Mutational properties of amino acid residues: Implications for evolvability of phosphorylatable residues

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 367, Issue 1602, 2012, Pages 2584-2593

  Creixell, Pau ^a   Schoof, Erwin M ^a   Tan, Chris Soon Heng ^b   Linding, Rune ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

Author keywords

Amino acid evolvability; Mutation; Phosphorylation site evolution

Indexed keywords

AMINO ACID; ANCESTRY; EVOLUTIONARY BIOLOGY; MOLECULAR ANALYSIS; MUTATION; NATURAL SELECTION; PHYSICOCHEMICAL PROPERTY; PROTEIN;

EID: 84865106483     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2012.0076     Document Type: Article

References (22)

1. Jacob, F. 1977 Evolution and tinkering. Science 196, 1161-1166. (doi:10.1126/science.860134)
2. Pastor-Satorras, R., Smith, E. & Solé, R. V. 2003 Evolving protein interaction networks through gene duplication. J. Theor. Biol. 222, 199-210. (doi:10.1016/S0022-5193 (03)00028-6)
3. Force, A., Lynch, M., Pickett, F. B., Amores, A., Yan, Y. L. & Postlethwait, J. 1999 Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531-1545.
4. Dayhoff, M. O., Schwartz, R. & Orcutt, B. C. 1978 A model of evolutionary change in proteins. In Atlas of protein sequence and structure, vol. 5, suppl. 3 (ed. M. O. Dayhoff), pp. 345-352. Washington, DC: National Biomedical Research Foundation.
5. Henikoff, S. & Henikoff, J. G. 1992 Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA 89, 109 15-109 19. (doi:10.1073/pnas.89.22.10915)
6. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. 1990 Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
7. Linding, R. 2010 (R)evolution of complex regulatory systems. Sci Signal. 3, eg4. (doi:10.1126/scisignal.3127eg4)
8. Tan, C. S. H., Pasculescu, A., Lim, W. A., Pawson, T., Bader, G. D. & Linding, R. 2009 Positive selection of tyrosine loss in metazoan evolution. Science 325, 1686-1688. (doi:10.1126/science.1174301)
9. Lim, W. A. & Pawson, T. 2010 Phosphotyrosine signaling: evolving a new cellular communication system. Cell 142, 661-667. (doi:10.1016/j.cell.2010.08.023)
10. Pincus, D., Letunic, I., Bork, P. & Lim, W. A. 2008 Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages. Proc. Natl Acad. Sci. USA 105, 9680-9684. (doi:10.1073/pnas.0803161105)
11. Manning, G., Young, S. L., Miller, W. T. & Zhai, Y. 2008 The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan. Proc. Natl Acad. Sci. USA 105, 9674-9679. (doi:10.1073/pnas.0801314105)
12. Koonin, E. V. & Novozhilov, A. S. 2009 Origin and evolution of the genetic code: the universal enigma. IUBMB Life 61, 99-111. (doi:10.1002/iub.146)
13. Pearlman, S., Serber Jr, Z. & Ferrell, J. E. 2011 A mechanism for the evolution of phosphorylation sites. Cell 147, 934-946. (doi:10.1016/j.cell.2011.08.052)
14. Tan, C. S. H., Schoof, E. M., Creixell, P., Pasculescu, A., Lim, W. A., Pawson, T., Bader, G. D. & Linding, R. 2011 Response to comment on positive selection of tyrosine loss in metazoan evolution. Science 332, 917. (doi:10.1126/science.1188535)
15. Remm, M., Storm, C. E. & Sonnhammer, E. L. 2001 Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314, 1041-1052. (doi:10.1006/jmbi.2000.5197)
16. Katoh, K. & Toh, H. 2008 Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinformatics 9, 286-298. (doi:10.1093/bib/bbn013)
17. Yang, Z. 2007 PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591. (doi:10.1093/molbev/msm088)
18. Hedges, S.B.2002The originand evolutionofmodel organisms. Nat. Rev. Genet. 3, 838-849. (doi:10.1038/nrg929)
19. 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. (doi:10.1093/oxfordjournals. molbev.a003851)
20. Hornbeck, P. V., Kornhauser, J. M., Tkachev, S., Zhang, B., Skrzypek, E., Murray, B., Latham, V. & Sullivan, M. 2012 PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40, D261-D270. (doi:10. 1093/nar/gkr1122)
21. Dinkel, H., Chica, C., Via, A., Gould, C. M., Jensen, L. J., Gibson, T. J. & Diella, F. 2010 Phospho. ELM: a database of phosphorylation sites-update 2011. Nucleic Acids Res. 39, D261-D267. (doi:10. 1093/nar/gkq1104)
22. Ward, J. J., McGuffin, L. J., Bryson, K., Buxton, B. F. & Jones, D. T. 2004 The DISOPRED server for the prediction of protein disorder. Bioinformatics 20, 2138-2139. (doi:10.1093/bioinformatics/bth195)