Molecular dynamics-solvated interaction energy studies of protein-protein interactions:: The MP1-p14 scaffolding complex
Molecular dynamics-solvated interaction energy studies of protein-protein interactions:: The MP1-p14 scaffolding complex
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DOI：
10.1016/j.jmb.2008.04.035
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发表时间：
2008-06-13
影响因子：
5.6
通讯作者：
O. Purisima, Enrico
中科院分区：
文献类型：
--
作者：
Cui, Qizhi;Sulea, Traian;O. Purisima, Enrico
使用MP 1-p14支架复合物作为模型系统的丝裂原活化蛋白激酶信号通路，我们探索了一种基于结构的计算协议，探测和表征结合亲和力热点蛋白质-蛋白质界面。热点位于虚拟丙氨酸扫描共识预测超过三个不同的能量函数和两个不同的单一结构的复杂表示。通过将第一原理方法如分子力学广义玻恩表面积（MM-GBSA）和溶剂化相互作用能（SIE）应用于突变和野生型复合物的分子动力学（MD）轨迹，对选择热点突变进行精细的结合亲和力预测。在这里，预测的热点残基实际上突变为丙氨酸，并确定突变复合物的晶体结构。研究了两种突变的MP 1-p14复合物，p14（Y 56 A）-突变的复合物和MP 1（L 63 A，L 65 A）-突变的复合物。还研究了产生突变复合物的MD系综的替代方法，而不依赖于突变复合物的晶体结构。的SIE功能，拟合蛋白质-配体结合亲和力，给出了绝对的结合亲和力预测与实验非常一致，并优于标准的MM-GBSA预测时，测试的MD合奏的Ras-Raf和Ras-RalGDS蛋白质-蛋白质复合物。对于野生型和突变型MP 1-p14复合物，SIE预测的相对结合亲和力的酵母双杂交试验，提供半定量的相对相互作用强度的支持。MP，I-突变的复合物的结果表明，如果突变的MD系综近似突变的野生型MD轨迹，SIE预测恶化。P14突变复合物的SIE数据表明，尽管突变后观察到局部结构差异，但从突变的野生型晶体结构产生突变的MD系综是可行的。出于能量方面的考虑，这将避免产生和结晶突变复合物的昂贵需求。这里确定的p14（Y 56 A）突变所提供的致敏蛋白质-蛋白质界面在基于筛选的第一代小分子命中的发现中具有实际应用，用于进一步开发成促分裂原活化蛋白激酶信号通路的特异性调节剂。皇冠版权所有（C）2008由爱思唯尔有限公司出版。保留所有权利。
Using the MP1-p14 scaffolding complex from the mitogen-activated protein kinase signaling pathway as model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein-protein interfaces. Hot spots are located by virtual alanine-scanning consensus predictions over three different energy functions and two different single-structure representations of the complex. Refined binding affinity predictions for select hot-spot mutations are carried out by applying first-principle methods such as the molecular mechanics generalized Born surface area (MM-GBSA) and solvated interaction energy (SIE) to the molecular dynamics (MD) trajectories for mutated and wild-type complexes. Here, predicted hot-spot residues were actually mutated to alanine, and crystal structures of the mutated complexes were determined. Two mutated MP1-p14 complexes were investigated, the p14(Y56A)-mutated complex and the MP1(L63A,L65A)-mutated complex. Alternative ways to generate MD ensembles for mutant complexes, not relying on crystal structures for mutated complexes, were also investigated. The SIE function, fitted on protein-ligand binding affinities, gave absolute binding affinity predictions in excellent agreement with experiment and outperformed standard MM-GBSA predictions when tested on the MD ensembles of Ras-Raf and Ras-RalGDS protein-protein complexes. For wild-type and mutant MP1-p14 complexes, SIE predictions of relative binding affinities were supported by a yeast two-hybrid assay that provided semiquantitative relative interaction strengths. Results on the MP,I-mutated complex suggested that SIE predictions deteriorate if mutant MD ensembles are approximated by just mutating the wild-type MD trajectory. The SIE data on the p14-mutated complex indicated feasibility for generating mutant MD ensembles from mutated wild-type crystal structure, despite local structural differences observed upon mutation. For energetic considerations, this would circumvent costly needs to produce and crystallize mutated complexes. The sensitized protein-protein interface afforded by the p14(Y56A) mutation identified here has practical applications in screening-based discovery of first-generation small-molecule hits for further development into specific modulators of the mitogen-activated protein kinase signaling pathway. Crown Copyright (C) 2008 Published by Elsevier Ltd. All rights reserved.