Jiang Sulin, Tovchigrechko Andrei, Vakser Ilya A
Department of Biochemistry, Weill Medical College of Cornell University, New York, NY 10021, USA.
Protein Sci. 2003 Aug;12(8):1646-51. doi: 10.1110/ps.0304503.
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.
蛋白质折叠和蛋白质识别主要方面之间的强烈相似性是蛋白质科学中正在浮现的基本原理之一。空间互补性在蛋白质识别中的至关重要性是一个已被充分证实的事实。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，即二级结构元件的堆积方面。虽然蛋白质结构的紧密堆积总体上是一个众所周知的事实，但对几何互补性在二级结构元件堆积中作用的系统研究一直缺乏。为了评估空间互补性的作用，我们使用对接程序，仅通过几何匹配来重现已知蛋白质结构中晶体学确定的二级结构元件堆积。对接结果显示出相当比例的正确预测堆积构型。不同类型的二级结构元件对显示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，不同类型对中空间匹配的相对贡献与已知蛋白质结构中此类对的数量相关。这种效应可能表明存在一种进化压力，促使选择紧密堆积的二级结构元件，以使整个结构的堆积最大化。总体结论是，空间匹配在二级结构元件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原理很重要，并且可能有助于开发更好的蛋白质结构预测方法。
