Dissecting the protein-RNA interface: The role of protein surface shapes and RNA secondary structures in protein-RNA recognition

Nucleic Acids Research

Volumn 40, Issue 8, 2012, Pages 3299-3306

  Iwakiri, Junichi ^a   Tateishi, Hiroki ^a   Chakraborty, Anirban ^a   Patil, Prakash ^a   Kenmochi, Naoya ^a  

^a UNIVERSITY OF MIYAZAKI   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ASPARTIC ACID; HYDROGEN; NUCLEOTIDE; PHOSPHATE; RNA PHOSPHATE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN SURFACE SHAPE; RNA STRUCTURE; STATIC ELECTRICITY; STRUCTURE ANALYSIS;

AMINO ACIDS; BASE PAIRING; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; RNA; RNA-BINDING PROTEINS; SURFACE PROPERTIES;

EID: 84860369519     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1225     Document Type: Article

References (34)

1. Garvie, C.W. and Wolberger, C. (2001) Recognition of specific DNA sequences. Mol. Cell, 8, 937-946.
2. Dixon, S.J., Costanzo, M., Baryshnikova, A., Andrews, B. and Boone, C. (2009) Systematic mapping of genetic interaction networks. Annu. Rev. Genet., 43, 601-625.
3. Mata, J., Marguerat, S. and Bahler, J. (2005) Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem. Sci., 30, 506-514.
4. Rohs, R., West, S., Sosinsky, A., Liu, P., Mann, R. and Honig, B. (2009) The role of DNA shape in protein-DNA recognition. Nature, 461, 1248-1253.
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. Allers, J. and Shamoo, Y. (2001) Structure-based analysis of protein-RNA interactions using the program ENTANGLE. J. Mol. Biol., 311, 75-86.
7. Bahadur, R.P., Zacharias, M. and Janin, J. (2008) Dissecting protein-RNA recognition sites. Nucleic Acids Res., 36, 2705-2716.
8. Ellis, J.J., Broom, M. and Jones, S. (2007) Protein-RNA interactions: structural analysis and functional classes. Proteins, 66, 903-911.
9. Sonavane, S. and Chakrabarti, P. (2009) Cavities in protein-DNA and protein-RNA interfaces. Nucleic Acids Res., 37, 4613-4620.
10. Ray, D., Kazan, H., Chan, E.T., Pena Castillo, L., Chaudhry, S., Talukder, S., Blencowe, B.J., Morris, Q. and Hughes, T.R. (2009) Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat. Biotechnol., 27, 667-670.
11. Wang, G. and Dunbrack, R.L. Jr (2005) PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res., 33, W94-W98.
12. Krissinel, E. and Henrick, K. (2007) Inference of macromolecular assemblies from crystalline state. J. Mol. Biol., 372, 774-797.
13. Pintar, A., Carugo, O. and Pongor, S. (2002) CX, an algorithm that identifies protruding atoms in proteins. Bioinformatics, 18, 980-984.
14. Yura, K. and Hayward, S. (2009) The interwinding nature of protein-protein interfaces and its implication for protein complex formation. Bioinformatics, 25, 3108-3113.
15. McDonald, I.K. and Thornton, J.M. (1994) Satisfying hydrogen bonding potential in proteins. J. Mol. Biol., 238, 777-793.
16. Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H. and Westhof, E. (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res., 31, 3450-3460.
17. Leontis, N.B. and Westhof, E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499-512.
18. McDonald, I.K. and Thornton, J.M. (1994) Satisfying hydrogen bonding potential in proteins. J. Mol. Biol., 238, 777-793.
19. Auweter, S.D., Oberstrass, F.C. and Allain, F.H. (2006) Sequence-specific binding of single-stranded RNA: is there a code for recognition? Nucleic Acids Res., 34, 4943-4959.
20. Price, S.R., Evans, P.R. and Nagai, K. (1998) Crystal structure of the spliceosomal U2B"-U2A' protein complex bound to a fragment of U2 small nuclear RNA. Nature, 394, 645-650.
21. Sankaranarayanan, R., Dock-Bregeon, A.C., Romby, P., Caillet, J., Springer, M., Rees, B., Ehresmann, C., Ehresmann, B. and Moras, D. (1999) The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Cell, 97, 371-381.
22. Kromayer, M., Neuhierl, B., Friebel, A. and Bock, A. (1999) Genetic probing of the interaction between the translation factor SelB and its mRNA binding element in Escherichia coli. Mol. Gen. Genet., 262, 800-806.
23. Lee, T.T., Agarwalla, S. and Stroud, R.M. (2005) A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell, 120, 599-611.
24. Moore, T., Zhang, Y., Fenley, M.O. and Li, H. (2004) Molecular basis of box C/D RNA-protein interactions; cocrystal structure of archaeal L7Ae and a box C/D RNA. Structure, 12, 807-818.
25. Gupta, A. and Gribskov, M. (2011) The role of RNA sequence and structure in RNA-protein interactions. J Mol. Biol., 409, 574-587.
26. Morozova, N., Allers, J., Myers, J. and Shamoo, Y. (2006) Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures. Bioinformatics, 22, 2746-2752.
27. Kondo, J. and Westhof, E. (2011) Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes. Nucleic Acids Res., 39, 8628-8637.
28. Kim, O.T., Yura, K. and Go, N. (2006) Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction. Nucleic Acids Res., 34, 6450-6460.
29. Shazman, S. and Mandel-Gutfreund, Y. (2008) Classifying RNA-binding proteins based on electrostatic properties. PLoS Comput. Biol., 4, e1000146.
30. Perez-Cano, L. and Fernandez-Recio, J. (2010) Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins. Proteins, 78, 25-35.
31. Chen, Y.C. and Lim, C. (2008) Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry. Nucleic Acids Res., 36, e29.
32. Shulman-Peleg, A., Shatsky, M., Nussinov, R. and Wolfson, H.J. (2008) Prediction of interacting single-stranded RNA bases by protein-binding patterns. J. Mol. Biol., 379, 299-316.
33. Terribilini, M., Lee, J.H., Yan, C., Jernigan, R.L., Honavar, V. and Dobbs, D. (2006) Prediction of RNA binding sites in proteins from amino acid sequence. RNA, 12, 1450-1462.
34. Liu, Z.P., Wu, L.Y., Wang, Y., Zhang, X.S. and Chen, L. (2010) Prediction of protein-RNA binding sites by a random forest method with combined features. Bioinformatics, 26, 1616-1622.