Refinement of protein structures in explicit solvent
Refinement of protein structures in explicit solvent
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DOI：
10.1002/prot.10299
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发表时间：
2003-02-15
影响因子：
2.9
通讯作者：
Nilges, M
中科院分区：
文献类型：
--
作者：
Linge, JP;Williams, MA;Nilges, M
我们提出了一个CPU有效的协议，在一个显式的溶剂和能量参数与完全修订二面角条款的薄层蛋白质结构的细化。我们的方法适用于由理论确定的蛋白质结构（例如，同源性建模或穿线）或实验方法（例如，NMR）。与其他最近提出的改进协议相比，我们非常强调与广泛接受的共价参数和计算效率的一致性。我们举例说明了三种蛋白质的NMR结构计算的方法：白细胞介素-4，ubiquitin，和crambin。我们显示了比较他们的结构合奏之前和之后，在水中的二面角的力场能量项和没有细化; crambin也精制在DMSO中。我们的研究结果表明，显着改善的结构质量的一个简短的细化在薄层溶剂。此外，他们表明，二面角能量项的力场是有益的结构计算和细化。我们讨论的最佳权重的能量常数的骨干角ω，包括广泛的讨论的意义和相关性的计算验证标准，特别是均方根Z分数的共价参数，如键长。(C)2003 Wiley-Liss，Inc.
We present a CPU efficient protocol for refinement of protein structures in a thin layer of explicit solvent and energy parameters with completely revised dihedral angle terms. Our approach is suitable for protein structures determined by theoretical (e.g., homology modeling or threading) or experimental methods (e.g., NMR). In contrast to other recently proposed refinement protocols, we put a strong emphasis on consistency with widely accepted covalent parameters and computational efficiency. We illustrate the method for NMR structure calculations of three proteins: interleukin-4, ubiquitin, and crambin. We show a comparison of their structure ensembles before and after refinement in water with and without a force field energy term for the dihedral angles; crambin was also refined in DMSO. Our results demonstrate the significant improvement of structure quality by a short refinement in a thin layer of solvent. Further, they show that a dihedral angle energy term in the force field is beneficial for structure calculation and refinement. We discuss the optimal weight for the energy constant for the backbone angle omega and include an extensive discussion of meaning and relevance of the calculated validation criteria, in particular root mean square Z scores for covalent parameters such as bond lengths. (C) 2003 Wiley-Liss, Inc.