Role of water mediated interactions in protein-protein recognition landscapes
Role of water mediated interactions in protein-protein recognition landscapes
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DOI：
10.1021/ja034729u
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发表时间：
2003-07-30
影响因子：
15
通讯作者：
Wolynes, PG
中科院分区：
文献类型：
--
作者：
Papoian, GA;Ulander, J;Wolynes, PG
蛋白质折叠和结合的能量景观图被用来优化蛋白质复合物界面中直接和水介导的相互作用的一些对势。我们发现，水介导的相互作用大大补充了直接的相互作用，在歧视各种类型的陷阱相互作用，这些模型存在于细胞中。我们强调的上下文依赖性的知识为基础的结合潜力，与自主折叠的情况相比。通过执行相应的相互作用矩阵的主成分分析（PCA），我们合理化的识别信号的强度为每个组合的接触类型和参考陷阱状态使用的差分在理想化的“典型”的天然和陷阱层的氨基酸组成。直接和水介导的接触电位矩阵的比较强调了部分溶剂化在稳定蛋白质界面中的带电基团的重要性。特定的水介导的interresidue相互作用，预计显着影响的动力学以及热力学的蛋白质协会。
The energy landscape picture of protein folding and binding is employed to optimize a number of pair potentials for direct and water-mediated interactions in protein complex interfaces. We find that water-mediated interactions greatly complement direct interactions in discriminating against various types of trap interactions that model those present in the cell. We highlight the context dependent nature of knowledge-based binding potentials, as contrasted with the situation for autonomous folding. By performing a Principal Component Analysis (PCA) of the corresponding interaction matrixes, we rationalize the strength of the recognition signal for each combination of the contact type and reference trap states using the differential in the idealized "canonical" amino acid compositions of native and trap layers. The comparison of direct and water-mediated contact potential matrixes emphasizes the importance of partial solvation in stabilizing charged groups in the protein interfaces. Specific water-mediated interresidue interactions are expected to influence significantly the kinetics as well as thermodynamics of protein association.