Structural context of exons in protein domains: Implications for protein modelling and design

Journal of Molecular Biology

Volumn 333, Issue 5, 2003, Pages 1045-1059

  Contreras Moreira, Bruno ^a   Jonsson, Pall F ^a   Bates, Paul A ^a  

^a THE FRANCIS CRICK INSTITUTE   (United Kingdom)

Author keywords

Comparative modelling; Intron exon boundaries; Protein design; Protein evolution

Indexed keywords

PROTEIN;

ALPHA HELIX; ARTICLE; EXON; GENETIC ANALYSIS; GENOMICS; HUMAN; INTRON; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY;

MURINAE;

EID: 0142216627     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.09.023     Document Type: Article

References (55)

1. Berget S.M., Moore C., Sharp P.A. Spliced segments at the 5′ terminus of adenovirus 2 late mRNA. Proc. Natl Acad. Sci. USA. 74:1977;3171-3175.
2. Chow L.T., Gelinas R.E., Broker T.R., Roberts R.J. An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA. Cell. 12:1977;1-8.
3. Gilbert W. The exon theory of genes. Cold Spring Harbor Symp. Quant. Biol. 52:1987;901-905.
4. Palmer J.D., Logsdon J.M. Jr. The recent origins of introns. Curr. Opin. Genet. Dev. 1:1991;470-477.
5. Fedorov A., Cao X., Saxonov S., de Souza S.J., Roy S.W., Gilbert W. Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns. Proc. Natl Acad. Sci. USA. 98:2001;13177-13182.
6. Fedorov A., Merican A.F., Gilbert W. Large-scale comparison of intron positions among animal, plant, and fungal genes. Proc. Natl Acad. Sci. USA. 99:2002;16128-16133.
7. Stoltzfus A., Spencer D.F., Zuker M., Logsdon J.M. Jr, Doolittle W.F. Testing the exon theory of genes: the evidence from protein structure. Science. 265:1994;202-207.
8. de Souza S.J., Long M., Schoenbach L., Roy S.W., Gilbert W. Intron positions correlate with module boundaries in ancient proteins. Proc. Natl Acad. Sci. USA. 93:1996;14632-14636.
9. de Souza S.J., Long M., Schoenbach L., Roy S.W., Gilbert W. The correlation between introns and the three-dimensional structure of proteins. Gene. 205:1997;141-144.
10. de Souza S.J., Long M., Klein R.J., Roy S., Lin S., Gilbert W. Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins. Proc. Natl Acad. Sci. USA. 95:1998;5094-5099.
11. Chothia C., Gough J., Vogel C., Teichmann S.A. Evolution of the protein repertoire. Science. 300:2003;1701-1703.
12. Padgett R.A., Grabowski P.J., Konarska M.M., Seiler S., Sharp P.A. Splicing of messenger RNA precursors. Annu. Rev. Biochem. 55:1986;1119-1150.
13. Alberts B., Bray D., Lewis J., Raff M., Roberts K., Watson J.D. Molecular Biology of the Cell. 3rd edit. 1994;Garland, New York.
14. Clark F., Thanaraj T.A. Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human. Hum. Mol. Genet. 11:2002;451-464.
15. Patthy L. Protein Evolution. 1999;Blackwell Science, Oxford.
16. Devos D., Valencia A. Practical limits of function prediction. Proteins: Struct. Funct. Genet. 41:2000;98-107.
17. Thornton J.M., Todd A.E., Milburn D., Borkakoti N., Orengo C.A. From structure to function: approaches and limitations. Nature Struct. Biol. 7:2000;991-994.
18. Doi N., Yanagawa H. Design of generic biosensors based on green fluorescent proteins with allosteric sites by directed evolution. FEBS Letters. 453:1999;305-307.
19. Looger L.L., Hellinga H.W. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. J. Mol. Biol. 307:2001;429-445.
20. Reina J., Lacroix E., Hobson S.D., Fernandez-Ballester G., Rybin V., Schwab M.S., et al. Computer-aided design of a PDZ domain to recognize new target sequences. Nature Struct. Biol. 9:2002;621-627.
21. Looger L.L., Dwyer M.A., Smith J.J., Hellinga H.W. Computational design of receptor and sensor proteins with novel functions. Nature. 423:2003;185-190.
22. Voigt C.A., Martinez C., Wang Z.G., Mayo S.L., Arnold F.H. Protein building blocks preserved by recombination. Nature Struct. Biol. 9:2002;553-558.
23. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., et al. The Protein Data Bank. Nucl. Acids Res. 28:2000;235-242.
24. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637.
25. Patthy L. Intron-dependent evolution: preferred types of exons and introns. FEBS Letters. 214:1987;1-7.
26. Berezovsky I.N., Grosberg A.Y., Trifonov E.N. Closed loops of nearly standard size: common basic element of protein structure. FEBS Letters. 466:2000;283-286.
27. Berezovsky I.N., Trifonov E.N. Van der Waals locks: loop-n-lock structure of globular proteins. J. Mol. Biol. 307:2001;1419-1426.
28. Betts M.J., Guigo R., Agarwal P., Russell R.B. Exon structure conservation despite low sequence similarity: a relic of dramatic events in evolution? EMBO J. 20:2001;5354-5360.
29. Wessler S.R. The splicing of maize transposable elements from pre-mRNA - a minireview. Gene. 82:1989;127-133.
30. Purugganan M., Wessler S. The splicing of transposable elements and its role in intron evolution. Genetica. 86:1992;295-303.
31. Yuan Y.C., Whitson R.H., Liu Q., Itakura K., Chen Y. A novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases. Nature Struct. Biol. 5:1998;959-964.
32. Whitson R.H., Huang T., Itakura K. The novel Mrf-2 DNA-binding domain recognizes a five-base core sequence through major and minor-groove contacts. Biochem. Biophys. Res. Commun. 258:1999;326-331.
33. Zhu L., Hu J., Lin D., Whitson R., Itakura K., Chen Y. Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA. Biochemistry. 40:2001;9142-9150.
34. Katona G., Berglund G.I., Hajdu J., Graf L., Szilagyi L. Crystal structure reveals basis for the inhibitor resistance of human brain trypsin. J. Mol. Biol. 315:2002;1209-1218.
35. Perona J.J., Craik C.S. Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold. J. Biol. Chem. 272:1997;29987-29990.
36. Janin J., Henrick K., Moult J., Eyck L.T., Sternberg M.J.E., Vajda S., et al. CAPRI: a critical assessment of predicted interactions. Proteins: Struct. Funct. Genet. 52:2003;2-9.
37. Petersen K., Taylor W.R. Modelling zinc-binding proteins with GADGET: genetic algorithm and distance geometry for exploring topology. J. Mol. Biol. 325:2003;1039-1059.
38. Contreras-Moreira B., Fitzjohn P.W., Bates P.A. In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling. J. Mol. Biol. 328:2003;593-608.
39. Tramontano A., Leplae R., Morea V. Analysis and assessment of comparative modeling predictions in CASP4. Proteins: Struct. Funct. Genet. Suppl:2001;22-38.
40. Tramontano A. Of men and machines. Nature Struct. Biol. 10:2003;87-90.
41. Fedorova L., Fedorov A. Introns in gene evolution. Genetica. 118:2003;123-131.
42. Bairoch A., Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucl. Acids Res. 28:2000;45-48.
43. Waterston R.H., Lindblad-Toh K., Birney E., Rogers J., Abril J.F., Agarwal P., et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420:2002;520-562.
44. Kent W.J. BLAT - the BLAST-like alignment tool. Genome Res. 12:2002;656-664.
45. Bates P.A., Kelley L.A., MacCallum R.M., Sternberg M.J. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins: Struct. Funct. Genet. 2001;39-46.
46. Contreras-Moreira B., Bates P.A. Domain fishing: a first step in protein comparative modelling. Bioinformatics. 18:2002;1141-1142.
47. Sayle R.A., Milner-White E.J. RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 20:1995;37-376.
48. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
49. Hu, J., Shen, X., Shao, Y., Bystroff, C. & Zaki, M. J. (2002). Mining protein contact maps. In BIOKDD02: Workshop on Data Mining in Bioinformatics (Zaki, M. J., Wang, J. T. L., Toivonen, H. T. T., eds), pp. 3-10, ACM, Edmonton, Canada.
50. Dunbrack R.L. Jr, Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J. Mol. Biol. 230:1993;543-574.
51. Robson B., Osguthorpe D.J. Refined models for computer simulation of protein folding. Applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor. J. Mol. Biol. 132:1979;19-51.
52. Eisenberg D., McLachlan A.D. Solvation energy in protein folding and binding. Nature. 319:1986;199-203.
53. Russell R.B., Barton G.J. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins: Struct. Funct. Genet. 14:1992;309-323.
54. Gerstein M., Levitt M. Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures. Proc. Intl Conf. Intell. Syst. Mol. Biol. 4:1996;59-67.
55. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680.