Assessing the Strength of Weak Ties for Interpreting Human Exome

遗传学中的一个主要挑战是鉴定驱动表型变异的遗传变异，以及对表型变异的分析。 人类蛋白质序列的自然变异是迎接挑战的重要途径。不强 非共价相互作用在蛋白质的折叠、组装和识别、结构分析、 人类蛋白质中的非共价相互作用如何从一个个体到另一个个体变化将是至关重要的。我们的结果 表明成千上万的非共价相互作用，特别是弱相互作用（例如，p相互作用， 阴离子四极（AQ）、氢键等），由于自然变异，人类蛋白质受到干扰。像 除p-相互作用外，AQ在大分子结构中也起着重要作用。然而，实力较弱 相互作用（例如，AQ）仍然知之甚少，因此，对 人类蛋白质序列的自然变异仍然是不可理解的。不知道 弱相互作用能量学和人类蛋白质中改变的所有弱相互作用的综合地图将 继续显着有助于缺乏对表型变异起源的理解。继续 这种知识差距的存在是一个重要的问题，因为，直到它被填补，如何遗传 对于有益的遗传干预来说，驱动表型变异的变异仍然是不可理解的。我们的长期 目的是更好地理解弱非共价相互作用在调节蛋白质功能中的作用。的 R15应用的目的是全面测量弱相互作用的强度 (e.g., AQ），并创建人类蛋白质结构中所有非共价相互作用的全面目录 这些基因是由于人类的自然序列变异而改变的。我们的基本原理是：（a）确定能量 弱相互作用（例如，AQ）很可能通过使后续对蛋白质的研究成为可能，提供新的见解 （B）自然结构细节的完整目录的可用性 所有人类蛋白质的错义变体将有助于探索遗传变体驱动的分子机制。 表型变异两个具体目标是：1）通过实验确定AQ的强度; 2）创建 人类蛋白质天然错义变体的3D结构图数据库。对于Aim-1，谨慎使用18 选择的蛋白质-肽界面，我们实验测量AQ的强度，发生在各种 结构背景进行全面估计。对于Aim-2，使用人外显子组聚集体 （ExAC）数据库，我们提供了一个全面的，精细的结构图，所有的非共价相互作用，在人类 由于自然变异而受到干扰的蛋白质结构。使用分子动力学模拟，我们还 探索ExAC突变在两种功能重要的人类蛋白质中的后果。该方法是 在原子分辨率下捕捉遗传和表型变异之间的联系。这项研究是 意义重大，因为它有望纵向扩展对遗传变异如何有助于 表型变异这将使人类蛋白质组的预防性和治疗性操作成为可能。

A major challenge in genetics is to identify genetic variants driving phenotypic variation, and the analysis of natural variation in human protein sequences is an important avenue to meet the challenge. As weak noncovalent interactions play critical role in protein folding, assembly and recognition, structural analysis of how noncovalent interactions in human proteins, from one individual to another, vary will be critical. Our results suggest that thousands of noncovalent interactions, particularly weak ones (e.g., p-interactions, anion-quadrupole (AQ), hydrogen bonds etc.), are perturbed in human proteins due to natural variation. Like other p-interactions, AQ also plays important role in macromolecular structure. However, the strength of weak interactions (e.g., AQ) remain poorly understood, and therefore, the interpretation of the consequences of natural variation of human protein sequences remain incomprehensible. The absence of the knowledge of weak-interaction energetics and the comprehensive map of all weak interactions altered in human proteins will continue to significantly contribute to the lack of understanding of the origin of phenotypic variation. Continued existence of this knowledge gap represents an important problem because, until it is filled, how genetic variants drive phenotypic variation remain incomprehensible for beneficial genetic interventions. Our long-term goal is to better understand the role of weak noncovalent interactions in regulating protein function. The objective for this particular R15 application is to comprehensively measure the strength of a weak interaction (e.g., AQ) and to create a comprehensive catalogue of all noncovalent interaction in human protein structures that are altered due to natural human sequence variation. Our rationale is that (a) determination of the energy of a weak interaction (e.g., AQ) is likely to provide new insights by enabling subsequent studies on protein function by manipulating AQ; (b) the availability of a complete catalogue of fine structural details of natural missense variants of all human proteins will facilitate probing molecular mechanism of genetic variants driving phenotypic variation. The two specific aims are: 1) Determine the strength of AQ experimentally; 2) Create a database of 3D structural maps of natural missense variants of human proteins. For Aim-1, using 18 carefully chosen protein-peptide interfaces, we experimentally measure the strength of AQ that occur in various structural contexts for a comprehensive estimate. For Aim-2, using human exome aggregation consortium (ExAC) database, we provide a comprehensive, fine structural map of all noncovalent interactions in human protein structures that are perturbed due to natural variation. Using molecular dynamic simulations, we also probe the consequences of ExAC mutations in two functionally important human proteins. The approach is innovative for capturing a link between genetic and phenotypic variations at atomic resolution. The research is significant, because it is expected to vertically expand the understanding of how genetic variations contribute to phenotypic variation. That will enable preventative, therapeutic manipulations of human proteome.