Statistical analysis of atomic contacts at RNA-protein interfaces
Statistical analysis of atomic contacts at RNA-protein interfaces
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DOI：
10.1002/jmr.534
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发表时间：
2001-07-01
影响因子：
2.7
通讯作者：
Westhof, E
中科院分区：
文献类型：
--
作者：
Treger, M;Westhof, E
对来自蛋白质数据库的45种蛋白质和RNA分子之间的复合物晶体进行了统计调查，以了解RNA组分（磷酸盐、核糖和四种碱基）与氨基酸侧链之间的接触数量。三组复合物被定义为：tRNA合成酶;核糖体复合物;第三组包含各种复合物。原子接触的类型被先验地分为离子型、中性氢键、C-H键。. O氢键或货车范德华相互作用。所有联系人都被组织到一个关系数据库中，以便进行统计分析。主要结论如下：（i）在所有三组复合物中，最优选的氨基酸（Arg、Asn、Ser、Lys）和较不优选的那些（Ala、Ile、Leu、瓦尔）相同; Trp和Cys很少观察到（在界面集合中分别为15和5个氨基酸）;（ii）在位于界面处的氨基酸总数中，22%是疏水性的，40%是带电的，（阳性32%，阴性8%），极性30%，Gly 8%;（iii）在核糖体复合物中，磷酸盐优先于核糖，核糖优先于碱基，但在其他两组中没有显著的优先性;（iv）在蛋白质-RNA界面处没有显著的碱基类型的流行，但是特别地Arg和Lys显示出对磷酸的偏好超过核糖和碱基; Pro和Asn偏好碱基超过核糖和磷酸; Met、Phe和Tyr偏好核糖超过磷酸和碱基。此外，Ile、Pro、Ser偏好A而不是其他; Leu偏好C; Asp和Gly偏好G;并且Asn偏好U。考虑到接触类型，可以得出以下结论：（i）23%的接触是通过潜在的氢键（包括CH）。. O H键和离子相互作用），72%属于货车德瓦尔斯相互作用，5%被认为是短接触;（ii）所有潜在的H键，54%是标准的，33%是C-H键。.（3）G的Watson-Crick位点、O_6（G）和主要的N_2（G）以及羟基O_2 ′参与氢键的频率高于预期，蛋白质主链参与32%，侧链参与68%;考虑到中性和离子H-键，以下配对比预期的更频繁-碱基A-Ser、碱基G-Asp/Glu、碱基U-Asn。RNA的CH基团优先与氧原子相互作用（62%在主链上，19%在侧链上）;（iv）碱基参与所有H-键的38%，并且超过26%的H-键在RNA上具有H供体基团;（v）原子O2 '参与所有H-键的21%，这个数字大于预期;（vi）与RNA组分直接接触的氨基酸不太频繁地通过它们的主链原子通过水分子与RNA原子相互作用;相反，那些经常观察到的直接接触的氨基酸，除Ser外，使用它们的侧链原子进行水桥接相互作用。版权所有（C）2001约翰威利父子有限公司
Forty-five crystals of complexes between proteins and RNA molecules from the Protein Data Bank have been statistically surveyed for the number of contacts between RNA components (phosphate, ribose and the four bases) and amino acid side chains. Three groups of complexes were defined: the tRNA synthetases; the ribosomal complexes; and a third group containing a variety of complexes. The types of atomic contacts were a priori classified into ionic, neutral H-bond, C-H . . .O H-bond, or van der Waals interaction. All the contacts were organized into a relational database which allows for statistical analysis. The main conclusions are the following: (i) in all three groups of complexes, the most preferred amino acids (Arg, Asn, Ser, Lys) and the less preferred ones (Ala, Ile, Leu, Val) are the same; Trp and Cys are rarely observed (respectively 15 and 5 amino acids in the ensemble of interfaces); (ii) of the total number of amino acids located at the interfaces 22% are hydrophobic, 40% charged (positive 32%, negative 8%), 30% polar and 8% are Gly; (iii) in ribosomal complexes, phosphate is preferred over ribose, which is preferred over the bases, but there is no significant preference in the other two groups; (iv) there is no significant prevalence of a base type at protein-RNA interfaces, but specifically Arg and Lys display a preference for phosphate over ribose and bases; Pro and Asn prefer bases over ribose and phosphate; Met, Phe and Tyr prefer ribose over phosphate and bases. Further, Ile, Pro, Ser prefer A over the others; Leu prefers C; Asp and Gly prefer G; and Asn prefers U. Considering the contact types, the following conclusions could be drawn: (i) 23% of the contacts are via potential H-bonds (including CH . . .O H-bonds and ionic interactions), 72% belong to van der Waals interactions and 5% are considered as short contacts; (ii) of all potential H-bonds, 54% are standard, 33% are of the C-H . . .O type and 13% are ionic; (iii) the Watson-Crick sites of G, O6(G) and principally N2(G) and the hydroxyl group O2 ' is more often involved in H-bonds than expected; the protein main chain is involved in 32% and the side chains in 68% of the H-bonds; considering the neutral and ionic H-bonds, the following couples are more frequent than expected-base A-Ser, base G-Asp/Glu, base U-Asn. The RNA CH groups interact preferentially with oxygen atoms (62% on the main chain and 19% on the side chains); (iv) the bases are involved in 38% of all H-bonds and more than 26% of the H-bonds have the H donor group on the RNA; (v) the atom O2 ' is involved in 21% of all H-bonds, a number greater than expected; (vi) amino acids less frequently in direct contact with RNA components interact frequently via their main chain atoms through water molecules with RNA atoms; in contrast, those frequently observed in direct contact, except Ser, use instead their side chain atoms for water bridging interactions. Copyright (C) 2001 John Wiley & Sons, Ltd.