E.I.2
  • 36
    • 84865730325 scopus 로고    scopus 로고
    • Protein biophysics explains why highly abundant proteins evolve slowly
    • Serohijos AW, Rimas Z, Shakhnovich EI (2012) Protein biophysics explains why highly abundant proteins evolve slowly. Cell Rep 2:249–256.
    • (2012) Cell Rep , vol.2 , pp. 249-256
    • Serohijos, A.W.1    Rimas, Z.2    Shakhnovich, E.I.3
  • 37
    • 0034213559 scopus 로고    scopus 로고
    • Conservation of polar residues as hot spots at protein interfaces
    • Hu Z, Ma B, Wolfson H, Nussinov R (2000) Conservation of polar residues as hot spots at protein interfaces. Proteins 39:331–342.
    • (2000) Proteins , vol.39 , pp. 331-342
    • Hu, Z.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 38
    • 84913534565 scopus 로고    scopus 로고
    • Changing folding and binding stability in a viral coat protein: a comparison between substitutions accessible through mutation and those fixed by natural selection
    • Miller CR, Lee KH, Wichman HA, Ytreberg FM (2014) Changing folding and binding stability in a viral coat protein: a comparison between substitutions accessible through mutation and those fixed by natural selection. PLoS One 9:e112988.
    • (2014) PLoS One , vol.9
    • Miller, C.R.1    Lee, K.H.2    Wichman, H.A.3    Ytreberg, F.M.4
  • 39
    • 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 111:088102.
    • (2013) Phys Rev Lett , vol.111 , pp. 088102
    • Manhart, M.1    Morozov, A.V.2
  • 40
    • 84922642514 scopus 로고    scopus 로고
    • Protein folding and binding can emerge as evolutionary spandrels through structural coupling
    • Manhart M, Morozov AV (2015) Protein folding and binding can emerge as evolutionary spandrels through structural coupling. Proc Natl Acad Sci USA 112:1797–1802.
    • (2015) Proc Natl Acad Sci USA , vol.112 , pp. 1797-1802
    • Manhart, M.1    Morozov, A.V.2
  • 41
    • 27744554173 scopus 로고    scopus 로고
    • Norovirus protein structure and function
    • Hardy ME (2005) Norovirus protein structure and function. FEMS Microbiol Lett 253:1–8.
    • (2005) FEMS Microbiol Lett , vol.253 , pp. 1-8
    • Hardy, M.E.1
  • 44
    • 78650045540 scopus 로고    scopus 로고
    • The phage-host arms race: shaping the evolution of microbes
    • Stern A, Sorek R (2011) The phage-host arms race: shaping the evolution of microbes. Bioessays 33:43–51.
    • (2011) Bioessays , vol.33 , pp. 43-51
    • Stern, A.1    Sorek, R.2
  • 46
    • 0032808947 scopus 로고    scopus 로고
    • The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes
    • Drake JW (1999) The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes. Ann NY Acad Sci 870:100–107.
    • (1999) Ann NY Acad Sci , vol.870 , pp. 100-107
    • Drake, J.W.1
  • 48
  • 50
    • 0345306751 scopus 로고    scopus 로고
    • The origins of genome complexity
    • Lynch M, Conery JS (2003) The origins of genome complexity. Science 302:1401–1404.
    • (2003) Science , vol.302 , pp. 1401-1404
    • Lynch, M.1    Conery, J.S.2
  • 51
    • 77955970107 scopus 로고    scopus 로고
    • Optimality models in the age of experimental evolution and genomics
    • Bull JJ, Wang IN (2010) Optimality models in the age of experimental evolution and genomics. J Evol Biol 23:1820–1838.
    • (2010) J Evol Biol , vol.23 , pp. 1820-1838
    • Bull, J.J.1    Wang, I.N.2
  • 52
    • 79960994072 scopus 로고    scopus 로고
    • Diversity against adversity: how adaptive immune system evolves potent antibodies
    • Muyoung H, Zeldovich KB, Shakhnovich EI (2011) Diversity against adversity: how adaptive immune system evolves potent antibodies. J Statist Phys 144:241–267.
    • (2011) J Statist Phys , vol.144 , pp. 241-267
    • Muyoung, H.1    Zeldovich, K.B.2    Shakhnovich, E.I.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.