Using protein structural information in evolutionary inference: Transmembrane proteins

Molecular Biology and Evolution

Volumn 16, Issue 12, 1999, Pages 1696-1710

  Liò, Pietro ^a   Goldman, Nick ^a,b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b ISAAC NEWTON INSTITUTE FOR MATHEMATICAL SCIENCES   (United Kingdom)

Author keywords

Hidden Markov model; Maximum likelihood; Molecular evolution; Phylogeny; Protein structure; Transmembrane proteins

Indexed keywords

CALCITONIN RECEPTOR; CYTOCHROME B; RECEPTOR SUBUNIT;

AMINO ACID SEQUENCE; ARTICLE; GENETIC MODEL; GENETIC TRANSFORMATION; MOLECULAR EVOLUTION; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE;

EID: 0032708723     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026083     Document Type: Article

References (60)

1. ARNASON, U., and A. GULLBERG. 1996. Cytochrome b nucleotide sequences and the identification of five primary lineages of extant Cetaceans. Mol. Biol. Evol. 13:407-417.
2. ASAI, T., D. ZAPOROJETS, C. SQUIRES, and C. L. SQUIRES. 1999. An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. Proc. Natl. Acad. Sci. USA 96:1971-1976.
3. BEN-EFRAIM, I., D. BACH, and Y. SHAI. 1993. Spectroscopic and functional characterization of the putative transmembrane segment of the minK potassium channel. Biochemistry 32:2371-2377.
4. CAO, Y., N. OKADA, and M. HASEGAWA. 1997. Phylogenetic position of guinea pigs revisited. Mol. Biol. Evol. 14:461-464.
5. CHOTHIA, C., and A. M. LESK. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:79-94.
6. CSERZO, M., E. WALLIN, I. SIMON, G. VON HEIJNE, and A. ELOFSSON. 1997. Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Eng. 10:673-676.
7. DAYHOFF, M. O., R. V. ECK, and C. M. PARK. 1972. A model of evolutionary change in proteins. Pp. 89-99 in M. O. DAYHOFF, ed. Atlas of protein sequence and structure. Vol. 5. National Biomedical Research Foundation, Washington, D.C.
8. DAYHOFF, M. O., R. M. SCHWARTZ, and B. C. ORCUTT. 1978. A model of evolutionary change in proteins. Pp. 345-352 in M. O. DAYHOFF, ed. Atlas of protein sequence and structure. Vol. 5, Suppl. 2. National Biomedical Research Foundation, Washington, D.C.
9. DEISENHOFER, J., and H. MICHEL. 1989. The photosynthetic reaction center from the purple bacterium Rhodopseudomonas viridis. Science 245:1463-1473.
10. DENG, H., R. LIU, W. ELLMEIER et al. (15 co-authors). 1996. Identification of a major co-receptor for primary isolates of HIV-1. Nature 381:661-666.
11. DRAGIC, T., V. LITWIN, G. P. ALLAWAY et al. (11 co-authors). 1996. HIV-1 entry into CD4(+) cells is mediated by the chemokine receptor CC-CKR-5. Nature 381:667-673.
12. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
13. _. 1995. PHYLIP (phylogenetic inference package). Version 3.57. Distributed by the author, Department of Genetics, University of Washington, Seattle.
14. FLUHMANN, B., R. MUFF, W. HUNZIKER, J. A. FISCHER, and W. BORN. 1995. A human orphan calcitonin receptor-like structure. Biochem. Biophys. Res. Commun. 206:341-347.
15. GAVEL, Y., and G. VON HEIJNE. 1992. The distribution of charged amino acids in mitochondrial inner membrane proteins suggests different modes of membrane integration for nuclearly and mitochondrially encoded proteins. Eur. J. Biochem. 205:1207-1215.
16. GOLDMAN, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198.
17. 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.
18. _. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149: 445-458.
19. GRISHIN, N. V. 1997. Estimation of evolutionary distances from protein spatial structures. J. Mol. Evol. 45:359-369.
20. HASEGAWA, M., J. ADACHI, and M. C. MILINKOVITCH. 1997. Novel phylogeny of whales supported by total molecular evidence. J. Mol. Evol. 44:s117-s120.
21. HEINZ, D. W., W. BAASE, F. D. DAHLQUIST, and B. W. MATTHEWS. 1993. How amino acid insertions are allowed in an α-helix of T4 lysozyme. Nature 361:561-564.
22. HIROKAWA, T., S. BOON-CHIENG, and S. MITAKU. 1998. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 14:378-379.
23. HOFMANN, K., and W. STOFFEL. 1993. TMbase: a database of membrane spanning proteins segments. Biol. Chem. Hoppe Seyler 347:166-171.
24. HUELSENBECK, J. P., and B. RANNALA. 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:227-232.
25. JONES, D. T. 1994. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33:3038-3049.
26. JONES, D. T., W. R. TAYLOR, and J. M. THORNTON. 1992. The rapid generation of mutation data matrices from protein sequences. CABIOS 8:275-282.
27. _. 1994. A mutation data matrix for transmembrane proteins. FEBS Lett. 339:269-275.
28. JONES, P. C., A. SIVAPRASADARAO, D. WRAY, and J. B. FINDLAY. 1996. A method for determining transmembrane protein structure. Mol. Membr. Biol. 13:53-60.
29. JURETIC, D., and A. LUCIN. 1998. The preference functions method for predicting protein helical turns with helical propensity. J. Chem. Inf. Comput. Sci. 38:575-585.
30. KABSCH, W., and C. SANDER. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 22:2577-2637.
31. KREUSCH, A., and G. E. SCHULZ. 1994. Refined structure of the porin from Rhodopseudomonas blastica - comparison with the porin from Rhodobacter capsulatus. J. Mol. Biol. 243:891-905.
32. KUHMANN, S. E., E. J. PLATT, S. L. KOZAK, and D. KABAT. 1997. Polymorphisms in the CCR5 genes of African green monkeys and mice implicate specific amino acids in infections by simian and human immunodeficiency viruses. J. Virol. 71:8642-8656.
33. LANE, D. J., A. P. HARRISON, J. R. STAHL, B. PACE, S. J. GIOVANNONI, G. J. OLSEN, and N. R. PACE. 1992. Evolutionary relationships among sulphur- and iron-oxidizing eubacteria. J. Bacteriol. 174:269-278.
34. LESK, A. M., and C. CHOTHIA. 1982. Evolution of proteins formed by beta-sheets. II. The core of the immunoglobulin domains. J. Mol. Biol. 160:325-342.
35. LIÒ, P., and N. GOLDMAN. 1998. Models of molecular evolution and phylogeny. Genome Res. 8:1233-1244.
36. LIÒ, P., N. GOLDMAN, J. L. THORNE, and D. T. JONES. 1998. Combining protein secondary structure prediction and evolutionary inference. Bioinformatics 14:726-733.
37. MIZUGUCHI, K., and N. GO. 1995. Comparison of spatial arrangements of the secondary structure elements in proteins. Protein Eng. 8:353-362.
38. NAGASHIMA, K. Y. P., A. HIRAISHI, K. SHIMADA, and K. MATSUURA. 1997a. Horizontal transfer of genes coding for the photosynthetic reaction centers of purple bacteria. J. Mol. Evol. 45:131-136.
39. NAGASHIMA, K. Y. P., K. MATSUURA, N. WAKAO, A. HIRAISHI, and K. SHIMADA. 1997b. Nucleotide sequences of genes coding for photosynthetic reaction centers of Acidiphilium rubrum and related aerobic acidophilic bacteria. Plant Cell Physiol. 38:1249-1258.
40. NAYLOR, G., and W. M. BROWN. 1997. Structural biology and phylogenetic estimation. Nature 388:527-528.
41. OMLAND, K. E. 1997. Correlated rates of molecular and morphological evolution. Evolution 51:1381-1393.
42. PAGEL, M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc. R. Soc. Lond. B Biol. Sci. 255:37-45.
43. PHILIPPE, H. 1997. Rodent monophyly: pitfalls of molecular phylogenies. J. Mol. Evol. 45:712-715.
44. Qu, C., L. LAI, X. Xu, and Y. TANG. 1993. Phyletic relationships of protein structures based on spatial preference of residues. J. Mol. Evol. 36:67-78.
45. ROST, B., R. CASADIO, P. FARISELLI, and C. SANDER. 1995. Transmembrane helices predicted at 95% accuracy. Protein Sci. 4:521-533.
46. ROST, B., P. FARISELLI, and R. CASADIO. 1996. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci. 5:1704-1718.
47. 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.
48. RZHETSKY, A. 1995. Estimating substitution rates in ribosomal RNA genes. Genetics 141:771-783.
49. SONNHAMMER, E. L. L., G. VON HEIJNE, and A. KROGH. 1998. A hidden Markov model for predicting transmembrane helices in protein sequences. ISMB 6:175-182.
50. SPRUIJT, R. B., C. J. WOLFS, J. W. VERVER, and M. A. HEMMINGA. 1996. Accessibility and environment probing using cystein residues introduced along the putative transmembrane domain of the major coat protein of bacteriophage M13. Biochemistry 35:10383-10391.
51. THORNE, J. L., N. GOLDMAN, and D. T. JONES. 1996. Combining protein evolution and secondary structure. Mol. Biol. Evol. 13:666-673.
52. TUSNÁDY, G. E., and I. SIMON. 1998. Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol. 283:489-506.
53. VON HEIJNE, G. 1992. Membrane protein structure prediction. J. Mol. Biol. 225:487-494.
54. WAKAO, N., N. YOKOI, N. ISOYAMA et al. (11 co-authors). 1996. Discovery of natural photosynthesis using Zn-containing bacteriochlorophyll in an aerobic bacterium Acidiphilium rubrum. Plant Cell Physiol. 37:889-893.
55. WOESE, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221-271.
56. WOESE, C. R., E. STACKEBRANDT, W. G. WEISBURG et al. (11 co-authors). 1984. The phylogeny of purple bacteria: the alpha subdivision. Syst. Appl. Microbiol. 5:315-326.
57. XIA, D., C. YU, H. KIM, J. XIA, A. M. KACHURIN, L. ZHANG, L. YU, and J. DEISENHOFER. 1997. Crystal structure of the cytochrome bc(1) complex from bovine heart mitochondria. Science 277:60-66.
58. 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.
59. _. 1995. Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem. Syst. Biol. 44: 384-399.
60. ZHANG, L., C. D. CARRUTHERS, T. HE, Y. HUANG, Y. CAO, G. WANG, B. HAHN, and D. D. HO. 1997. HIV type 1 subtypes, coreceptor usage, and CCR5 polymorphism. AIDS Res. Hum. Retroviruses 13:1357-1366.