Protein structural influences in rhodopsin evolution

Molecular Biology and Evolution

Volumn 22, Issue 4, 2005, Pages 894-904

  Marsh, Lorraine ^a   Griffiths, Carole S ^a,b  

^a LONG ISLAND UNIVERSITY   (United States)

^b DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

Extra steps; Homoplasy; Protein structure; Rhodopsin; Substitution rate

Indexed keywords

RHODOPSIN;

ALLIGATOR; ALPHA HELIX; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; AMPHIBIA; ARTICLE; BIRD; CORRELATION ANALYSIS; COW; LIPID BILAYER; MAMMAL; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; MOLECULAR MODEL; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PARSIMONY ANALYSIS; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; SURFACE PROPERTY; VERTEBRATE;

AMINO ACID SUBSTITUTION; ANIMALS; EVOLUTION, MOLECULAR; FOURIER ANALYSIS; PHYLOGENY; PROTEIN CONFORMATION; RHODOPSIN;

EID: 16344388218     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi081     Document Type: Article

References (42)

1. Amrine-Madsen, H., K. Koepfli, R. K. Wayne, and M. S. Springer. 2003. A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships. Mol. Phylogenet. Evol. 28:225-240.
2. Bowie, J. U., J. F. Reidhaar-Olson, W. A. Lim, and R. Sauer. 1990. Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science 247:1306-1310.
3. Breikers, G., P. H. Bovee-Geurts, G. L. DeCaluwe, and W. J. DeGrip. 2001. A structural role for Asp83 in the photoactivation of rhodopsin. Biol. Chem. 382:1263-1270.
4. Chen, W., C. Bonillo, and G. Lecointre. 2003. Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Telostei) with larger number of taxa. Mol. Phylogenet. Evol. 26:262-288.
5. Cotton, J. A., and R. D. Page. 2002. Going nuclear: gene family evolution and vertebrate phylogeny reconciled. Proc. R. Soc. Lond. B Biol. Sci. 269:1555-1561.
6. 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 sequences and structure, Vol. 5, Suppl. 3. National Biomedical Research Foundation, Washington, D. C.
7. Dimmic, M. W., D. P. Mindell, and R. A. Goldstein. 2000. Modeling evolution at the protein level using an adjustable amino acid fitness model. Pac. Symp. Biocomput. 2000:18-29.
8. Donnelly, D., J. P. Overington, S. V. Ruffle, J. H. A. Nugent, and T. L. Blundell. 1993. Modeling α-helical transmembrane domains: the calculation and use of substitution tables for lipid-facing residues. Protein Sci. 2:55-70.
9. Eisenberg, D., R. M. Weiss, and T. C. Terwillinger. 1984. The hydrophobic moment detects periodicity in protein hydrophobicity. Proc. Natl. Acad. Sci. USA 81:140-144.
10. Elmerot, C., U. Arnason, T. Gojobori, and A. Janke. 2002. The mitochondrial genome of the pufferfish, Fugu rubripes, and the ordinal telostean relationships. Gene 295:163-172.
11. Fares, M. A., S. F. Elana, J. Ortiz, A. Moya, and E. Barrio. 2002. A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses. J. Mol. Evol. 55:509-521.
12. Goldman, N., J. L. Thorne, and D. T. Jones. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149:445-458.
13. Goldman, N., and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-736.
14. Griffiths, C. S., G. F. Barrowclough, J. G. Groth, and L. Mertz. 2004. Phylogeny of the Falconidae (Aves): a comparison of the efficacy of morphological, mitochondrial, and nuclear data. Mol. Phylogenet. Evol. 32:100-109.
15. Gu, X., and J. Zhang. 1997. A simple method for estimating the parameter of substitution rate variation among sites. Mol. Biol. Evol. 14:1106-1113.
16. Hillis, D. M. 1995. Approaches for assessing phylogenetic accuracy. Syst. Biol. 44:3-16.
17. Kabsch, W. M., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
18. Koshi, J. M., and R. A. Goldstein. 1998. Mathematical models of natural amino acid site mutations. Proteins 32:289-295.
19. Kosiol, C., N. Goldman, and N. H. Buttimore. 2004. A new criterion and method for amino acid classification. J. Theor. Biol. 228:97-106.
20. Lee, B., and F. M. Richards. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.
21. Li, W.-H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36:96-99.
22. Lio, P., and M. Vannucci. 2000. Wavelet change-point prediction of transmembrane proteins. Bioinformatics 16:376-382.
23. Lopez, P., D. Casane, and H. Philippe. 2002. Heterotachy, an important process of protein evolution. Mol. Biol. Evol. 19:1-7.
24. Miya, M., H. Takeshima, H. Endo et al. (12 co-authors). 2003. Major patterns of higher teleostean phytogenies; a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol. 26:121-138.
25. Mizuguchi, K., and T. Blundell. 2000. Analysis of conservation and substitution of secondary structure elements within protein superfamilies. Bioinformatics 16:1111-1119.
26. Muse, S. V., and B. S. Gaut. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:715-734.
27. Naylor, G., and F. Kraus. 1995. The relationship between S and M and the retention index. Syst. Biol. 44:559-562.
28. Naylor, G. J. P., and W. M. Brown. 1997. Structural biology and phylogenetic estimation. Nature 388:528-530.
29. Ng, P. C., J. G. Henikoff, and D. Henikoff. 2000. PHAT: a transmembrane-specific substitution matrix. Bioinformatics 16:760-766.
30. Palczewski, K., T. Kumasaka, T. Hori et al. (12 co-authors).2000. Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289:739-745.
31. Pamilo, P., and N. O. Bianchi. 1993. Evolution of the ZFX and ZFY genes: rates and interdependence between the genes. Mol. Biol. Evol. 10:271-281.
32. Sanchez, R., and A. Sali. 1997. Advances in comparative protein-structure modeling. Curr. Opin. Struct. Biol. 7:206-214.
33. Schadt, E., and K. Lange. 2002. Codon and rate variation models in molecular phylogeny. Mol. Biol. Evol. 19:1534-1539.
34. Simmons, M. P., and M. Miya. 2004. Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 teleost fishes. Mol. Phylogenet. Evol. 31:351-362.
35. Soyer, O., M. W. Dimmic, R. R. Neubig, and R. A. Goldstein. 2002. Using evolutionary methods to study G-protein coupled receptors. Pac. Symp. Biocomput. 2002:625-637.
36. Stevens, T. J., and I. T. Arkin. 2001. Substitution rates in α-helical transmembrane proteins. Protein Sci. 10:2507-2517.
37. Suzuki, Y. 2004. Three-dimensional window analysis for detecting positive selection at structural regions of proteins. Mol. Biol. Evol. 21:2352-2359.
38. Swofford, D. L. 1999. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass.
39. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pp. 407-514 in D. M. Hillis, C. Moritz, and B. K. Mable, eds. Molecular Systematics, Sinauer Associates, Sunderland, Mass.
40. Walker, J. S. 1999. A primer on wavelets and their scientific applications. CRC Press, LLC, New York, N.Y.
41. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
42. -. 1996. Among-site variation and its impact on phylogenetic analysis. Trends Ecol. Evol. 11:367-372.