Local packing density is the main structural determinant of the rate of protein sequence evolution at site level

BioMed Research International

Volumn 2014, Issue , 2014, Pages

  Yeh, So Wei ^a   Huang, Tsun Tsao ^a   Liu, Jen Wei ^a   Yu, Sung Huan ^a   Shih, Chien Hua ^a   Hwang, Jenn Kang ^a   Echave, Julian ^b  

^a NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^b UNIVERSIDAD NACIONAL DE SAN MARTÍN   (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

MONOMER; PROTEIN; SOLVENT;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CONSURF RATE OF EVOLUTION; CONTACT NUMBER; CONTROLLED STUDY; ENTROPY; EVOLUTIONARY RATE; EVOLUTIONARY TRACE SCORE; KARLIN AND BROCCHIERI SUM OF PAIRS SCORE; LOCAL PACKING DENSITY; MOLECULAR EVOLUTION; PHYLOGENETIC TREE; RELATIVE SOLVENT ACCESSIBILITY; SCORING SYSTEM; SEQUENCE ALIGNMENT; SHANNON ENTROPY; SOLVENT ACCESSIBILITY; VALDAR AND THORNTON SUM OF PAIRS SCORE; WEIGHTED CONTACT NUMBER; CHEMISTRY; PROTEIN DATABASE;

AMINO ACID SEQUENCE; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; PROTEINS; SOLVENTS;

EID: 84904630632     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2014/572409     Document Type: Article

References (47)

1. Pál C., Papp B., Lercher M. J., An integrated view of protein evolution. Nature Reviews Genetics 2006 7 5 337 348 10.1038/nrg1838 2-s2.0-33646182934
2. Thorne J. L., Protein evolution constraints and model-based techniques to study them. Current Opinion in Structural Biology 2007 17 3 337 341 10.1016/j.sbi.2007.05.006 2-s2.0-34347383963 (Pubitemid 47021360)
3. Worth C. L., Gong S., Blundell T. L., Structural and functional constraints in the evolution of protein families. Nature Reviews Molecular Cell Biology 2009 10 10 709 720 10.1038/nrm2762 2-s2.0-70349470948
4. Wilke C. O., Drummond D. A., Signatures of protein biophysics in coding sequence evolution. Current Opinion in Structural Biology 2010 20 3 385 389 10.1016/j.sbi.2010.03.004 2-s2.0-77955574001
5. Grahnen J. A., Nandakumar P., Kubelka J., Liberles D. A., Biophysical and structural considerations for protein sequence evolution. BMC Evolutionary Biology 2011 11 1, article 361 10.1186/1471-2148-11-361 2-s2.0-83455238341
6. Liberles D. A., Teichmann S. A., Bahar I., Bastolla U., Bloom J., Bornberg-Bauer E., Colwell L. J., De Koning A. P. J., Dokholyan N. V., Echave J., Elofsson A., Gerloff D. L., Goldstein R. A., Grahnen J. A., Holder M. T., Lakner C., Lartillot N., Lovell S. C., Naylor G., Perica T., Pollock D. D., Pupko T., Regan L., Roger A., Rubinstein N., Shakhnovich E., Sjølander K., Sunyaev S., Teufel A. I., Thorne J. L., Thornton J. W., Weinreich D. M., Whelan S., The interface of protein structure, protein biophysics, and molecular evolution. Protein Science 2012 21 6 769 785 10.1002/pro.2071 2-s2.0-84861434946
7. Bustamante C. D., Townsend J. P., Hartl D. L., Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Molecular Biology and Evolution 2000 17 2 301 308 10.1093/oxfordjournals. molbev.a026310 2-s2.0-0033969946 (Pubitemid 30075599)
8. Dean A. M., Neuhauser C., Grenier E., Golding G. B., The pattern of amino acid replacements in α / β -barrels. Molecular Biology and Evolution 2002 19 11 1846 1864 10.1093/oxfordjournals.molbev.a004009 2-s2.0-0036856289 (Pubitemid 35388108)
9. Franzosa E. A., Xia Y., Structural determinants of protein evolution are context-sensitive at the residue level. Molecular Biology and Evolution 2009 26 10 2387 2395 10.1093/molbev/msp146 2-s2.0-70349911882
10. Ramsey D. C., Scherrer M. P., Zhou T., Wilke C. O., The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Genetics 2011 188 2 479 488 10.1534/genetics.111.128025 2-s2.0-79958187925
11. Yeh S.-W., Liu J.-W., Yu S.-H., Shih C.-H., Hwang J.-K., Echave J., Site-specific structural constraints on protein sequence evolutionary divergence: local packing density vs. solvent exposure. Molecular Biology and Evolution 2014 31 1 135 139 10.1093/molbev/mst178
12. Liao H., Yeh W., Chiang D., Jernigan R. L., Lustig B., Protein sequence entropy is closely related to packing density and hydrophobicity. Protein Engineering, Design and Selection 2005 18 2 59 64 10.1093/protein/gzi009 2-s2.0-17644407653 (Pubitemid 40562553)
13. Shih C., Chang C., Lin Y., Lo W., Hwang J., Evolutionary information hidden in a single protein structure. Proteins: Structure, Function and Bioinformatics 2012 80 6 1647 1657 10.1002/prot.24058 2-s2.0-84862785625
14. Huang T. T., del Valle Marcos M. L., Hwang J. K., Echave J., A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility. BMC Evolutionary Biology 2014 14, article 78
15. 2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 2001 17 8 700 712 10.1093/bioinformatics/17.8.700 2-s2.0-0034843597 (Pubitemid 32851378)
16. Valdar W. S. J., Scoring residue conservation. Proteins: Structure, Function and Genetics 2002 48 2 227 241 10.1002/prot.10146 2-s2.0-0036681416 (Pubitemid 34743413)
17. Johansson F., Toh H., A comparative study of conservation and variation scores. BMC Bioinformatics 2010 11, article 388 10.1186/1471-2105-11-388 2-s2.0-77954686958
18. Tien M. Z., Meyer A. G., Sydykova D. K., Spielman S. J., Wilke C. O., Maximum allowed solvent accessibilites of residues in proteins. PloS ONE 2013 8 11 e80635
19. International Union of Biochemistry and Molecular Biology, Nomenclature Committee, Edwin Clifford Webb, Enzyme Nomenclature 1992: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes 1992 International Union of Biochemistry and Molecular Biology by Academic Press
20. Murzin A. G., Brenner S. E., Hubbard T., Chothia C., SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 1995 247 4 536 540 10.1006/jmbi.1995. 0159 2-s2.0-0028961335
21. Goldenberg O., Erez E., Nimrod G., Ben-Tal N., The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. Nucleic Acids Research 2009 37 1 D323 D327 10.1093/nar/gkn822 2-s2.0-57049150788
22. Ashkenazy H., Erez E., Martz E., Pupko T., Ben-Tal N., ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Research 2010 38 2 W529 W533 10.1093/nar/gkq399 2-s2.0-77954257799
23. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 1997 25 17 3389 3402 10.1093/nar/25.17.3389 2-s2.0-0030801002 (Pubitemid 27359211)
24. UniProt Consortium, The universal protein resource (UniProt). Nucleic Acids Research 2007 35 D193 D197
25. Li W., Godzik A., Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006 22 13 1658 1659 10.1093/bioinformatics/btl158 2-s2.0-33745634395 (Pubitemid 43985301)
26. Edgar R. C., MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 2004 32 5 1792 1797 10.1093/nar/gkh340 2-s2.0-3042666256 (Pubitemid 38832724)
27. Pupko T., Bell R. E., Mayrose I., Glaser F., Ben-Tal N., Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 2002 18 supplement 1 S71 S77 10.1093/bioinformatics/18.suppl-1. S71 2-s2.0-0002218484 (Pubitemid 41185639)
28. Mayrose I., Graur D., Ben-Tal N., Pupko T., Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Molecular Biology and Evolution 2004 21 9 1781 1791 10.1093/molbev/msh194 2-s2.0-4143051195 (Pubitemid 39096894)
29. Mihalek I., Reš I., Lichtarge O., A family of evolution-entropy hybrid methods for ranking protein residues by importance. Journal of Molecular Biology 2004 336 5 1265 1282 10.1016/j.jmb.2003.12.078 2-s2.0-1242339659 (Pubitemid 38229712)
30. Waterman M. S., Introduction to Computational Biology 1995 London, UK Chapman & Hall
31. Karlin S., Brocchieri L., Evolutionary conservation of RecA genes in relation to protein structure and function. Journal of Bacteriology 1996 178 7 1881 1894 2-s2.0-0029935769 (Pubitemid 26110530)
32. Valdar W. S., Thornton J. M., Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 2001 42 1 108 124 10.1002/1097-0134(20010101)42:1<108::AID-PROT110>3.0.CO;2-O
33. Sander C., Schneider R., Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Structure, Function and Genetics 1991 9 1 56 68 2-s2.0-0026030641
34. Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H., Shindyalov I. N., Bourne P. E., The protein data bank. Nucleic Acids Research 2000 28 1 235 242 10.1093/nar/28.1.235 2-s2.0-0033954256 (Pubitemid 30047768)
35. Lin C., Huang S., Lai Y., Yen S., Shih C., Lu C., Huang C., Hwang J., Deriving protein dynamical properties from weighted protein contact number. Proteins: Structure, Function and Genetics 2008 72 3 929 935 10.1002/prot.21983 2-s2.0-47349097554 (Pubitemid 352000870)
36. Kabsch W., Sander C., Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers-Peptide Science Section 1983 22 12 2577 2637 10.1002/bip.360221211 2-s2.0-0020997912
37. Rose G. D., Geselowitz A. R., Lesser G. J., Lee R. H., Zehfus M. H., Hydrophobicity of amino acid residues in globular proteins. Science 1985 229 4716 834 838 10.1126/science.4023714 2-s2.0-0022412192 (Pubitemid 16246583)
38. Miller S., Janin J., Lesk A. M., Chothia C., Interior and surface of monomeric proteins. Journal of Molecular Biology 1987 196 3 641 656 10.1016/0022-2836(87)90038-6 2-s2.0-0023645203
39. Cohen J., Applied Multiple Regression/Correlation Analysis for the Behavioral Sciences 2003 3rd Mahwah, NJ, USA L. Erlbaum Associates
40. Warner R. M., Applied Statistics: From Bivariate Through Multivariate Techniques 2013 2nd Thousand Oaks, Calif, USA SAGE
41. Halle B., Flexibility and packing in proteins. Proceedings of the National Academy of Sciences of the United States of America 2002 99 3 1274 1279 10.1073/pnas.032522499 2-s2.0-0037022347 (Pubitemid 34136483)
42. Scherrer M. P., Meyer A. G., Wilke C. O., Modeling coding-sequence evolution within the context of residue solvent accessibility. BMC Evolutionary Biology 2012 12 1, article 179 10.1186/1471-2148-12-179 2-s2.0-84866021249
43. Flatow D., Leelananda S. P., Skliros A., Kloczkowski A., Jernigan R. L., Volumes and surface areas: geometries and scaling relationships between coarse- grained and atomic structures. Current Pharmaceutical Design 2014 20 8 1208 1222 10.2174/13816128113199990067
44. Parisi G., Echave J., Structural constraints and emergence of sequence patterns in protein evolution. Molecular Biology and Evolution 2001 18 5 750 756 10.1093/oxfordjournals.molbev.a003857 2-s2.0-0035028705 (Pubitemid 32372945)
45. Fornasari M. S., Parisi G., Echave J., Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations. Molecular Biology and Evolution 2002 19 3 352 356 10.1093/oxfordjournals.molbev.a004089 2-s2.0-0036184351 (Pubitemid 34184606)
46. Parisi G., Echave J., Generality of the structurally constrained protein evolution model: assessment on representatives of the four main fold classes. Gene 2005 345 1 45 53 10.1016/j.gene.2004.11.025 2-s2.0-13444305208 (Pubitemid 40208500)
47. Chang C. M., Huang Y. W., Shih C. H., Hwang J. K., On the relationship between the sequence conservation and the packing density profiles of the protein complexes. Proteins: Structure, Function and Bioinformatics 2013 81 7 1192 1199 10.1002/prot.24268 2-s2.0-84879421722