Assessing the impact of secondary structure and solvent accessibility on protein evolution

Genetics

Volumn 149, Issue 1, 1998, Pages 445-458

  Goldman, Nick ^a   Thorne, Jeffrey L ^b   Jones, David T ^c  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL DEHYDROGENASE; AMINO ACID; GLUCOSE 1 PHOSPHATE ADENYLYLTRANSFERASE; GLUTAMATE DEHYDROGENASE; GLYCOPROTEIN GP 120; GUANINE NUCLEOTIDE BINDING PROTEIN; MATRIX PROTEIN; PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP); PROTEIN; SOLVENT; SUCROSE SYNTHASE; SYNTHETASE; UNCLASSIFIED DRUG; XYLAN ENDO 1,3 BETA XYLOSIDASE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE;

DATABASES, FACTUAL; EVOLUTION, MOLECULAR; MARKOV CHAINS; MODELS, CHEMICAL; PROTEIN STRUCTURE, SECONDARY; SOLVENTS;

EID: 0031805465     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (51)

1. ADACHI, J., and M. HASEGAWA, 1995 MOLPHY: Programs for Molecular Phylogenetics, Ver. 2.3. Institute of Statistical Mathematics, Tokyo.
2. ASAI, K., S. HAYAMIZU and K. HANDA, 1993 Prediction of protein secondary structure by the hidden Markov model. CABIOS 9: 141-146.
3. BENNER, S. A., I. BADCOE, M. A. COHEN and D. L. GERLOFF, 1994 Bona fide prediction of aspects of protein conformation: assigning interior and surface residues from patterns of variation and conservation in homologous sequences. J. Mol. Biol. 235: 926-958.
4. BERNSTEIN, F. C., T. F. KOETZLE, G. J. B. WILLIAMS, E. F. MEYER, M. D. BRICE et al., 1977 The protein data bank: a computer-based archival file for macromolecular structures. Eur. J. Biochem. 80: 319-324.
5. BLEASBY, A. J., and J. C. WOOTTON, 1990 Construction of validated, non-redundant composite protein sequence databases. Prot. Eng. 3: 153-159.
6. BROWN, M., R. HUGHEY, A. KROGH, I. S. MIAN. K. SJOLANDER et al., 1993 Using Dirichlet mixture priors to derive hidden Markov models for protein families, pp. 47-55 in Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, edited by L. HUNTER, D. SEARLS and J. SHAVLIK. AIII Press, Menlo Park, CA.
7. BRUNO, W. J., 1996 Modelling residue usage in aligned protein sequences via maximum likelihood. Mol. Biol. Evol. 13: 1368-1374.
8. CAO, Y., J. ADACHI, A. JANKE, S. PÄÄBO and M. HASEGAWA, 1994 Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial, proteins: instability of a tree based on a single gene. J. Mol. Evol. 39: 519-527.
9. CHOTHIA, C., and A. M. LESK, 1986 The relation between the divergence of sequence and structure in proteins. EMBO J. 5: 823-826.
10. CHURCHILL, G. A., 1989 Stochastic models for heterogeneous DNA sequences. Bull. Math. Biol. 51: 79-94.
11. DAYHOFF, M. O., R. V. ECK and C. M. PARK, 1972 A model of evolutionary change in proteins, pp. 89-99 in Atlas of Protein Sequence and Structure, edited by M. O. DAYHOFF. National Biomedical Research Foundation, Washington, DC.
12. DAYHOFF, M. O., R. M. SCHWARTZ and B. C. ORCUTT, 1978 A model of evolutionary change in proteins, pp. 345-352 in Atlas of Protein Sequence and Structure, edited by M. O. DAYHOFF. National Biomedical Research Foundation, Washington, DC.
13. EFRON, B., and R. J. TIBSHIRANI, 1993 An Introduction to the Bootstrap. Chapman and Hall, New York.
14. FELSENSTEIN, J., 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368-376.
15. FELSENSTEIN, J., 1985 Phylogenies and the comparative method. Am. Nat. 125: 1-15.
16. FELSENSTEIN, J., 1995 PHYLIP (Phylogenetic Inference Package), Ver. 3.57. Department of Genetics, University of Washington, Seattle.
17. FELSENSTEIN, J., and G. A. CHURCHILL, 1996 A hidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13: 93-104.
18. FRIEDLANDER, T. P., J. C. REGIER, C. MITTER and D. L. WAGNER, 1996 A nuclear gene for higher-level phylogenetics-phosphoenolpy-ruvate carboxykinase tracks Mesozoic-age divergences within Lepidoptera (Insecta). Mol. Biol. Evol. 13: 594-604.
19. GOLDMAN, N., 1993 Statistical tests of models of DNA substitution. J. Mol. Evol. 36: 182-198.
20. GOLDMAN, N., and Z. YANG, 1994 A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11: 725-736.
21. GOLDMAN, N., J. L. THORNE and D. T. JONES, 1996 Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J. Mol. Biol. 263: 196-208.
22. GOTOH, O., 1982 An improved algorithm for matching biological sequences. J. Mol. Biol. 162: 705-708.
23. HANSEN, J. E., O. LUND, J. O. NIELSEN, S. BRUNAK and J.-E. S. HANSEN, 1996 Prediction of the secondary structure of HIV-1 gp120. Proteins 25: 1-11.
24. HARVEY, P. H., and M. D. PAGEL, 1991 The Comparative Method in Evolutionary Biology. Oxford University Press, Oxford. UK.
25. HASEGAWA, M., H. KISHINO and T. A. YANO, 1985 Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160-174.
26. JONES, D. T., W. R. TAVLOR and J. M. THORNTON, 1992 The rapid generation of mutation data matrices from protein sequences. CABIOS 8: 275-282.
27. JONES, D. T., W. R. TAYLOR and J. M. THORNTON, 1994 A mutation data matrix for transmembrane proteins. FEBS Letts. 339: 269-275.
28. JUKES, T. H., and C. R. CANTOR, 1969 Evolution of protein molecules, pp. 21-132 in Mammalian Protein Metabolism, edited by H. N. MUNRO. Academic Press, New York.
29. KABSCH, W., and C. SANDER, 1983 Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 22: 2577-2637.
30. KIMURA, M., 1983 The Neutral Theory of Molecular Evolution, Cambridge University Press, Cambridge, UK.
31. KOSHI, J. M., and R. A. GOLDSTEIN, 1995 Context-dependent optimal substitution matrices. Prot. Eng. 8: 641-645.
32. LÜTHY, R., A. D. MCLACHLAN and D. EISENBERG, 1991 Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins 10: 229-239.
33. NAYLOR, G. J. P., and W. M. BROWN, 1997 Structural biology and phylogeny estimation. Nature 388: 527-528.
34. OVERINGTON, J., M. S. JOHNSON, A. ŠALI and T. L. BLUNDELL, 1990 Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc. R. Soc. Lond. Ser B 241: 132-145.
35. ROBERTSON, D. L., B. H. HAHN and P. M. SHARP, 1995 Recombination in AIDS viruses. J. Mol. Evol. 40: 249-259.
36. RUSSELL, R. B., M. A. S. SAQI, R. A. SAYLE, P. A. BATES and M. J. E. STERNBERG, 1997 Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J. Mol. Biol. 269: 423-439.
37. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL and D. M. HILLIS, 1996 Phylogenetic inference, pp. 407-514 in Molecular Systematics, Ed. 2, edited by D. M. HILLIS, C. MORTTZ and B. K. MABLE. Sinauer Associates, Sunderland, MA.
38. TAYLOR, W. R., 1988 A flexible method to align large numbers of biological sequences. J. Mol. Evol. 28: 161-169.
39. TELLER, J. K., P. J. BAKER, K. L. BRITTON, P. C. ENGEL, D. W. RICE at al., 1995 Correlation of intron-exon organisation with the three-dimensional structure in glutamate dehydrogenase. Biochim. Biophys. Acta 1247: 231-238.
40. THORNE, J. L., N. GOLDMAN and D. T. JONES, 1996 Combining protein evolution and secondary structure. Mol. Biol. Evol. 13: 666-673.
41. TOPHAM, C. M., A. MCLEOD, F. EISENMENGER, J. P. OVERINGTON, M. S. JOHNSON et al, 1993 Fragment ranking in modelling of protein structure: conformationally constrained substitution tables. J. Mol. Biol. 229: 194-220.
42. WAKO, H., and T. L. BLUNDELL, 1994 Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. I. Solvent accessibility classes. J. Mol. Biol. 238: 682-692.
43. WHITE, J. V., C. M. STULTZ and T. F. SMITH, 1994 Protein classification by stochastic modeling and optimal filtering of amino-acid sequences. Math. Biosci. 119: 35-75.
44. YANG, Z., 1994 Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39: 306-314.
45. YANG, Z., 1995 A space-time process model for the evolution of DNA sequences. Genetics 139: 993-1005.
46. YANG, Z., 1996 Among-site rate variation and its impact on phylogenetic analysis. TREE 11: 367-372.
47. YANG, Z., 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13: 555-556.
48. YANG, Z., N. GOLDMAN and A. FRIDAY, 1994 Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol. 11: 316-324.
49. YANG, Z., I. J. LAUDER and H. J. LIN, 1995 Molecular evolution of the hepatitis B virus genome. J. Mol. Evol. 41: 587-596.
50. YOKOYAMA, S., and W. T. STARMER, 1992 Phylogeny and evolutionary rates of G protein α subunit genes. J. Mol. Evol. 35: 230-238.
51. YOKOYAMA, S., and D. E. HARRY, 1993 Molecular phylogeny and evolutionary rates of alcohol dehydrogenases in vertebrates and plants. Mol. Biol. Evol. 10: 1215-1226.