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A new perspective on analysis of helix-helix packing preferences in globular proteins

机译:球蛋白螺旋-螺旋堆积偏好分析的新视角

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摘要

For many years, statistical analysis of protein databanks has led to the belief that the steric compatibility of helix interfaces may be the source of observed preferences for particular angles between neighboring helices. Several elegant models describing how side chains on helices can interdigitate without steric clashes were able to account quite reasonably for the observed distributions. However, it was later recognized that the 'bare' measured angle distribution should be corrected to avoid statistical bias.(1,2) Disappointingly, the resealed distributions dramatically lost their similarity with theoretical predictions, casting doubts on the validity of the geometrical assumptions and models. In this article, we elucidate a few points concerning the proper choice of a random reference distribution. In particular we demonstrate the need for corrections induced by unavoidable uncertainties in determining whether two helices are in face-to-face contact or not and their relative orientations. By using this new resealing, we show that 'true' packing angle preferences are well described by regular packing models, thus proving that preferential angles between contacting helices do exist.
机译:多年来,对蛋白质数据库的统计分析已导致人们相信,螺旋界面的空间相容性可能是观察到的相邻螺旋之间特定角度偏好的来源。一些优雅的模型描述了螺旋上的侧链如何在不发生空间碰撞的情况下可以相互交叉,这些模型能够相当合理地解释观察到的分布。但是,后来人们认识到应纠正``裸露''的测角分布以避免统计偏差。(1,2)令人失望的是,重新密封的分布极大地丧失了与理论预测的相似性,令人怀疑几何假设和楷模。在本文中,我们阐明了有关随机参考分布的正确选择的几点。特别是,我们证明了在确定两个螺旋是否面对面接触以及它们的相对方向时,不可避免的不确定性引起的校正是必要的。通过使用这种新的重新密封,我们表明常规包装模型可以很好地描述“真实”的包装角度偏好,从而证明确实存在接触螺旋之间的优选角度。

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    TROVATO A.; SENO F;

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  • 年度 2004
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