Bryant S H, Lawrence C E
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20879.
Proteins. 1993 May;16(1):92-112. doi: 10.1002/prot.340160110.
In this paper we present a new residue contact potential derived by statistical analysis of protein crystal structures. This gives mean hydrophobic and pairwise contact energies as a function of residue type and distance interval. To test the accuracy of this potential we generate model structures by "threading" different sequences through backbone folding motifs found in the structural data base. We find that conformational energies calculated by summing contact potentials show perfect specificity in matching the correct sequences with each globular folding motif in a 161-protein data set. They also identify correct models with the core folding motifs of hemerythrin and immunoglobulin McPC603 V1-domain, among millions of alternatives possible when we align subsequences with alpha-helices and beta-strands, and allow for variation in the lengths of intervening loops. We suggest that contact potentials reflect important constraints on nonbonded interaction in native proteins, and that "threading" may be useful for structure prediction by recognition of folding motif.
在本文中，我们展示了一种通过对蛋白质晶体结构进行统计分析得出的新的残基接触势。这给出了作为残基类型和距离间隔函数的平均疏水和成对接触能。为了测试这种势的准确性，我们通过将不同序列“穿线”到结构数据库中发现的主链折叠基序来生成模型结构。我们发现，通过对接触势求和计算得到的构象能在将正确序列与161个蛋白质数据集里的每个球状折叠基序进行匹配时显示出完美的特异性。当我们将子序列与α螺旋和β链进行比对，并考虑中间环长度的变化时，它们还能在数百万种可能的替代结构中识别出血红蛋白和免疫球蛋白McPC603 V1结构域的核心折叠基序的正确模型。我们认为接触势反映了对天然蛋白质中非键相互作用的重要限制，并且“穿线”可能通过识别折叠基序对结构预测有用。
