Sutch Brian T, Chambers Eric J, Bayramyan Melina Z, Gallaher Timothy K, Haworth Ian S
Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, USA.
J Chem Inf Model. 2009 Sep;49(9):2139-46. doi: 10.1021/ci900154a.
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.
我们开发了一种用于确定蛋白质 - RNA 复合物对相似性的方法，我们将其称为 SIMA（通过同一性和基序比对实现相似性）。SIMA 方法的关键要素是除了单个氢键和范德华接触外，还根据基序（盐桥、芳香族堆积相互作用、非芳香族堆积、疏水相互作用和氢键基序）来描述蛋白质 - RNA 界面。基于将基序比对与蛋白质和 RNA 序列同一性相结合的成对评分函数，我们为任何一对蛋白质 - RNA 复合物定义了一个 SIMA 分数。正分数表示复合物之间的相似性。我们使用 SIMA 方法从 RCSB 数据库获得的 382 个非核糖体蛋白质 - RNA 结构文件中的 776 个此类复合物中鉴定出 284 个非冗余二元蛋白质 - RNA 复合物。SIMA 允许对蛋白质 - RNA 界面进行快速和定量的比较，并且可能对具有潜在功能和进化意义的界面分类有用。
