Similarity of Protein-RNA Interfaces Based on Motif Analysis

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• 作者：Brian T. Sutch ; Eric J. Chambers ; Melina Z. Bayramyan ; Timothy K. Gallaher ; Ian S. Haworth
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2009
• 出版时间：September 28, 2009
• 年：2009
• 卷：49
• 期：9
• 页码：2139-2146
• 全文大小：291K
• 年卷期：v.49,no.9(September 28, 2009)
• ISSN：1549-960X

文摘

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.