A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding.
A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding.
复制标题
具有各向异性氢键的粗粒 α-碳蛋白模型。
DOI：
10.1002/prot.21515
复制
发表时间：
2008
期刊：
影响因子：
2.9
通讯作者：
Head-Gordon,Teresa
中科院分区：
文献类型：
--
作者：
Yap,Eng-Hui;Fawzi,NicolasLux;Head-Gordon,Teresa
我们开发了一个基于序列的α-碳模型，以结合平均场估计的多肽链的取向依赖性，产生特定的氢键配对，以稳定α-螺旋和β-折叠。我们说明了新的蛋白质模型在捕获蛋白质L和G的热力学措施和折叠机制的成功。与我们以前的粗粒度模型相比，新模型显示出更大的折叠协同性和蛋白质序列可设计性的改进，以及预测蛋白质L和G的动力学速率和机制的正确趋势。我们相信该模型广泛适用于其他蛋白质折叠和蛋白质-蛋白质共组装过程，并且除了天然状态的拓扑描述之外不需要实验输入。即使没有三级拓扑信息，它也可以作为一个中分辨率蛋白质模型，用于更详尽的构象搜索策略，可以桥接到多肽链的原子描述。Proteins 2008.© 2007 Wiley利斯公司
We develop a sequence based α‐carbon model to incorporate a mean field estimate of the orientation dependence of the polypeptide chain that gives rise to specific hydrogen bond pairing to stabilize α‐helices and β‐sheets. We illustrate the success of the new protein model in capturing thermodynamic measures and folding mechanism of proteins L and G. Compared to our previous coarse‐grained model, the new model shows greater folding cooperativity and improvements in designability of protein sequences, as well as predicting correct trends for kinetic rates and mechanism for proteins L and G. We believe the model is broadly applicable to other protein folding and protein–protein co‐assembly processes, and does not require experimental input beyond the topology description of the native state. Even without tertiary topology information, it can also serve as a mid‐resolution protein model for more exhaustive conformational search strategies that can bridge back down to atomic descriptions of the polypeptide chain. Proteins 2008. © 2007 Wiley‐Liss, Inc.