Li Xiang, Keskin Ozlem, Ma Buyong, Nussinov Ruth, Liang Jie
Department of Bioengineering, University of Illinois at Chicago, MC-063, Chicago, IL 60607, USA.
J Mol Biol. 2004 Nov 26;344(3):781-95. doi: 10.1016/j.jmb.2004.09.051.
Energetic hot spots account for a significant portion of the total binding free energy and correlate with structurally conserved interface residues. Here, 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 are disfavored in unfilled pockets. For the three available protein-protein complexes with complemented pockets where both members of the complex were alanine-scanned, 62% of all hot spots (DeltaDeltaG>2kcal/mol) are within these pockets, and 60% of the residues in the complemented pockets are hot spots. 93% of all red-hot residues (DeltaDeltaG>/=4kcal/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 energetic 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 18 protein-protein complexes with complemented pockets whose unbound structures are available, in 16 the pockets are identified to pre-exist in the unbound structures. The root-mean-squared deviations of the atoms lining the pockets between the bound and unbound states is as small as 0.9A, suggesting that such pockets constitute features of the populated native state that may be used in docking.
高能热点在总结合自由能中占很大比例，且与结构保守的界面残基相关。在此，我们绘制实验确定的热点和结构保守残基，以研究它们的几何组织。未填充口袋是蛋白质 - 蛋白质复合后仍未填充的口袋，而互补口袋是结合后消失的口袋，代表紧密契合区域。我们发现结构保守残基和高能热点强烈倾向于位于互补口袋中，而在未填充口袋中则不受青睐。对于三个有互补口袋且复合物的两个成员都进行了丙氨酸扫描的可用蛋白质 - 蛋白质复合物，所有热点（ΔΔG>2kcal/mol）中有62%在这些口袋内，互补口袋中60%的残基是热点。所有超热残基（ΔΔG≥4kcal/mol）中有93%要么突入互补口袋，要么位于互补口袋中。互补口袋中热点和保守残基的出现突出了局部紧密堆积在蛋白质缔合中的作用，并合理化了它们的能量贡献和保守性。互补口袋及其相应的突出残基是蛋白质 - 蛋白质相互作用中最重要的几何特征之一。通过筛选溶剂，这种组织屏蔽了主链氢键和电荷 - 电荷相互作用。互补口袋通常在结合前就已存在。对于18个有互补口袋且其未结合结构可用的蛋白质 - 蛋白质复合物，在16个中确定口袋在未结合结构中预先存在。结合态和未结合态之间口袋内衬原子的均方根偏差小至0.9Å，表明这些口袋构成了可能用于对接的丰富天然态的特征。
