메뉴 건너뛰기




Volumn 24, Issue 12, 2014, Pages 2050-2058

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

EID: 84913588353     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.176214.114     Document Type: Article
Times cited : (114)

References (59)
  • 1
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • The 1000 Genomes Project Consortium. 2012. An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.
    • (2012) Nature , vol.491 , pp. 56-65
  • 2
    • 80053453491 scopus 로고    scopus 로고
    • Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites
    • Adikesavan AK, Katsonis P, Marciano DC, Lua R, Herman C, Lichtarge O. 2011. Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites. PLoS Genet 7: e1002244.
    • (2011) PLoS Genet , vol.7 , pp. e1002244
    • Adikesavan, A.K.1    Katsonis, P.2    Marciano, D.C.3    Lua, R.4    Herman, C.5    Lichtarge, O.6
  • 4
    • 84887309484 scopus 로고    scopus 로고
    • Prediction and experimental validation of enzyme substrate specificity in protein structures
    • Amin S, Erdin S, Ward R, Lua R, Lichtarge O. 2013. Prediction and experimental validation of enzyme substrate specificity in protein structures. Proc Natl Acad Sci 110: 45.
    • (2013) Proc Natl Acad Sci , vol.110 , pp. 45
    • Amin, S.1    Erdin, S.2    Ward, R.3    Lua, R.4    Lichtarge, O.5
  • 5
    • 44349132708 scopus 로고    scopus 로고
    • Common and rare variants in multifactorial susceptibility to common diseases
    • Bodmer W, Bonilla C. 2008. Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 40: 695-701.
    • (2008) Nat Genet , vol.40 , pp. 695-701
    • Bodmer, W.1    Bonilla, C.2
  • 6
    • 0037373275 scopus 로고    scopus 로고
    • Discovering genotypes underlying human phenotypes: Past successes for Mendelian disease, future approaches for complex disease
    • Botstein D, Risch N. 2003. Discovering genotypes underlying human phenotypes: past successes for Mendelian disease, future approaches for complex disease. Nat Genet 33: 228-237.
    • (2003) Nat Genet , vol.33 , pp. 228-237
    • Botstein, D.1    Risch, N.2
  • 9
    • 57149120304 scopus 로고    scopus 로고
    • Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences
    • Choi SC, Redelings BD, Thorne JL. 2008. Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences. Phil Trans R Soc B 363: 3931-3939.
    • (2008) Phil Trans R Soc B , vol.363 , pp. 3931-3939
    • Choi, S.C.1    Redelings, B.D.2    Thorne, J.L.3
  • 11
    • 69749122314 scopus 로고    scopus 로고
    • Identification of deleterious mutations within three human genomes
    • Chun S, Fay J. 2009. Identification of deleterious mutations within three human genomes. Genome Res 19: 1553.
    • (2009) Genome Res , vol.19 , pp. 1553
    • Chun, S.1    Fay, J.2
  • 12
    • 0032574346 scopus 로고    scopus 로고
    • The evolutionary genetics of speciation
    • Coyne JA, Orr HA. 1998. The evolutionary genetics of speciation. Phil Trans R Soc B 353: 287-305.
    • (1998) Phil Trans R Soc B , vol.353 , pp. 287-305
    • Coyne, J.A.1    Orr, H.A.2
  • 14
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 15
    • 77649271360 scopus 로고    scopus 로고
    • Evolutionary trace annotation of protein function in the structural proteome
    • Erdin S, Ward R, Venner E, Lichtarge O. 2010. Evolutionary trace annotation of protein function in the structural proteome. J Mol Biol 396: 1451-1473.
    • (2010) J Mol Biol , vol.396 , pp. 1451-1473
    • Erdin, S.1    Ward, R.2    Venner, E.3    Lichtarge, O.4
  • 16
    • 34447546660 scopus 로고    scopus 로고
    • The distribution of fitness effects of new mutations
    • Eyre-Walker A, Keightley PD. 2007. The distribution of fitness effects of new mutations. Nat Rev Genet 8: 610-618.
    • (2007) Nat Rev Genet , vol.8 , pp. 610-618
    • Eyre-Walker, A.1    Keightley, P.D.2
  • 18
    • 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
  • 19
    • 0030574072 scopus 로고    scopus 로고
    • Compensatory nearly neutral mutations: Selection without adaptation
    • Hartl DL, Taubes CH. 1996. Compensatory nearly neutral mutations: selection without adaptation. J Theor Biol 182: 303-309.
    • (1996) J Theor Biol , vol.182 , pp. 303-309
    • Hartl, D.L.1    Taubes, C.H.2
  • 20
    • 0026458378 scopus 로고
    • Amino acid substitutionmatrices from protein blocks
    • Henikoff S, Henikoff J. 1992. Amino acid substitutionmatrices from protein blocks. Proc Natl Acad Sci 89: 10915.
    • (1992) Proc Natl Acad Sci , vol.89 , pp. 10915
    • Henikoff, S.1    Henikoff, J.2
  • 21
    • 79957621519 scopus 로고    scopus 로고
    • Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed
    • Hicks S, Wheeler DA, Plon SE, Kimmel M. 2011. Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Hum Mutat 32: 661-668.
    • (2011) Hum Mutat , vol.32 , pp. 661-668
    • Hicks, S.1    Wheeler, D.A.2    Plon, S.E.3    Kimmel, M.4
  • 22
    • 0037816165 scopus 로고    scopus 로고
    • Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis
    • Kato S, Han S, Liu W, Otsuka K, Shibata H, Kanamaru R, Ishioka C. 2003. Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis. Proc Natl Acad Sci 100: 8424.
    • (2003) Proc Natl Acad Sci , vol.100 , pp. 8424
    • Kato, S.1    Han, S.2    Liu, W.3    Otsuka, K.4    Shibata, H.5    Kanamaru, R.6    Ishioka, C.7
  • 23
    • 84855455959 scopus 로고    scopus 로고
    • Rates and fitness consequences of new mutations in humans
    • Keightley PD. 2012. Rates and fitness consequences of new mutations in humans. Genetics 190: 295-304.
    • (2012) Genetics , vol.190 , pp. 295-304
    • Keightley, P.D.1
  • 24
    • 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
  • 25
    • 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
  • 27
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary tracemethod defines binding surfaces common to protein families
    • Lichtarge O, Bourne H, Cohen F. 1996. An evolutionary tracemethod defines binding surfaces common to protein families. J Mol Biol 257: 342-358.
    • (1996) J Mol Biol , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.2    Cohen, F.3
  • 28
    • 0031555477 scopus 로고    scopus 로고
    • Identification of functional surfaces of the zinc binding domains of intracellular receptors
    • Lichtarge O, Yamamoto KR, Cohen FE. 1997. Identification of functional surfaces of the zinc binding domains of intracellular receptors. J Mol Biol 274: 325-337.
    • (1997) J Mol Biol , vol.274 , pp. 325-337
    • Lichtarge, O.1    Yamamoto, K.R.2    Cohen, F.E.3
  • 29
    • 0027764344 scopus 로고
    • Proteinsequence alignments: A strategy for the hierarchical analysis of residue conservation
    • Livingstone CD, Barton GJ. 1993. Proteinsequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput Appl Biosci 9: 745-756.
    • (1993) Comput Appl Biosci , vol.9 , pp. 745-756
    • Livingstone, C.D.1    Barton, G.J.2
  • 33
    • 0036300444 scopus 로고    scopus 로고
    • Structural clusters of evolutionary trace residues are statistically significant and common in proteins
    • Madabushi S, Yao H, Marsh M, Kristensen DM, Philippi A, Sowa ME, Lichtarge O. 2002. Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J Mol Biol 316: 139-154.
    • (2002) J Mol Biol , vol.316 , pp. 139-154
    • Madabushi, S.1    Yao, H.2    Marsh, M.3    Kristensen, D.M.4    Philippi, A.5    Sowa, M.E.6    Lichtarge, O.7
  • 34
    • 1542379652 scopus 로고    scopus 로고
    • Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions
    • Madabushi S, Gross AK, Philippi A, Meng EC, Wensel TG, Lichtarge O. 2004. Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions. J Biol Chem 279: 8126-8132.
    • (2004) J Biol Chem , vol.279 , pp. 8126-8132
    • Madabushi, S.1    Gross, A.K.2    Philippi, A.3    Meng, E.C.4    Wensel, T.G.5    Lichtarge, O.6
  • 35
    • 0028076771 scopus 로고
    • Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence
    • Markiewicz P, Kleina L, Cruz C, Ehret S, Miller J. 1994. Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence. J Mol Biol 240: 421.
    • (1994) J Mol Biol , vol.240 , pp. 421
    • Markiewicz, P.1    Kleina, L.2    Cruz, C.3    Ehret, S.4    Miller, J.5
  • 37
    • 58149347486 scopus 로고    scopus 로고
    • Genome-wide association studies: Potential next steps on a genetic journey
    • McCarthy MI, Hirschhorn JN. 2008. Genome-wide association studies: potential next steps on a genetic journey. Hum Mol Genet 17: R156-R165.
    • (2008) Hum Mol Genet , vol.17 , pp. R156-R165
    • McCarthy, M.I.1    Hirschhorn, J.N.2
  • 38
    • 1242339659 scopus 로고    scopus 로고
    • A family of evolution-entropy hybrid methods for ranking protein residues by importance
    • Mihalek I, Res I, Lichtarge O. 2004. A family of evolution-entropy hybrid methods for ranking protein residues by importance. J Mol Biol 336: 1265-1282.
    • (2004) J Mol Biol , vol.336 , pp. 1265-1282
    • Mihalek, I.1    Res, I.2    Lichtarge, O.3
  • 39
    • 34547616501 scopus 로고    scopus 로고
    • The new mutation theory of phenotypic evolution
    • Nei M. 2007. The new mutation theory of phenotypic evolution. Proc Natl Acad Sci 104: 12235-12242.
    • (2007) Proc Natl Acad Sci , vol.104 , pp. 12235-12242
    • Nei, M.1
  • 40
    • 0035026704 scopus 로고    scopus 로고
    • Predicting deleterious amino acid substitutions
    • Ng P, Henikoff S. 2001. Predicting deleterious amino acid substitutions. Genome Res 11: 863.
    • (2001) Genome Res , vol.11 , pp. 863
    • Ng, P.1    Henikoff, S.2
  • 42
    • 0027020232 scopus 로고
    • The nearly neutral theory of molecular evolution
    • Ohta T. 1992. The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23: 263-286.
    • (1992) Annu Rev Ecol Syst , vol.23 , pp. 263-286
    • Ohta, T.1
  • 43
    • 13144257707 scopus 로고    scopus 로고
    • The genetic theory of adaptation: A brief history
    • Orr HA. 2005. The genetic theory of adaptation: a brief history. Nat Rev Genet 6: 119-127.
    • (2005) Nat Rev Genet , vol.6 , pp. 119-127
    • Orr, H.A.1
  • 44
    • 0027062943 scopus 로고
    • Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds
    • Overington J, Donnelly D, Johnson MS, Sali A, Blundell TL. 1992. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci 1: 216-226.
    • (1992) Protein Sci , vol.1 , pp. 216-226
    • Overington, J.1    Donnelly, D.2    Johnson, M.S.3    Sali, A.4    Blundell, T.L.5
  • 45
    • 0034843597 scopus 로고    scopus 로고
    • AL2CO: Calculation of positional conservation in a protein sequence alignment
    • Pei J, Grishin NV. 2001. AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 17: 700-712.
    • (2001) Bioinformatics , vol.17 , pp. 700-712
    • Pei, J.1    Grishin, N.V.2
  • 46
    • 34248379012 scopus 로고    scopus 로고
    • Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: Lessons from recent developments in the IARC TP53 database
    • Petitjean A, Mathe E, Kato S, Ishioka C, Tavtigian S, Hainaut P, Olivier M. 2007. Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database. Hum Mutat 28: 622-629.
    • (2007) Hum Mutat , vol.28 , pp. 622-629
    • Petitjean, A.1    Mathe, E.2    Kato, S.3    Ishioka, C.4    Tavtigian, S.5    Hainaut, P.6    Olivier, M.7
  • 47
    • 0025955349 scopus 로고
    • Systematic mutation of bacteriophage T4 lysozyme
    • Rennell D, Bouvier S, Hardy L, Poteete A. 1991. Systematic mutation of bacteriophage T4 lysozyme. J Mol Biol 222: 67-86.
    • (1991) J Mol Biol , vol.222 , pp. 67-86
    • Rennell, D.1    Bouvier, S.2    Hardy, L.3    Poteete, A.4
  • 48
    • 77952356281 scopus 로고    scopus 로고
    • Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors
    • Rodriguez G, Yao R, Lichtarge O, Wensel T. 2010. Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors. Proc Natl Acad Sci 107: 7787.
    • (2010) Proc Natl Acad Sci , vol.107 , pp. 7787
    • Rodriguez, G.1    Yao, R.2    Lichtarge, O.3    Wensel, T.4
  • 49
    • 84868159034 scopus 로고    scopus 로고
    • Two mechanisms produce mutation hotspots at DNA breaks in Escherichia coli
    • Shee C, Gibson JL, Rosenberg SM. 2012. Two mechanisms produce mutation hotspots at DNA breaks in Escherichia coli. Cell Rep 2: 714-721.
    • (2012) Cell Rep , vol.2 , pp. 714-721
    • Shee, C.1    Gibson, J.L.2    Rosenberg, S.M.3
  • 50
    • 0014935646 scopus 로고
    • Natural selection and the concept of a protein space
    • Smith JM 1970. Natural selection and the concept of a protein space. Nature 225: 563-564
    • (1970) Nature , vol.225 , pp. 563-564
    • Smith, J.M.1
  • 51
    • 0346220017 scopus 로고    scopus 로고
    • Dimerization in aminergic G-protein-coupled receptors: Application of a hidden-site class model of evolution
    • Soyer OS, Dimmic MW, Neubig RR, Goldstein RA. 2003. Dimerization in aminergic G-protein-coupled receptors: application of a hidden-site class model of evolution. Biochemistry 42: 14522-14531.
    • (2003) Biochemistry , vol.42 , pp. 14522-14531
    • Soyer, O.S.1    Dimmic, M.W.2    Neubig, R.R.3    Goldstein, R.A.4
  • 52
    • 22244437614 scopus 로고    scopus 로고
    • Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity
    • Stone E, Sidow A. 2005. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome Res 15: 978-986.
    • (2005) Genome Res , vol.15 , pp. 978-986
    • Stone, E.1    Sidow, A.2
  • 53
    • 34347388470 scopus 로고    scopus 로고
    • UniRef: Comprehensive and non-redundant UniProt reference clusters
    • Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. 2007. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23: 1282-1288.
    • (2007) Bioinformatics , vol.23 , pp. 1282-1288
    • Suzek, B.E.1    Huang, H.2    McGarvey, P.3    Mazumder, R.4    Wu, C.H.5
  • 54
    • 0036681416 scopus 로고    scopus 로고
    • Scoring residue conservation
    • Valdar WS. 2002. Scoring residue conservation. Proteins 48: 227-241.
    • (2002) Proteins , vol.48 , pp. 227-241
    • Valdar, W.S.1
  • 55
    • 65649110443 scopus 로고    scopus 로고
    • Evolutionary Trace Annotation Server: Automated enzyme function prediction in protein structures using 3D templates
    • Ward RM, Venner E, Daines B, Murray S, Erdin S, Kristensen DM, Lichtarge O. 2009. Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates. Bioinformatics 25: 1426-1427.
    • (2009) Bioinformatics , vol.25 , pp. 1426-1427
    • Ward, R.M.1    Venner, E.2    Daines, B.3    Murray, S.4    Erdin, S.5    Kristensen, D.M.6    Lichtarge, O.7
  • 57
    • 0000907353 scopus 로고
    • The roles of mutation, inbreeding, crossbreeding, and selection in evolution
    • Genetics Society of America, Ithaca, NY
    • Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding, and selection in evolution. In Proceedings of the 6th International Congress of Genetics, Vol. 1, pp. 356-366. Genetics Society of America, Ithaca, NY.
    • (1932) Proceedings of the 6th International Congress of Genetics , vol.1 , pp. 356-366
    • Wright, S.1
  • 59
    • 33748267918 scopus 로고    scopus 로고
    • Rank information: A structure-independent measure of evolutionary trace quality that improves identification of protein functional sites
    • Yao H, Mihalek I, Lichtarge O. 2006. Rank information: a structure-independent measure of evolutionary trace quality that improves identification of protein functional sites. Proteins 65: 111-123.
    • (2006) Proteins , vol.65 , pp. 111-123
    • Yao, H.1    Mihalek, I.2    Lichtarge, O.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.