Analyzing protein structure and function using ancestral gene reconstruction

Current Opinion in Structural Biology

Volumn 20, Issue 3, 2010, Pages 360-366

  Harms, Michael J ^a   Thornton, Joseph W ^a  

^a UNIVERSITY OF OREGON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

G PROTEIN COUPLED RECEPTOR; GLUCOCORTICOID RECEPTOR; GLYCINE; GREEN FLUORESCENT PROTEIN; LEUCINE; MINERALOCORTICOID RECEPTOR; OPSIN;

AMINO ACID COMPOSITION; AMINO ACID SUBSTITUTION; CRYSTAL STRUCTURE; EPISTASIS; EVOLUTION; GENE MUTATION; GENETIC CONSERVATION; GENETIC VARIABILITY; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW;

EVOLUTION, MOLECULAR; GREEN FLUORESCENT PROTEINS; HUMANS; OPSINS; PROTEINS; RECEPTORS, STEROID;

EID: 77955584075     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2010.03.005     Document Type: Review

References (49)

1. Smith J. Natural selection and the concept of a protein space. Nature 1970, 225:563-564.
2. Romero P.A., Arnold F.H. Exploring protein fitness landscapes by directed evolution. Nat Rev Mol Cell Biol 2009, 10:866-876.
3. Buske F.A., Their R., Gillam E.M.J., Bodén M. In silico characterization of protein chimeras: relating sequence and function within the same fold. Proteins: Struct Funct Bioinf 2009, 77:111-120.
4. Chakrabarti S., Lanczycki C.J. Analysis and prediction of functionally important sites in proteins. Protein Sci 2007, 16:4-13.
5. Capra J.A., Singh M. Characterization and prediction of residues determining protein functional specificity. Bioinformatics 2008, 10.1093/bioinformatics/btn214.
6. Donald J.E., Shakhnovich E.I. SDR: a database of predicted specificity-determining residues in proteins. Nucl Acids Res 2009, 37:D191-194.
7. Datta A.K. Comparative sequence analysis in the sialyltransferase protein family: analysis of motifs. Curr Drug Targets 2009, 10:483-498.
8. Desai T.A., Rodionov D.A., Gelfand M.S., Alm E.J., Rao C.V. Engineering transcription factors with novel DNA-binding specificity using comparative genomics. Nucleic Acids Res 2009, 37:2493-2503.
9. Maita N., Nyirenda J., Igura M., Kamishikiryo J., Kohda D. Comparative structural biology of eubacterial and archaeal oligosaccharyltransferases. J Biol Chem 2010, 285:4941-4950.
10. Neidhart D.J., Kenyon G.L., Gerlt J.A., Petsko G.A. Mandelate racemase and muconate lactonizing enzyme are mechanistically distinct and structurally homologous. Nature 1990, 347:692-694.
11. Hoffman M. On the road to mandelate ... racemase. Science 1991, 251:31-32.
12. Gerlt J.A., Babbitt P.C. Enzyme (re)design: lessons from natural evolution and computation. Curr Opin Chem Biol 2009, 13:10-18.
13. Xiang H., Luo L., Taylor K.L., Dunaway-Mariano D. Interchange of catalytic activity within the 2-enoyl-coenzyme a hydratase/isomerase superfamily based on a common active site template. Biochemistry 1999, 38:7638-7652.
14. Ijima Y., Matoishi K., Terao Y., Doi N., Yanagawa H., Ohta H. Inversion of enantioselectivity of asymmetric biocatalytic decarboxylation by site-directed mutagenesis based on the reaction mechanism. Chem Commun 2005, 10.1039/b416398b.
15. Bershtein S., Segal M., Bekerman R., Tokuriki N., Tawfik D.S. Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 2006, 444:929-932.
16. Hayashi Y., Aita T., Toyota H., Husimi Y., Urabe I., Yomo T. Experimental rugged fitness landscape in protein sequence space. PLoS ONE 2006, 1:e96.
17. Phillips P.C. Epistasis - the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 2008, 9:855-867.
18. Parera M., Perez-Alvarez N., Clotet B., Martínez M.A. Epistasis among deleterious mutations in the HIV-1 protease. J Mol Biol 2009, 392:243-250.
19. O'Maille P.E., Malone A., Dellas N., Andes Hess B., Smentek L., Sheehan I., Greenhagen B.T., Chappell J., Manning G., Noel J.P. Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases. Nat Chem Biol 2008, 4:617-623.
20. Bloom J.D., Labthavikul S.T., Otey C.R., Arnold F.H. Protein stability promotes evolvability. Proc Natl Acad Sci U S A 2006, 103:5869-5874.
21. Bridgham J.T., Ortlund E.A., Thornton J.W. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 2009, 461:515-519.
22. Ortlund E.A., Bridgham J.T., Redinbo M.R., Thornton J.W. Crystal structure of an ancient protein: evolution by conformational epistasis. Science 2007, 317:1544-1548.
23. Thornton J.W. Resurrecting ancient genes: experimental analysis of extinct molecules. Nat Rev Genet 2004, 5:366-375.
24. Liberles D.A. Ancestral Sequence Reconstruction 2007, Oxford University Press, USA.
25. Pauling L., Zuckerkandl E. Chemical paleogenetics: molecular "restoration studies" of extinct forms of life. Acta Chem Scand 1963, 17:S9-S16.
26. Ugalde J.A., Chang B.S.W., Matz M.V. Evolution of coral pigments recreated. Science 2004, 305:1433.
27. Field S.F., Matz M.V. Retracing evolution of red fluorescence in GFP-like proteins from Faviina corals. Mol Biol Evol 2010, 27:225-233.
28. Bridgham J.T., Carroll S.M., Thornton J.W. Evolution of hormone-receptor complexity by molecular exploitation. Science 2006, 312:97-101.
29. Carroll S.M., Bridgham J.T., Thornton J.W. Evolution of hormone signaling in elasmobranchs by exploitation of promiscuous receptors. Mol Biol Evol 2008, 25:2643-2652.
30. Yokoyama S., Yang H., Starmer W.T. Molecular basis of spectral tuning in the red- and green-sensitive (M/LWS) pigments in vertebrates. Genetics 2008, 179:2037-2043.
31. Yokoyama S., Radlwimmer F.B. The molecular genetics and evolution of red and green color vision in vertebrates. Genetics 2001, 158:1697-1710.
32. Yokoyama S., Tada T., Zhang H., Britt L. Elucidation of phenotypic adaptations: molecular analyses of dim-light vision proteins in vertebrates. Proc Natl Acad Sci U S A 2008, 105:13480-13485.
33. Kaiser S.M., Malik H.S., Emerman M. Restriction of an extinct retrovirus by the human TRIM5{alpha} antiviral protein. Science 2007, 316:1756-1758.
34. Kuang D., Yao Y., MacLean D., Wang M., Hampson D.R., Chang B.S.W. Ancestral reconstruction of the ligand-binding pocket of Family C G protein-coupled receptors. Proc Natl Acad Sci U S A 2006, 103:14050-14055.
35. Gaucher E.A., Thomson J.M., Burgan M.F., Benner S.A. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 2003, 425:285-288.
36. Gaucher E.A., Govindarajan S., Ganesh O.K. Palaeotemperature trend for Precambrian life inferred from resurrected proteins. Nature 2008, 451:704-707.
37. Thomson J.M., Gaucher E.A., Burgan M.F., De Kee D.W., Li T., Aris J.P., Benner S.A. Resurrecting ancestral alcohol dehydrogenases from yeast. Nat Genet 2005, 37:630-635.
38. Yang Z., Kumar S., Nei M. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 1995, 141:1641-1650.
39. Asenjo A.B., Rim J., Oprian D.D. Molecular determinants of human red/green color discrimination. Neuron 1994, 12:1131-1138.
40. Field S., Bulina M., Kelmanson I., Bielawski J., Matz M. Adaptive evolution of multicolored fluorescent proteins in reef-building corals. J Mol Evol 2006, 62:332-339.
41. Li Y., Suino K., Daugherty J., Xu H.E. Structural and biochemical mechanisms for the specificity of hormone binding and coactivator assembly by mineralocorticoid receptor. Mol Cell 2005, 19:367-380.
42. Weinreich D.M., Delaney N.F., DePristo M.A., Hartl D.L. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 2006, 312:111-114.
43. Wagner A. Neutralism and selectionism: a network-based reconciliation. Nat Rev Genet 2008, 9:965-974.
44. Bloom J., Arnold F. In the light of directed evolution: pathways of adaptive protein evolution. Proc Natl Acad Sci U S A 2009, 106:9995-10000.
45. Tokuriki N., Tawfik D.S. Protein dynamism and evolvability. Science 2009, 324:203-207.
46. Anfinsen C. Molecular Basis of Evolution 1959, John Wiley & Sons.
47. Blundell T.L., Wood S.P. Is the evolution of insulin Darwinian or due to selectively neutral mutation?. Nature 1975, 257:197-203.
48. Perutz M.F. Species adaptation in a protein molecule. Mol Biol Evol 1983, 1:1-28.
49. Serrano L., Day A.G., Fersht A.R. Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability. J Mol Biol 1993, 233:305-312.