Protein-RNA interactions: a structural analysis.

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.

[1]  B. Ganem RNA world , 1987, Nature.

[2]  P. Argos An investigation of protein subunit and domain interfaces. , 1988, Protein engineering.

[3]  W R Taylor,et al.  Protein structure alignment. , 1989, Journal of molecular biology.

[4]  Y. Li,et al.  Protein-RNA interactions in an icosahedral virus at 3.0 A resolution. , 1989, Science.

[5]  B. Kastner,et al.  Structure of spliceosomal snRNPs and their role in pre-mRNA splicing. , 1990, Biochimica et biophysica acta.

[6]  C. Fishwick,et al.  Use of synthetic oligoribonucleotides to probe RNA-protein interactions in the MS2 translational operator complex. , 1990, Nucleic acids research.

[7]  T. Steitz,et al.  Structural studies of protein–nucleic acid interaction: the sources of sequence-specific binding , 1990, Quarterly Reviews of Biophysics.

[8]  S. Harrison,et al.  A structural taxonomy of DNA-binding domains , 1991, Nature.

[9]  A. R. Srinivasan,et al.  The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. , 1992, Biophysical journal.

[10]  K. Nagai RNA-protein interactions , 1992 .

[11]  I. Mattaj RNA recognition: A family matter? , 1993, Cell.

[12]  J. Thornton,et al.  Satisfying hydrogen bonding potential in proteins. , 1994, Journal of molecular biology.

[13]  D. Draper,et al.  Protein-RNA recognition. , 1995, Annual review of biochemistry.

[14]  S. Jones,et al.  Principles of protein-protein interactions. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[15]  A Klug,et al.  Ribozymes: structure and mechanism in RNA catalysis. , 1996, Trends in biochemical sciences.

[16]  K. Nagai RNA-protein complexes. , 1996, Current opinion in structural biology.

[17]  S. Jones,et al.  Analysis of protein-protein interaction sites using surface patches. , 1997, Journal of molecular biology.

[18]  D. Moras,et al.  Structural and functional considerations of the aminoacylation reaction. , 1997, Trends in biochemical sciences.

[19]  S. Jones,et al.  Prediction of protein-protein interaction sites using patch analysis. , 1997, Journal of molecular biology.

[20]  G. Varani,et al.  RNA recognition by RNP proteins during RNA processing. , 1998, Annual review of biophysics and biomolecular structure.

[21]  T. Tarasow,et al.  Dressed for success: Realizing the catalytic potential of RNA , 1998 .

[22]  P. Moore,et al.  The three-dimensional structure of the ribosome and its components. , 1998, Annual review of biophysics and biomolecular structure.

[23]  J M Thornton,et al.  Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis. , 1998, Protein engineering.

[24]  M. Summers,et al.  Protein–RNA recognition , 1998, Biopolymers.

[25]  W. Scott RNA catalysis. , 1998, Current opinion in structural biology.

[26]  V. Ramakrishnan,et al.  Ribosomal protein structures: insights into the architecture, machinery and evolution of the ribosome. , 1998, Trends in biochemical sciences.

[27]  D. Draper Themes in RNA-protein recognition. , 1999, Journal of molecular biology.

[28]  H M Berman,et al.  Protein-DNA interactions: A structural analysis. , 1999, Journal of molecular biology.

[29]  C. Orengo CORA—Topological fingerprints for protein structural families , 2008, Protein science : a publication of the Protein Society.

[30]  S. Cusack RNA-protein complexes. , 1999, Current opinion in structural biology.

[31]  J. McCutcheon,et al.  A Detailed View of a Ribosomal Active Site The Structure of the L11–RNA Complex , 1999, Cell.

[32]  F. Schluenzen,et al.  Structure of Functionally Activated Small Ribosomal Subunit , 2000 .

[33]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[34]  F. Schluenzen,et al.  Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Å Resolution , 2000, Cell.

[35]  J. Williamson,et al.  Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain. , 2000, Science.

[36]  C. Vonrhein,et al.  Structure of the 30S ribosomal subunit , 2000, Nature.

[37]  A Yonath,et al.  Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. , 2000, Cell.

[38]  J. Williamson Induced fit in RNA–protein recognition , 2000, Nature Structural Biology.

[39]  J. Thornton,et al.  An overview of the structures of protein-DNA complexes , 2000, Genome Biology.

[40]  K. Hall,et al.  RNA-protein interactions. , 2002, Current opinion in structural biology.