Nucleic Acids Research, 2001, Vol. 29, No. 4 943-954
© 2001 Oxford University Press
Protein–RNA interactions: a structural analysis
1Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, UK, 2Department of Chemistry, Rutgers, The State University, Piscataway, NJ 08855-0939, USA and 3Department of Crystallography, Birkbeck College, Malet Street, London WC1 7HX, UK
A detailed computational analysis of 32 protein–RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein–double-stranded DNA and protein–single-stranded DNA complexes. The interface properties of the protein–RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein–RNA and protein–DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein–RNA complexes, backbone contacts were more dominant in the protein–DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level.
* To whom correspondence should be addressed at: Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1 6BT, UK. Tel: +44 207 679 7048; Fax: +44 207 916 8499; Email: thornton@biochem.ucl.ac.uk
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. Samanta, D. Mukhopadhyay, S. Chowdhury, J. Ghosh, S. Pal, A. Basu, A. Bhattacharya, A. Das, D. Das, and C. DasGupta Protein Folding by Domain V of Escherichia coli 23S rRNA: Specificity of RNA-Protein Interactions J. Bacteriol., May 1, 2008; 190(9): 3344 - 3352. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. P. Bahadur, M. Zacharias, and J. Janin Dissecting protein-RNA recognition sites Nucleic Acids Res., May 1, 2008; 36(8): 2705 - 2716. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. C. Chen and C. Lim Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry Nucleic Acids Res., March 1, 2008; 36(5): e29 - e29. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Gunawardana, H.-C. Cheng, and K. R. Gayler Identification of functional domains in Arabidopsis thaliana mRNA decapping enzyme (AtDcp2) Nucleic Acids Res., January 17, 2008; 36(1): 203 - 216. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Terribilini, J. D. Sander, J.-H. Lee, P. Zaback, R. L. Jernigan, V. Honavar, and D. Dobbs RNABindR: a server for analyzing and predicting RNA-binding sites in proteins Nucleic Acids Res., July 13, 2007; 35(suppl_2): W578 - W584. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. E. Sanderson and O. C. Uhlenbeck The 51-63 base pair of tRNA confers specificity for binding by EF-Tu RNA, June 1, 2007; 13(6): 835 - 840. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. R. A. Jonker, S. Ilin, S. K. Grimm, J. Wohnert, and H. Schwalbe L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy Nucleic Acids Res., January 28, 2007; 35(2): 441 - 454. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. E. Walden, A. I. Selezneva, J. Dupuy, A. Volbeda, J. C. Fontecilla-Camps, E. C. Theil, and K. Volz Structure of Dual Function Iron Regulatory Protein 1 Complexed with Ferritin IRE-RNA Science, December 22, 2006; 314(5807): 1903 - 1908. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. T. P. Kim, K. Yura, and N. Go Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction Nucleic Acids Res., December 5, 2006; (2006) gkl819v2. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Morozova, J. Allers, J. Myers, and Y. Shamoo Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures Bioinformatics, November 15, 2006; 22(22): 2746 - 2752. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Terribilini, J.-H. Lee, C. Yan, R. L. Jernigan, V. Honavar, and D. Dobbs Prediction of RNA binding sites in proteins from amino acid sequence RNA, August 1, 2006; 12(8): 1450 - 1462. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. G Clarke, S. A Hope, S. Byers, and R. J Rodgers Formation of ovarian follicular fluid may be due to the osmotic potential of large glycosaminoglycans and proteoglycans Reproduction, July 1, 2006; 132(1): 119 - 131. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Wang and S. J. Brown BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W243 - W248. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. KHANNA, H. WU, C. JOHANSSON, M. CAIZERGUES-FERRER, and J. FEIGON Structural study of the H/ACA snoRNP components Nop10p and the 3' hairpin of U65 snoRNA. RNA, January 1, 2006; 12(1): 40 - 52. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Stetler, C. Winograd, J. Sayegh, A. Cheever, E. Patton, X. Zhang, S. Clarke, and S. Ceman Identification and characterization of the methyl arginines in the fragile X mental retardation protein Fmrp Hum. Mol. Genet., January 1, 2006; 15(1): 87 - 96. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Reh, C. Korn, O. Gimadutdinow, and G. Meiss Structural Basis for Stable DNA Complex Formation by the Caspase-activated DNase J. Biol. Chem., December 16, 2005; 280(50): 41707 - 41715. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Kolosov, L. Frolova, A. Seit-Nebi, V. Dubovaya, A. Kononenko, N. Oparina, J. Justesen, A. Efimov, and L. Kisselev Invariant amino acids essential for decoding function of polypeptide release factor eRF1 Nucleic Acids Res., November 10, 2005; 33(19): 6418 - 6425. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. J. Oparina, O. V. Kalinina, M. S. Gelfand, and L. L. Kisselev Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications Nucleic Acids Res., September 14, 2005; 33(16): 5226 - 5234. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Kleinjung and F. Fraternali POPSCOMP: an automated interaction analysis of biomolecular complexes Nucleic Acids Res., July 1, 2005; 33(suppl_2): W342 - W346. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Reguera, E. Grueso, A. Carreira, C. Sanchez-Martinez, J. M. Almendral, and M. G. Mateu Functional Relevance of Amino Acid Residues Involved in Interactions with Ordered Nucleic Acid in a Spherical Virus J. Biol. Chem., May 6, 2005; 280(18): 17969 - 17977. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Guallar and K. W. Borrelli A binding mechanism in protein-nucleotide interactions: Implication for U1A RNA binding PNAS, March 15, 2005; 102(11): 3954 - 3959. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. J. DAY-STORMS, S. NIRANJANAKUMARI, and C. A. FIERKE Ionic interactions between PRNA and P protein in Bacillus subtilis RNase P characterized using a magnetocapture-based assay RNA, October 20, 2004; 10(10): 1595 - 1608. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Chen, T. Kortemme, T. Robertson, D. Baker, and G. Varani A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys Nucleic Acids Res., September 30, 2004; 32(17): 5147 - 5162. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. M. Hoffman, M. A. Khrapov, J. C. Cox, J. Yao, L. Tong, and A. D. Ellington AANT: the Amino Acid-Nucleotide Interaction Database Nucleic Acids Res., January 1, 2004; 32(90001): D174 - 181. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Sauter, J. Basquin, and D. Suck Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli Nucleic Acids Res., July 15, 2003; 31(14): 4091 - 4098. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. D. CILLEY and J. R. WILLIAMSON Structural mimicry in the phage {phi}21 N peptide-boxB RNA complex RNA, June 1, 2003; 9(6): 663 - 676. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zuo and M. P. Deutscher Mechanism of Action of RNase T. II. A STRUCTURAL AND FUNCTIONAL MODEL OF THE ENZYME J. Biol. Chem., December 13, 2002; 277(51): 50160 - 50164. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. K. Evans and V. Lundblad The Est1 Subunit of Saccharomyces cerevisiae Telomerase Makes Multiple Contributions to Telomere Length Maintenance Genetics, November 1, 2002; 162(3): 1101 - 1115. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zuo and M. P. Deutscher The Physiological Role of RNase T Can Be Explained by Its Unusual Substrate Specificity J. Biol. Chem., August 9, 2002; 277(33): 29654 - 29661. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Fraternali and L. Cavallo Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome Nucleic Acids Res., July 1, 2002; 30(13): 2950 - 2960. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Brazzolotto, P. Timmins, Y. Dupont, and J.-M. Moulis Structural Changes Associated with Switching Activities of Human Iron Regulatory Protein 1 J. Biol. Chem., March 29, 2002; 277(14): 11995 - 12000. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Seit-Nebi, L. Frolova, J. Justesen, and L. Kisselev Class-1 translation termination factors: invariant GGQ minidomain is essential for release activity and ribosome binding but not for stop codon recognition Nucleic Acids Res., October 1, 2001; 29(19): 3982 - 3987. [Abstract] [Full Text] [PDF]
|
|