메뉴 건너뛰기




Volumn 9, Issue 11, 2014, Pages

Changing folding and binding stability in a viral coat protein: A comparison between substitutions accessible through mutation and those fixed by natural selection

Author keywords

[No Author keywords available]

Indexed keywords

COAT PROTEIN; COAT PROTEIN F; UNCLASSIFIED DRUG; CAPSID PROTEIN; PROTEIN BINDING;

EID: 84913534565     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0112988     Document Type: Article
Times cited : (14)

References (51)
  • 1
    • 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. doi:10.1534/genetics.106.061754.
    • (2007) Genetics , vol.175 , pp. 255-266
    • Bloom, J.D.1    Raval, A.2    Wilke, C.O.3
  • 2
    • 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. doi:10.1038/nrg1672.
    • (2005) Nat Rev Genet , vol.6 , pp. 678-687
    • DePristo, M.A.1    Weinreich, D.M.2    Hartl, D.L.3
  • 3
    • 37749052245 scopus 로고    scopus 로고
    • Prediction of protein stability upon point mutations
    • Gromiha MM (2007) Prediction of protein stability upon point mutations. Biochem Soc Trans 35: 1569-1573. doi:10.1042/BST0351569.
    • (2007) Biochem Soc Trans , vol.35 , pp. 1569-1573
    • Gromiha, M.M.1
  • 5
    • 23144461249 scopus 로고    scopus 로고
    • I-Mutant2.0: Predicting stability changes upon mutation from the protein sequence or structure
    • Capriotti E, Fariselli P, Casadio R (2005) I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res 33: W306-W310. doi:10.1093/nar/gki375.
    • (2005) Nucleic Acids Res , vol.33 , pp. W306-W310
    • Capriotti, E.1    Fariselli, P.2    Casadio, R.3
  • 7
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
    • Guerois R, Nielsen JE, Serrano L (2002) Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. J Mol Biol 320: 369-387. doi:10.1016/S0022-2836(02)00442-4.
    • (2002) J Mol Biol , vol.320 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 10
    • 0000159569 scopus 로고    scopus 로고
    • Protein structure and the energetics of protein stability
    • Robertson A, Murphy KP (1997) Protein structure and the energetics of protein stability. Chem Rev 97: 1251-1267.
    • (1997) Chem Rev , vol.97 , pp. 1251-1267
    • Robertson, A.1    Murphy, K.P.2
  • 11
    • 77951977004 scopus 로고    scopus 로고
    • Protein kinetic stability
    • Sanchez-Ruiz JM (2010) Protein kinetic stability. Biophys Chem 148: 1-15. doi:10.1016/j.bpc.2010.02.004.
    • (2010) Biophys Chem , vol.148 , pp. 1-15
    • Sanchez-Ruiz, J.M.1
  • 12
    • 31344453994 scopus 로고    scopus 로고
    • Horizontal gene transfer and the evolution of microvirid coliphage genomes
    • Rokyta DR, Burch CL, Caudle SB, Wichman HA (2006) Horizontal gene transfer and the evolution of microvirid coliphage genomes. J Bacteriol 188: 1134-1142. doi:10.1128/JB.188.3.1134-1142.2006.
    • (2006) J Bacteriol , vol.188 , pp. 1134-1142
    • Rokyta, D.R.1    Burch, C.L.2    Caudle, S.B.3    Wichman, H.A.4
  • 13
    • 77952706843 scopus 로고    scopus 로고
    • Performance of protein stability predictors
    • Khan S, Vihinen M (2010) Performance of protein stability predictors. Hum Mutat 31: 675-684. doi:10.1002/humu.21242.
    • (2010) Hum Mutat , vol.31 , pp. 675-684
    • Khan, S.1    Vihinen, M.2
  • 14
    • 13144249171 scopus 로고    scopus 로고
    • Conformational stability and thermodynamics of folding of ribonucleases Sa, Sa2 and Sa3
    • Pace CN, Hebert EJ, Shaw KL, Schell D, Both V, et al. (1998) Conformational stability and thermodynamics of folding of ribonucleases Sa, Sa2 and Sa3. J Mol Biol 279: 271-286.
    • (1998) J Mol Biol , vol.279 , pp. 271-286
    • Pace, C.N.1    Hebert, E.J.2    Shaw, K.L.3    Schell, D.4    Both, V.5
  • 15
    • 77956478911 scopus 로고    scopus 로고
    • Experimental evolution of viruses: Microviridae as a model system
    • Wichman HA, Brown CJ (2010) Experimental evolution of viruses: Microviridae as a model system. Phil Trans R Soc B 365: 2495-2501. doi:10.1098/rstb.2010.0053.
    • (2010) Phil Trans R Soc B , vol.365 , pp. 2495-2501
    • Wichman, H.A.1    Brown, C.J.2
  • 16
    • 79953881781 scopus 로고    scopus 로고
    • Contribution of hydrophobic interactions to protein stability
    • Pace CN, Fu H, Fryar KL, Landua J, Trevino SR, et al. (2011) Contribution of Hydrophobic Interactions to Protein Stability. J Mol Biol 408: 514-528. doi:10.1016/j.jmb.2011.02.053.
    • (2011) J Mol Biol , vol.408 , pp. 514-528
    • Pace, C.N.1    Fu, H.2    Fryar, K.L.3    Landua, J.4    Trevino, S.R.5
  • 17
    • 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. doi:10.1016/j.jmb.2007.03.069.
    • (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
  • 18
    • 0019889063 scopus 로고
    • Thermodynamics of protein association reactions: Forces contributing to stability?
    • Ross PD, Subramanian S (1981) Thermodynamics of Protein Association Reactions: Forces Contributing to Stability? Biochemistry 20: 3096-3102.
    • (1981) Biochemistry , vol.20 , pp. 3096-3102
    • Ross, P.D.1    Subramanian, S.2
  • 20
    • 70349901079 scopus 로고    scopus 로고
    • Stability effects of mutations and protein evolvability
    • Tokuriki N, Tawfik DS (2009) Stability effects of mutations and protein evolvability. Curr Opin Struct Biol 19: 596-604. doi:10.1016/j.sbi.2009.08.003.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 596-604
    • Tokuriki, N.1    Tawfik, D.S.2
  • 21
    • 0034035485 scopus 로고    scopus 로고
    • Big-benefit mutations in a bacteriophage inhibited with heat
    • Bull JJ, Badgett MR, Wichman HA (2000) Big-benefit mutations in a bacteriophage inhibited with heat. Mol Biol Evol 17: 942-950.
    • (2000) Mol Biol Evol , vol.17 , pp. 942-950
    • Bull, J.J.1    Badgett, M.R.2    Wichman, H.A.3
  • 22
    • 0035860350 scopus 로고    scopus 로고
    • Tyrosine hydrogen bonds make a large contribution to protein stability
    • Pace CN, Horn G, Hebert EJ, Bechert J, Shaw K, et al. (2001) Tyrosine hydrogen bonds make a large contribution to protein stability. J Mol Biol 312: 393-404. doi:10.1006/jmbi.2001.4956.
    • (2001) J Mol Biol , vol.312 , pp. 393-404
    • Pace, C.N.1    Horn, G.2    Hebert, E.J.3    Bechert, J.4    Shaw, K.5
  • 23
    • 80053315010 scopus 로고    scopus 로고
    • First-Step Mutations for Adaptation at Elevated Temperature Increase Capsid Stability in a Virus
    • Lee KH, Miller CR, Nagel AC, Wichman HA, Joyce P, et al. (2011) First-Step Mutations for Adaptation at Elevated Temperature Increase Capsid Stability in a Virus. PLoS ONE 6: e25640. doi:10.1371/journal.pone.0025640.t001.
    • (2011) PLoS ONE , vol.6 , pp. e25640
    • Lee, K.H.1    Miller, C.R.2    Nagel, A.C.3    Wichman, H.A.4    Joyce, P.5
  • 24
    • 2542435875 scopus 로고    scopus 로고
    • PH and cationinduced thermodynamic stability of human hyaluronan binding protein 1 regulates its hyaluronan affinity
    • Jha BK, Mitra N, Rana R, Surolia A, Salunke DM, et al. (2004) pH and cationinduced thermodynamic stability of human hyaluronan binding protein 1 regulates its hyaluronan affinity. J Biol Chem 279: 23061-23072. doi:10.1074/jbc.M310676200.
    • (2004) J Biol Chem , vol.279 , pp. 23061-23072
    • Jha, B.K.1    Mitra, N.2    Rana, R.3    Surolia, A.4    Salunke, D.M.5
  • 25
    • 63449112107 scopus 로고    scopus 로고
    • Hotter is better and broader: Thermal sensitivity of fitness in a population of bacteriophages
    • Knies JL, Kingsolver JG, Burch CL (2009) Hotter is better and broader: thermal sensitivity of fitness in a population of bacteriophages. Am Nat 173: 419-430.
    • (2009) Am Nat , vol.173 , pp. 419-430
    • Knies, J.L.1    Kingsolver, J.G.2    Burch, C.L.3
  • 26
    • 33748454832 scopus 로고    scopus 로고
    • Natural selection for kinetic stability is a likely origin of correlations between mutational effects on protein energetics and frequencies of amino acid occurrences in sequence alignments
    • Godoy-Ruiz R, Ariza F, Rodriguez-Larrea D, Perez-Jimenez R, Ibarra-Molero B, et al. (2006) Natural selection for kinetic stability is a likely origin of correlations between mutational effects on protein energetics and frequencies of amino acid occurrences in sequence alignments. J Mol Biol 362: 966-978. doi:10.1016/j.jmb.2006.07.065.
    • (2006) J Mol Biol , vol.362 , pp. 966-978
    • Godoy-Ruiz, R.1    Ariza, F.2    Rodriguez-Larrea, D.3    Perez-Jimenez, R.4    Ibarra-Molero, B.5
  • 27
    • 84875058100 scopus 로고    scopus 로고
    • Adaptive regulatory substitutions affect multiple stages in the life cycle of the bacteriophage QX174
    • Brown CJ, Stancik AD, Roychoudhury P, Krone SM (2013) Adaptive regulatory substitutions affect multiple stages in the life cycle of the bacteriophage QX174. BMC Evol Biol 13: 66. doi:10.1146/annurev.mi.03.100149.002103.
    • (2013) BMC Evol Biol , vol.13 , pp. 66
    • Brown, C.J.1    Stancik, A.D.2    Roychoudhury, P.3    Krone, S.M.4
  • 28
    • 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: 85-95. doi:10.1016/S0022-2836(02)00400-X.
    • (2002) J Mol Biol , vol.320 , pp. 85-95
    • Wang, X.1    Minasov, G.2    Shoichet, B.K.3
  • 29
    • 0036384211 scopus 로고    scopus 로고
    • Structural bases of stability-function tradeoffs in enzymes
    • Beadle BM, Shoichet BK (2002) Structural bases of stability-function tradeoffs in enzymes. J Mol Biol 321: 285-296. doi:10.1016/S0022-2836(02)00599-5.
    • (2002) J Mol Biol , vol.321 , pp. 285-296
    • Beadle, B.M.1    Shoichet, B.K.2
  • 30
    • 48349090111 scopus 로고    scopus 로고
    • Protein aggregation and protein instability govern familial amyotrophic lateral sclerosis patient survival
    • Wang Q, Johnson JL, Agar NYR, Agar JN (2008) Protein aggregation and protein instability govern familial amyotrophic lateral sclerosis patient survival. PLoS Biol 6: e170. doi:10.1371/journal.pbio.0060170.
    • (2008) PLoS Biol , vol.6 , pp. e170
    • Wang, Q.1    Johnson, J.L.2    Agar, N.Y.R.3    Agar, J.N.4
  • 31
    • 0347357617 scopus 로고    scopus 로고
    • Protein folding and misfolding
    • Dobson CM (2003) Protein folding and misfolding. Nature 426: 884-890. doi:10.1038/nature02261.
    • (2003) Nature , vol.426 , pp. 884-890
    • Dobson, C.M.1
  • 32
    • 25144523127 scopus 로고    scopus 로고
    • Loss of protein structure stability as a major causative factor in monogenic disease
    • Yue P, Li Z, Moult J (2005) Loss of protein structure stability as a major causative factor in monogenic disease. J Mol Biol 353: 459-473. doi:10.1016/j.jmb.2005.08.020.
    • (2005) J Mol Biol , vol.353 , pp. 459-473
    • Yue, P.1    Li, Z.2    Moult, J.3
  • 33
    • 80052351483 scopus 로고    scopus 로고
    • In vitro assembly of the øx174 procapsid from external scaffolding protein oligomers and early pentameric assembly intermediates
    • Cherwa JE, Organtini LJ, Ashley RE, Hafenstein SL, Fane BA (2011) In Vitro Assembly of the øX174 Procapsid from External Scaffolding Protein Oligomers and Early Pentameric Assembly Intermediates. J Mol Biol 412: 387-396. doi:10.1016/j.jmb.2011.07.070.
    • (2011) J Mol Biol , vol.412 , pp. 387-396
    • Cherwa, J.E.1    Organtini, L.J.2    Ashley, R.E.3    Hafenstein, S.L.4    Fane, B.A.5
  • 34
    • 0026544322 scopus 로고
    • Atomic structure of single-stranded DNA bacteriophage QX174 and its functional implications
    • McKenna R, Xia D, Willingmann P, Ilag LL, Krishnaswamy S, et al. (1992) Atomic structure of single-stranded DNA bacteriophage QX174 and its functional implications. Nature 355: 137-143. doi:10.1038/355137a0.
    • (1992) Nature , vol.355 , pp. 137-143
    • Mckenna, R.1    Xia, D.2    Willingmann, P.3    Ilag, L.L.4    Krishnaswamy, S.5
  • 37
    • 0032967636 scopus 로고    scopus 로고
    • The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus FX174
    • Dokland T, Bernal RA, Burch AD, Pletnev S, Fane BA, et al. (1999) The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus FX174. J Mol Biol 288: 595-608. doi:10.1006/jmbi.1999.2699.
    • (1999) J Mol Biol , vol.288 , pp. 595-608
    • Dokland, T.1    Bernal, R.A.2    Burch, A.D.3    Pletnev, S.4    Fane, B.A.5
  • 38
    • 46249083761 scopus 로고    scopus 로고
    • Assembly reflects evolution of protein complexes
    • Levy ED, Erba EB, Robinson CV, Teichmann SA (2008) Assembly reflects evolution of protein complexes. Nature 453: 1262-1265. doi:10.1038/nature06942.
    • (2008) Nature , vol.453 , pp. 1262-1265
    • Levy, E.D.1    Erba, E.B.2    Robinson, C.V.3    Teichmann, S.A.4
  • 39
    • 33646948530 scopus 로고    scopus 로고
    • Parkinson's disease brain mitochondrial complex i has oxidatively damaged subunits and is functionally impaired and misassembled
    • Keeney PM, Xie J, Capaldi RA, Bennett JP Jr (2006) Parkinson's Disease Brain Mitochondrial Complex I Has Oxidatively Damaged Subunits and Is Functionally Impaired and Misassembled. J Neurosci 26: 5256-5264. doi:10.1523/JNEUROSCI.0984-06.2006.
    • (2006) J Neurosci , vol.26 , pp. 5256-5264
    • Keeney, P.M.1    Xie, J.2    Capaldi, R.A.3    Bennett, J.P.4
  • 40
    • 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: 805-808. doi:10.1038/nature01891.
    • (2003) Nature , vol.424 , pp. 805-808
    • Chiti, F.1    Stefani, M.2    Taddei, N.3    Ramponi, G.4    Dobson, C.M.5
  • 42
    • 3242875210 scopus 로고    scopus 로고
    • ElNemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement
    • Suhre K, Sanejouand Y-H (2004) ElNemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 32: W610-W614. doi:10.1093/nar/gkh368.
    • (2004) Nucleic Acids Res , vol.32 , pp. W610-W614
    • Suhre, K.1    Sanejouand, Y.-H.2
  • 43
    • 0033575348 scopus 로고    scopus 로고
    • Different trajectories of parallel evolution during viral adaptation
    • Wichman HA, Badgett MR, Scott L, Boulianne CM, Bull JJ (1999) Different trajectories of parallel evolution during viral adaptation. Science 285: 422-424.
    • (1999) Science , vol.285 , pp. 422-424
    • Wichman, H.A.1    Badgett, M.R.2    Scott, L.3    Boulianne, C.M.4    Bull, J.J.5
  • 44
    • 0033978271 scopus 로고    scopus 로고
    • Evolutionary reversals during viral adaptation to alternating hosts
    • Crill W, Wichman HA, Bull JJ (2000) Evolutionary reversals during viral adaptation to alternating hosts. Genetics 154: 27-37.
    • (2000) Genetics , vol.154 , pp. 27-37
    • Crill, W.1    Wichman, H.A.2    Bull, J.J.3
  • 45
    • 0034731035 scopus 로고    scopus 로고
    • Experimental evolution recapitulates natural evolution
    • Wichman HA, Scott LA, Yarber CD, Bull JJ (2000) Experimental evolution recapitulates natural evolution. Phil Trans R Soc B 355: 1677-1684. doi:10.1098/rstb.2000.0731.
    • (2000) Phil Trans R Soc B , vol.355 , pp. 1677-1684
    • Wichman, H.A.1    Scott, L.A.2    Yarber, C.D.3    Bull, J.J.4
  • 46
    • 20444382446 scopus 로고    scopus 로고
    • Adaptive molecular evolution for 13, 000 phage generations: A possible arms race
    • Wichman HA, Millstein J, Bull JJ (2005) Adaptive molecular evolution for 13, 000 phage generations: A possible arms race. Genetics 170: 19-31. doi:10.1534/genetics.104.034488.
    • (2005) Genetics , vol.170 , pp. 19-31
    • Wichman, H.A.1    Millstein, J.2    Bull, J.J.3
  • 47
    • 55549105742 scopus 로고    scopus 로고
    • Genomic evolution in a virus under specific selection for host recognition
    • Pepin KM, Domsic J, McKenna R (2008) Genomic evolution in a virus under specific selection for host recognition. Infection, Genetics and Evolution 8: 825- 834. doi:10.1016/j.meegid.2008.08.008.
    • (2008) Infection, Genetics and Evolution , vol.8 , pp. 825-834
    • Pepin, K.M.1    Domsic, J.2    Mckenna, R.3
  • 49
    • 84875281425 scopus 로고    scopus 로고
    • Selection affects genes involved in replication during long-term evolution in experimental populations of the bacteriophage QX174
    • Brown CJ, Millstein J, Williams CJ, Wichman HA (2013) Selection affects genes involved in replication during long-term evolution in experimental populations of the bacteriophage QX174. PLoS ONE 8: e60401. doi:10.1371/journal.- pone.0060401.
    • (2013) PLoS ONE , vol.8 , pp. e60401
    • Brown, C.J.1    Millstein, J.2    Williams, C.J.3    Wichman, H.A.4
  • 50
    • 42049093984 scopus 로고    scopus 로고
    • Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage QX 174
    • Pepin KM, Wichman HA (2008) Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage QX 174. BMC Evol Biol 8: 85. doi:10.1186/1471-2148-8-85.
    • (2008) BMC Evol Biol , vol.8 , pp. 85
    • Pepin, K.M.1    Wichman, H.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.