The role of geometric complementarity in secondary structure packing: A systematic docking study
The role of geometric complementarity in secondary structure packing: A systematic docking study
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DOI：
10.1110/ps.0304503
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发表时间：
2003-08-01
期刊：
影响因子：
8
通讯作者：
Vakser, IA
中科院分区：
文献类型：
--
作者：
Jiang, SL;Tovchigrechko, A;Vakser, IA
蛋白质折叠和蛋白质识别的主要方面之间的强相似性是蛋白质科学中新兴的基本原理之一。空间互补性在蛋白质识别中的至关重要性是一个众所周知的事实。本研究的目的是评估空间互补性在蛋白质折叠中的重要性，即在二级结构元件的包装中。虽然蛋白质结构的紧密堆积，在一般情况下，是一个众所周知的事实，几何互补性的作用，包装的二级结构元素一直缺乏系统的研究。为了评估空间互补性的作用，我们使用了对接程序，通过仅使用几何匹配来重建已知蛋白质结构中二级结构元件的晶体学确定的包装。对接的结果显示了一个显着的百分比正确预测的包装配置。不同类型的二级结构元件对表现出不同程度的空间互补性（从高到低：β-β，环-环，α-α和α-β）。有趣的是，在不同类型的对的空间匹配的相对贡献与已知的蛋白质结构中这样的对的数量相关。这种效应可能表明进化的压力，以选择紧密堆积的二级结构的元素，以最大限度地提高整个结构的包装。总体结论是，空间匹配在二级结构元素的堆积中起着至关重要的作用。这些结果对于更好地理解蛋白质结构的原理具有重要意义，并可能有助于开发更好的蛋白质结构预测方法。
A strong similarity between the major aspects of protein folding and protein recognition is one of the emerging fundamental principles in protein science. A crucial importance of steric complementarity in protein recognition is a well-established fact. The goal of this study was to assess the importance of the steric complementarity in protein folding, namely, in the packing of the secondary structure elements. Although the tight packing of protein structures, in general, is a well-known fact, a systematic study of the role of geometric complementarity in the packing of secondary structure elements has been lacking. To assess the role of the steric complementarity, we used a docking procedure to recreate the crystallographically determined packing of secondary structure elements in known protein structures by using the geometric match only. The docking results revealed a significant percentage of correctly predicted packing configurations. Different types of pairs of secondary structure elements showed different degrees of steric complementarity (from high to low: beta-beta, loop-loop, alpha-alpha, and alpha-beta). Interestingly, the relative contribution of the steric match in different types of pairs was correlated with the number of such pairs in known protein structures. This effect may indicate an evolutionary pressure to select tightly packed elements of secondary structure to maximize the packing of the entire structure. The overall conclusion is that the steric match plays an essential role in the packing of secondary structure elements. The results are important for better understanding of principles of protein structure and may facilitate development of better methods for protein structure prediction.