Similarity of protein-RNA interfaces based on motif analysis.
We have developed a method for determination of the similarity of pairs of protein-RNA complexes, which we refer to as SIMA (Similarity by Identity and Motif Alignment). The key element in the SIMA method is the description of the protein-RNA interface in terms of motifs (salt bridges, aromatic stacking interactions, nonaromatic stacks, hydrophobic interactions, and hydrogen-bonded motifs), in addition to single hydrogen bonds and van der Waals contacts. Based on a pairwise scoring function combining motif alignment with identity of the protein and RNA sequences, we define a SIMA score for any pair of protein-RNA complexes. A positive score indicates similarity between the complexes. We used the SIMA method to identify 284 nonredundant binary protein-RNA complexes out of 776 such complexes in 382 nonribosomal protein-RNA structure files obtained from the RCSB database. SIMA allows rapid and quantitative comparison of protein-RNA interfaces and may be useful for interface classification with potential functional and evolutionary implications.
Sutch
Brian T
BT
Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, USA.
Chambers
Eric J
EJ
Bayramyan
Melina Z
MZ
Gallaher
Timothy K
TK
Haworth
Ian S
IS
D000595:Amino Acid Sequence; D001483:Base Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012313:RNA / Q000737:chemistry* / Q000378:metabolism*
D011506:Proteins; D012313:RNA