Bahar I, Jernigan R L
Molecular Structure Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5677, USA.
Fold Des. 1996;1(5):357-70. doi: 10.1016/S1359-0278(96)00051-X.
Two opposite views have been advanced for the packing of sidechains in globular proteins. The first is the jigsaw puzzle model, in which the complementarity of size and shape is essential. The second, the nuts-and-bolts model, suggests that constraints induced by steric complementarity or pairwise specificity have little influence. Here, the angular distributions of sidechains around amino acids of different types are analyzed, in order to capture the preferred (if any) coordination loci in the neighborhood of a given type of amino acid.
Some residue pairs select specific coordination states with probabilities about ten times higher than expected for random distributions. This selectivity becomes more pronounced at closer separations leading to an effective free energy of stabilization as large as -2 RT for some sidechain pairs. A list of the most probable coordination sites around each residue type is presented, along with their statistical weights.
These data provide guidance as to how to pack selectively the nonbonded sidechains in the neighborhood of a central residue for computer generation of unknown protein structures.
对于球状蛋白质中侧链的堆积，存在两种相反的观点。第一种是拼图模型，其中大小和形状的互补性至关重要。第二种是螺母和螺栓模型，表明空间互补性或成对特异性所引起的限制影响很小。在此，分析了不同类型氨基酸周围侧链的角度分布，以获取给定类型氨基酸附近的优选（如果有的话）配位位点。
一些残基对选择特定配位状态的概率比随机分布预期的高出约十倍。这种选择性在更近的距离处变得更加明显，导致一些侧链对的有效稳定自由能高达 -2RT。列出了每种残基类型周围最可能的配位位点及其统计权重。
这些数据为在计算机生成未知蛋白质结构时如何在中心残基附近选择性地堆积非键合侧链提供了指导。
