title: Signatures of protein biophysics in coding sequence evolution.
abstract: Since the early days of molecular evolution, the conventional wisdom has been that the evolution of protein-coding genes is primarily determined by functional constraints. Yet recent evidence indicates that the evolution of these genes is strongly shaped by the biophysical processes of protein synthesis, protein folding, and specific as well as nonspecific protein-protein interactions. Selection pressures related to these biophysical processes affect primarily the amino-acid sequence of genes, but they also leave their mark on synonymous sites at the nucleotide level. While evidence for specific selection pressures related to protein biophysics is strong, there is currently no unifying framework that integrates the various selection pressures on coding sequences and disentangles their relative importance.
authors.affiliation: Center for Computational Biology and Bioinformatics, Institute for Cell and Molecular Biology, and Section of Integrative Biology, The University of Texas at Austin, Austin, TX, USA. cwilke@mail.utexas.edu
authors.forename: Claus O
authors.initials: CO
authors.lastname: Wilke
authors.forename: D Allan
authors.initials: DA
authors.lastname: Drummond
mesh_terms: D000818:Animals; D055592:Biophysical Phenomena; D019143:Evolution, Molecular; D016678:Genome / Q000235:genetics*; D014176:Protein Biosynthesis; D011506:Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012641:Selection, Genetic
chemical_list: D011506:Proteins
references.citation: Genome Res. 2000 Jul;10(7):991-1000
references.pmid: 10899148
references.citation: Proc Natl Acad Sci U S A. 2009 May 5;106(18):7273-80
references.pmid: 19351897
references.citation: Mol Biol Evol. 2009 Oct;26(10):2387-95
references.pmid: 19597162
references.citation: Mol Biol Evol. 2006 Sep;23(9):1751-61
references.pmid: 16782762
references.citation: Genetics. 2006 May;173(1):473-81
references.pmid: 16489231
references.citation: Genetics. 1998 May;149(1):445-58
references.pmid: 9584116
references.citation: PLoS Comput Biol. 2007 Nov;3(11):e203
references.pmid: 18039025
references.citation: Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10930-5
references.pmid: 16043700
references.citation: Nat Struct Mol Biol. 2009 Mar;16(3):274-80
references.pmid: 19198590
references.citation: Phys Rev Lett. 2003 May 30;90(21):218101
references.pmid: 12786593
references.citation: J Mol Evol. 2008 Apr;66(4):395-404
references.pmid: 18379715
references.citation: Genetics. 1994 Mar;136(3):927-35
references.pmid: 8005445
references.citation: FEBS Lett. 1999 Dec 3;462(3):387-91
references.pmid: 10622731
references.citation: Proc Natl Acad Sci U S A. 2009 Apr 14;106(15):6197-202
references.pmid: 19339491
references.citation: Science. 2006 Dec 22;314(5807):1938-41
references.pmid: 17185604
references.citation: Mol Syst Biol. 2008;4:210
references.pmid: 18682700
references.citation: Science. 2007 Jan 26;315(5811):525-8
references.pmid: 17185560
references.citation: PLoS Comput Biol. 2010 Feb 05;6(2):e1000664
references.pmid: 20140241
references.citation: Proc Biol Sci. 2006 Jun 22;273(1593):1507-15
references.pmid: 16777745
references.citation: Mol Biol Evol. 2007 Apr;24(4):1005-11
references.pmid: 17264066
references.citation: Nat Rev Genet. 2009 Oct;10(10):715-24
references.pmid: 19763154
references.citation: Mol Biol Evol. 2007 May;24(5):1113-21
references.pmid: 17347158
references.citation: Mol Biol Evol. 2010 Mar;27(3):609-21
references.pmid: 19923193
references.citation: Nat Rev Mol Cell Biol. 2009 Oct;10(10):709-20
references.pmid: 19756040
references.citation: BMC Evol Biol. 2003 May 23;3:11
references.pmid: 12769820
references.citation: Mol Biol Evol. 2006 Feb;23(2):327-37
references.pmid: 16237209
references.citation: Proteins. 2001 Jan 1;42(1):108-24
references.pmid: 11093265
references.citation: Mol Biol Evol. 2010 Mar;27(3):735-41
references.pmid: 19910385
references.citation: BMC Evol Biol. 2003 Oct 02;3:21
references.pmid: 14525624
references.citation: Biol Direct. 2008 Oct 07;3:40
references.pmid: 18840284
references.citation: Proc Natl Acad Sci U S A. 2005 Oct 4;102(40):14338-43
references.pmid: 16176987
references.citation: Science. 2002 Apr 26;296(5568):750-2
references.pmid: 11976460
references.citation: Structure. 2007 Nov;15(11):1442-51
references.pmid: 17997970
references.citation: Genome Res. 2003 Oct;13(10):2229-35
references.pmid: 14525925
references.citation: J Mol Biol. 1999 Aug 6;291(1):177-96
references.pmid: 10438614
references.citation: Science. 2009 Apr 10;324(5924):255-8
references.pmid: 19359587
references.citation: Biochem Biophys Res Commun. 2002 Apr 26;293(1):537-41
references.pmid: 12054634
references.citation: Mol Syst Biol. 2010;6:340
references.pmid: 20087338
references.citation: RNA. 2007 Jan;13(1):87-96
references.pmid: 17095544
references.citation: Proc Natl Acad Sci U S A. 2007 Sep 18;104(38):14952-7
references.pmid: 17848524
references.citation: PLoS Comput Biol. 2009 Jun;5(6):e1000413
references.pmid: 19521505
references.citation: Cell. 2008 Jul 25;134(2):341-52
references.pmid: 18662548
references.citation: Biochem Soc Trans. 2009 Aug;37(Pt 4):756-61
references.pmid: 19614589
references.citation: Mol Biol Evol. 2007 Feb;24(2):374-81
references.pmid: 17101719
references.citation: Mol Biol Evol. 2005 May;22(5):1345-54
references.pmid: 15746013
references.citation: Mol Biol Evol. 2009 Jul;26(7):1571-80
references.pmid: 19349643
references.citation: J Mol Evol. 2002 Jul;55(1):104-10
references.pmid: 12165847