Probing protein ensemble rigidity and hydrogen–deuterium exchange
Probing protein ensemble rigidity and hydrogen–deuterium exchange
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DOI：
10.1088/1478-3975/10/5/056013
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发表时间：
2013-04
期刊：
影响因子：
2
通讯作者：
Adnan Sljoka;Derek J. Wilson
中科院分区：
文献类型：
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作者：
Adnan Sljoka;Derek J. Wilson
利用软盘包涵和刚性子结构形貌（FIRST）程序可以准确有效地分析蛋白质的刚性和柔韧性。先前使用FIRST的研究旨在使用单个静态（快照）结构分析蛋白质的刚性和灵活性。然而，众所周知，即使在非常有利于良好定义的天然结构的条件下，蛋白质也可以进行自发的亚分子展开和再折叠，或构象动力学。这些（局部）展开事件产生了大量彼此差别很小的构象。在这种情况下，蛋白质被更好地表示为“天然”结构的热力学集合，而不仅仅是单一的静态低能结构。利用这一概念，我们引入了一种新的基于first的方法，通过(i)平均整个集合的氢键强度和（ii）改进氢键的数学模型来预测蛋白质集合的刚性/灵活性。此外，我们将我们的第一系综刚性预测与主链酰胺的系综溶剂可及性数据结合起来，提出了一种新的计算方法，该方法同时使用刚性和溶剂可及性来预测氢-氘交换（HDX）。为了验证我们的预测，我们报道了一项新的位点特异性HDX实验，该实验表征了来自超嗜热菌Sulfolobus solfataricus （Sso AcP）的酰基磷酸酶的天然结构集合。HDX数据观测到的亚结构构象动力学与第一系综刚度预测非常吻合，这是传统的单一“快照”刚度分析无法获得的。此外，对受HDX保护的区域和发生交换的区域的计算预测与Sso AcP的HDX实验剖面非常吻合。
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program floppy inclusion and rigid substructure topography (FIRST). Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure. It is however well known that proteins can undergo spontaneous sub-molecular unfolding and refolding, or conformational dynamics, even under conditions that strongly favor a well-defined native structure. These (local) unfolding events result in a large number of conformers that differ from each other very slightly. In this context, proteins are better represented as a thermodynamic ensemble of ‘native-like’ structures, and not just as a single static low-energy structure. Working with this notion, we introduce a novel FIRST-based approach for predicting rigidity/flexibility of the protein ensemble by (i) averaging the hydrogen bonding strengths from the entire ensemble and (ii) by refining the mathematical model of hydrogen bonds. Furthermore, we combine our FIRST-ensemble rigidity predictions with the ensemble solvent accessibility data of the backbone amides and propose a novel computational method which uses both rigidity and solvent accessibility for predicting hydrogen–deuterium exchange (HDX). To validate our predictions, we report a novel site specific HDX experiment which characterizes the native structural ensemble of Acylphosphatase from hyperthermophile Sulfolobus solfataricus (Sso AcP). The sub-structural conformational dynamics that is observed by HDX data, is closely matched with the FIRST-ensemble rigidity predictions, which could not be attained using the traditional single ‘snapshot’ rigidity analysis. Moreover, the computational predictions of regions that are protected from HDX and those that undergo exchange are in very good agreement with the experimental HDX profile of Sso AcP.