Biomolecular Recognition and Binding Mechanisms

蛋白质是细胞的“工作马”。它们的作用涵盖了分子机器和信号传递等多种功能。它们进行催化反应，运输，形成病毒衣壳，穿过膜并形成调节通道，将信息从DNA传递到RNA，使新蛋白质的合成成为可能，并且它们负责降解不必要的蛋白质和核酸。它们是免疫反应的载体，负责病毒进入细胞。鉴于其重要性，相当大的努力集中在蛋白质功能的预测上。预测蛋白质功能的主要方法是通过识别结合伴侣。如果至少一种与蛋白质相互作用的组分的功能是已知的，这应该有助于确定其功能和其发挥作用的途径。这是因为它们在活细胞中的绝大多数工作都涉及蛋白质-蛋白质相互作用。蛋白质在孤立状态下从不发挥作用。因此，通过蛋白质-蛋白质相互作用的复杂网络，我们可以绘制细胞通路，它们的相互联系和它们的动态调节。蛋白质间相互作用的鉴定是功能基因组学的核心。蛋白质相互作用的预测对于药物发现至关重要。该途径的知识，其拓扑结构，长度和动力学可以为预测副作用提供有用的信息。然而，预测蛋白质-蛋白质相互作用的目标是艰巨的。有些联想是强制性的，而另一些则是不断形成和分离的。原则上，从物理学的角度来看，任何两种蛋白质都可以相互作用。问题是在什么条件下，以什么强度。蛋白质相互作用的原理是通用的：两个蛋白质的非共价相互作用主要是疏水作用的结果。疏水效应驱动蛋白质-蛋白质相互作用。此外，氢键和静电相互作用也起着重要作用。因此，在体外观察到的许多相互作用是实验过度表达的结果。这使功能预测复杂化。能量热点占总结合自由能的重要部分，并与结构保守的界面残基相关。我们映射实验确定的热点和结构保守的残基，以研究它们的几何组织。“未填充的口袋”是在蛋白质-蛋白质复合后保持未填充的口袋，而“补充的口袋”是在结合后消失的口袋，代表紧密配合的区域。我们发现，结构保守的残基和充满活力的热点强烈倾向于位于互补的口袋里，而不利于在未填充的口袋里。对于具有互补口袋的三种可用的蛋白质-蛋白质复合物，其中两种复合物-成员都被丙氨酸扫描，所有热点（Δ Δ G大于2kcal/mol）的62%在这些口袋内，并且互补口袋中的60%的残基是热点。93%的所有“红热”残基（Δ Δ G大于4千卡/摩尔）突出到或位于互补的口袋中。热点和保守残基在互补口袋中的出现突出了蛋白质缔合中局部紧密堆积的作用，并使其能量贡献和守恒合理化。互补口袋及其相应的突出残基是蛋白质相互作用中最重要的几何特征之一。通过屏蔽溶剂，这种组织屏蔽了骨架氢键和电荷-电荷相互作用。补充口袋往往预先存在约束力。对于19种蛋白质-蛋白质复合物，其未结合结构也是可用的，其中16种蛋白质-蛋白质复合物的未结合结构中预先存在口袋。

Proteins are the "working horse" of the cell. Their roles span functions as diverse as being molecular machines and signaling. They carry out catalytic reactions, transport, form the viral capsids, traverse the membranes and form regulated channels, transmit the information from the DNA to RNA, making possible the synthesis of new proteins, and they are responsible for the degradation of the unnecessary proteins and nucleic acids. They are the vehicles of the immune response and are responsible for viral entry into the cell. Given their importance, considerable effort has been centered on the prediction of protein function. A prime way to predict protein function is through identification of binding partners. If the function of at least one of the components with which the protein interacts is known, that should facilitate assigning its function(s) and the pathway(s) in which it plays a role. This holds since the vast majority of their chores in the living cell involve protein-protein interactions. Proteins never function in isolation. Hence, through the intricate network of protein-protein interactions we can map cellular pathways, their interconnectivities and their dynamic regulation. Identification of protein-protein interactions is at the heart of functional genomics. Prediction of protein-protein interactions is crucial for drug discovery. Knowledge of the pathway, its topology, length, and dynamics may provide useful information for forecasting side effects. Yet, the goal of predicting protein-protein interaction is daunting. Some associations are obligatory, whereas others are continuously forming and dissociating. In principle, from the physical standpoint, any two proteins can interact. The question is under what conditions and at which strength. The principles of protein-protein interactions are general: The non-covalent interactions of two proteins are largely the outcome of the hydrophobic effect. The hydrophobic effect drives protein-protein interactions. In addition, hydrogen bonds and electrostatic interactions play important roles. Thus, many of the interactions observed in vitro are the outcome of experimental over-expression. This complicates the functional prediction. Energetic hot spots account for a significant portion of the total binding free energy and correlate with structurally conserved interface residues. We map experimentally determined hot spots and structurally conserved residues to investigate their geometrical organization. 'Unfilled pockets' are pockets that remain unfilled after protein-protein complexation, while 'complemented pockets' are pockets that disappear upon binding, representing tightly fit regions. We find that structurally conserved residues and energetic hot spots are strongly favored to be located in complemented pockets, and disfavored in unfilled pockets. For the three available protein-protein complexes with complemented pockets where both complex-members were alanine-scanned, 62% of all hot spots (DeltaDeltaG greater than 2 kcal/mol) are within these pockets, and 60% of the residues in the complemented pockets are hot spots. 93% of all "redhot" residues (DeltaDeltaG greater than 4 kcal/mol) either protrude into or are located in complemented pockets. The occurrence of hot spots and conserved residues in complemented pockets highlights the role of local tight packing in protein associations, and rationalizes their energy contribution and conservation. Complemented pockets and their corresponding protruding residues emerge among the most important geometric features in protein-protein interactions. By screening the solvent, this organization shields backbone hydrogen bonds and charge-charge interactions. Complemented pockets often pre-exist binding. For 19 protein-protein complexes with complemented pockets whose unbound structures are also available, in 16 the pockets pre-exist in the unbound structures.