Water in protein structure prediction
Water in protein structure prediction
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DOI：
10.1073/pnas.0307851100
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发表时间：
2004-03-09
影响因子：
11.1
通讯作者：
Wolynes, PG
中科院分区：
文献类型：
--
作者：
Papoian, GA;Ulander, J;Wolynes, PG
蛋白质已经进化到使用水来帮助引导折叠。一个物理动机，nonpairwise-additive模型的水介导的相互作用添加到一个蛋白质结构预测哈密顿产量显着改善较大的蛋白质的结构预测的质量。自由能剖面分析表明，远程水介导的潜力指导折叠和平滑的底层折叠漏斗。分析模拟轨迹提供了直接的证据，水介导的相互作用促进原生一样的包装supersecondclary结构元素。亲水基团的长程配对是蛋白质结构的组成部分。特异性水介导的相互作用是生物分子识别景观在折叠和结合中的普遍特征。
Proteins have evolved to use water to help guide folding. A physically motivated, nonpairwise-additive model of water-mediated interactions added to a protein structure prediction Hamiltonian yields marked improvement in the quality of structure prediction for larger proteins. Free energy profile analysis suggests that long-range water-mediated potentials guide folding and smooth the underlying folding funnel. Analyzing simulation trajectories gives direct evidence that water-mediated interactions facilitate native-like packing of superseconclary structural elements. Long-range pairing of hydrophilic groups is an integral part of protein architecture. Specific water-mediated interactions are a universal feature of biomolecular recognition landscapes in both folding and binding.