Prediction of RNA binding sites in proteins from amino acid sequence

RNA

Volumn 12, Issue 8, 2006, Pages 1450-1462

  Terribilini, Michael ^a   Lee, Jae Hyung ^a   Yan, Changhui ^b   Jernigan, Robert L ^a   Honavar, Vasant ^a,b,c   Dobbs, Drena ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b Utah State University ^*  (United States)

^c Iowa State University   (United States)

Author keywords

Bioinformatics; Prediction; RNA binding site; RNA protein interactions; RNABindR; Telomerase

Indexed keywords

MESSENGER RNA; RNA BINDING PROTEIN; TELOMERASE REVERSE TRANSCRIPTASE;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; BIOLOGY; GENE CONTROL; GENE EXPRESSION; MACHINE; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN MOTIF; PROTEIN RNA BINDING; PROTEIN SYNTHESIS; RNABINDR; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS; VIRUS ASSEMBLY; VIRUS REPLICATION; WEB BROWSER;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; AMINO ACIDS; ANIMALS; ARTIFICIAL INTELLIGENCE; BAYES THEOREM; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PREDICTIVE VALUE OF TESTS; PROTEIN CONFORMATION; PROTEINS; REPRODUCIBILITY OF RESULTS; RNA; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 33746526551     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2197306     Document Type: Article

References (58)

1. Allers, J. and Shamoo, Y. 2001. Structure-based analysis of protein-RNA interactions using the program ENTANGLE. J. Mol. Biol. 311: 75-86.
2. Autexier, C. and Lue, N.F. 2006. The structure and function of telomerase reverse transcriptase. Annu. Rev. Biochem. 75: 493-517.
3. Bachand, F. and Autexier, C. 2001. Functional regions of human telomerase reverse transcriptase and human telomerase RNA required for telomerase activity and RNA-protein interactions. Mol. Cell. Biol. 21: 1888-1897.
4. Baldi, P., Brunak, S., Chauvin, Y., Andersen, C.A., and Nielsen, H. 2000. Assessing the accuracy of prediction algorithms for classification: An overview. Bioinformatics 16: 412-424.
5. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
6. Blackburn, E.H. 2005. Telomeres and telomerase: Their mechanisms of action and the effects of altering their functions. FEBS Lett. 579: 859-862.
7. Bradford, J.R. and Westhead, D.R. 2004. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 21: 1487-1494.
8. Bryan, T.M., Goodrich, K.J., and Cech, T.R. 2000. Telomerase RNA bound by protein motifs specific to telomerase reverse transcriptase. Mol. Cell 6: 493-499.
9. Buntine, W. 1991. Theory refinement on Bayesian networks. Morgan-Kaufmann, San Mateo, CA.
10. Cai, Y.D. and Lin, S.L. 2003. Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence. Biochim. Biophys. Acta 1648: 127-133.
11. Chen, Y. and Varani, G. 2005. Protein families and RNA recognition. FEBS J. 272: 2088-2097.
12. Cusack, S. 1999. RNA-protein complexes. Curr. Opin. Struct. Biol. 9: 66-73.
13. de Vries, S.J., van Dijk, A.D.J., and Bonvin, A.M.J.J. 2006. WHISCY: What information does surface conservation yield? Application to data-driven docking. Proteins 63: 479-489.
14. Draper, D.E. 1999. Themes in RNA-protein recognition. J. Mol. Biol. 293: 255-270.
15. Eisenberg, D., Weiss, R.M., and Terwilliger, T.C. 1984. The hydrophobic moment detects periodicity in protein hydrophobicity. Proc. Natl. Acad. Sci. 81: 140-144.
16. Fischer, D. and Eisenberg, D. 1999. Finding families for genomic ORFans. Bioinformatics 15: 759-762.
17. Gomis-Ruth, F.X., Dessen, A., Timmins, J., Bracher, A., Kolesnikowa, L., Becker, S., Klenk, H.D., and Weissenhorn, W. 2003. The matrix protein VP40 from Ebola virus octamerizes into pore-like structures with specific RNA binding properties. Structure 11: 423-433.
18. Hall, K.B. 2002. RNA-protein interactions. Curr. Opin. Struct. Biol. 12: 283-288.
19. Han, L.Y., Cai, C.Z., Lo, S.L., Chung, M.C., and Chen, Y.Z. 2004. Prediction of RNA-binding proteins from primary sequence by a support vector machine approach. RNA 10: 355-368.
20. Hoffman, M.M., Khrapov, M.A., Cox, J.C., Yao, J., Tong, L., and Ellington, A.D. 2004. AANT: The amino acid-nucleotide interaction database. Nucleic Acids Res. 32: D174-D181.
21. Hoskins, J., Lovell, S., and Blundell, T.L. 2006. An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements. Protein Sci. 15: 1017-1029.
22. Hulo, N., Sigrist, C.J., Le Saux, V., Langendijk-Genevaux, P.S., Bordoli, L., Gattiker, A., De Castro, E., Bucher, P., and Bairoch, A. 2004. Recent improvements to the PROSITE database. Nucleic Acids Res. 32: D134-D137.
23. Jacobs, S.A., Podell, E.R., Wuttke, D.S., and Cech, T.R. 2005. Soluble domains of telomerase reverse transcriptase identified by high-throughput screening. Protein Sci. 14: 2051-2058.
24. Jacobs, S.A., Podell, E.R., and Cech, T.R. 2006. Crystal structure of the essential N-terminal domain of telomerase reverse transcriptase. Nat. Struct. Mol. Biol. 13: 218-225.
25. Jeong, E. and Miyano, S. 2006. A weighted profile method for protein-RNA interacting residue prediction. Trans. Comput. Syst. Biol. IV: 123-139.
26. Jeong, E., Chung, I., and Miyano, S. 2004. A neural network method for identification of RNA-interacting residues in protein. Genome Inform. Ser. Workshop Genome Inform. 15: 105-116.
27. Jones, S., Daley, D.T., Luscombe, N.M., Berman, H.M., and Thornton, J.M. 2001. Protein-RNA interactions: A structural analysis. Nucleic Acids Res. 29: 943-954.
28. Kim, H., Jeong, E., Lee, S.W., and Han, K. 2003. Computational analysis of hydrogen bonds in protein-RNA complexes for interaction patterns. FEBS Lett. 552: 231-239.
29. Klein, D.J., Schmeing, T.M., Moore, P.B., and Steitz, T.A. 2001. The kink-turn: A new RNA secondary structure motif. EMBO J. 20: 4214-4221.
30. Kyte, J. and Doolittle, R.F. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157: 105-132.
31. Lai, C.K., Mitchell, J.R., and Collins, K. 2001. RNA binding domain of telomerase reverse transcriptase. Mol. Cell. Biol. 21: 990-1000.
32. Lai, C.K., Miller, M.C., and Collins, K. 2002. Template boundary definition in Tetrahymena telomerase. Genes & Dev. 16: 415-420.
33. Lustig, B., Arora, S., and Jernigan, R.L. 1997. RNA base-amino acid interaction strengths derived from structures and sequences. Nucleic Acids Res. 25: 2562-2565.
34. Mitchell, T. 1997. Machine learning. McGraw-Hill, Boston, MA.
35. Moriarty, T.J., Huard, S., Dupuis, S., and Autexier, C. 2002. Functional multimerization of human telomerase requires an RNA interaction domain in the N terminus of the catalytic subunit. Mol. Cell. Biol. 22: 1253-1265.
36. Moriarty, T.J., Marie-Egyptienne, D.T., and Autexier, C. 2004. Functional organization of repeat addition processivity and DNA synthesis determinants in the human telomerase multimer. Mol. Cell. Biol. 24: 3720-3733.
37. Moriarty, T.J., Ward, R.J., Taboski, M.A., and Autexier, C. 2005. An anchor site-type defect in human telomerase that disrupts telomere length maintenance and cellular immortalization. Mol. Biol. Cell 16: 3152-3161.
38. Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Barrell, D., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., et al. 2003. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res. 31: 315-318.
39. Neuvirth, H., Raz, R., and Schreiber, G. 2004. ProMate: A structure based prediction program to identify the location of protein-protein binding sites. J. Mol. Biol. 338: 181-199.
40. Nissink, J.W. and Taylor, R. 2004. Combined use of physicochemical data and small-molecule crystallographic contact propensities to predict interactions in protein binding sites. Org. Biomol. Chem. 2: 3238-3249.
41. O'Connor, C.M., Lai, C.K., and Collins, K. 2005. Two purified domains of telomerase reverse transcriptase reconstitute sequence-specific interactions with RNA. J. Biol. Chem. 280: 17533-17539.
42. Ofran, Y. and Rost, B. 2003. Predicted protein-protein interaction sites from local sequence information. FEBS Lett. 544: 236-239.
43. Pan, H., Agarwalla, S., Moustakas, D.T., Finer-Moore, J., and Stroud, R.M. 2003. Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit. Proc. Natl. Acad. Sci. 100: 12648-12653.
44. Pang, P.S., Jankowsky, E., Wadley, L.M., and Pyle, A.M. 2004. Prediction of functional tertiary interactions and intermolecular interfaces from primary sequence data. J. Exp. Zoolog. B Mol. Dev. Evol. 304: 50-63.
45. Rost, B., Liu, J., Nair, R., Wrzeszczynski, K.O., and Ofran, Y. 2003. Automatic prediction of protein function. Cell. Mol. Life Sci. 60: 2637-2650.
46. Ryter, J.M. and Schultz, S.C. 1998. Molecular basis of double-stranded RNA-protein interactions: Structure of a dsRNA-binding domain complexed with dsRNA. EMBO J. 17: 7505-7513.
47. Sen, T.Z., Kloczkowski, A., Jernigan, R.L., Yan, C., Honavar, V., Ho, K.M., Wang, C.Z., Ihm, Y., Cao, H., Gu, X., et al. 2004. Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. BMC Bioinformatics 5: 205.
48. Shanahan, H.P., Garcia, M.A., Jones, S., and Thornton, J.M. 2004. Identifying DNA-binding proteins using structural motifs and the electrostatic potential. Nucleic Acids Res. 32: 4732-4741.
49. Siew, N. and Fischer, D. 2004. Structural biology sheds light on the puzzle of genomic ORFans. J. Mol. Biol. 342: 369-373.
50. Terribilini, M., Lee, J.H., Yan, C., Jernigan, R.L., Carpenter, S., Honavar, V., and Dobbs, D. 2006. Identifying interaction sites in "recalcitrant" proteins: Predicted protein and RNA binding sites in Rev proteins of HIV-1 and EIAV agree with experimental data. Pac. Symp. Biocomput. 2006: 415-426.
51. Tian, B., Bevilacqua, P.C., Diegelman-Parente, A., and Mathews, M.B. 2004. The double-stranded-RNA-binding motif: Interference and much more. Nat. Rev. Mol. Cell Biol. 5: 1013-1023.
52. Wang, G. and Dunbrack Jr., R.L. 2003. PISCES: A protein sequence culling server. Bioinformatics 19: 1589-1591.
53. Weiss, M.A. and Narayana, N. 1998. RNA recognition by argininerich peptide motifs. Biopolymers 48: 167-180.
54. Witten, I.H. and Frank, E. 2005. Data mining: Practical machine learning tools and techniques. Morgan Kaufmann, San Francisco.
55. Yan, C., Dobbs, D., and Honavar, V. 2004a. Identification of interface residues in protease-inhibitor and antigen-antibody complexes: A support vector machine approach. Neural Comput. Appl. 13: 123-129.
56. _. 2004b. A two-stage classifier for identification of protein-protein interface residues. Bioinformatics (Suppl 1)20: I371-I378.
57. Yan, C., Terribilini, M., Wu, F., Jernigan, R.L., Dobbs, D., and Honavar, V. 2006. Predicting DNA-binding sites in proteins from amino acid sequence. BMC Bioinformatics 7: 262.
58. Yu, X., Cao, J., Cai, Y., Shi, T., and Li, Y. 2006. Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines. J. Theor. Biol. 240: 175-184.