"Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins.
"Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins.
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DOI：
10.1021/acs.jpcb.7b04113
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发表时间：
2017-07-13
期刊：
影响因子：
--
通讯作者：
McCammon JA
中科院分区：
文献类型：
--
作者：
Ricci CG;Li B;Cheng LT;Dzubiella J;McCammon JA
溶剂化是许多生物过程中的基本驱动力，包括生物分子识别和自组装，更不用说蛋白质折叠，动力学和功能。变分隐式溶剂法（VISM）是目前开发和优化的一种理论工具，用于估计非常复杂拓扑结构的系统（如生物分子）的溶剂化自由能。VISM的理论框架使其独特，因为它耦合疏水，货车的德瓦尔斯，和静电相互作用作为溶剂化界面的功能。通过最小化该泛函，VISM产生溶剂化界面作为理论的输出。在这项工作中，我们将VISM推向更大规模的应用，将其与适应于MARTINI框架的粗粒度溶质哈密顿量相结合，MARTINI框架是一个成熟的用于模拟大规模生物分子组装的介观力场。我们展示了如何MARTINI-VISM（MVISM）相比，原子VISM（AVISM）的一小部分蛋白质的大小，形状和电荷分布不同。我们还证明了MVISM的适用性研究溶剂化性质的一个有趣的遭遇复杂，barnase barstar。有希望的结果表明，粗粒化的蛋白质与MARTINI力场确实是一个有价值的步骤，以扩大VISM的和MARTINI的应用在不久的将来。
Solvation is a fundamental driving force in many biological processes including biomolecular recognition and self-assembly, not to mention protein folding, dynamics, and function. The variational implicit solvent method (VISM) is a theoretical tool currently developed and optimized to estimate solvation free energies for systems of very complex topology, such as biomolecules. VISM’s theoretical framework makes it unique because it couples hydrophobic, van der Waals, and electrostatic interactions as a functional of the solvation interface. By minimizing this functional, VISM produces the solvation interface as an output of the theory. In this work, we push VISM to larger scale applications by combining it with coarse-grained solute Hamiltonians adapted from the MARTINI framework, a well-established mesoscale force field for modeling large-scale biomolecule assemblies. We show how MARTINI-VISM (MVISM) compares with atomistic VISM (AVISM) for a small set of proteins differing in size, shape, and charge distribution. We also demonstrate MVISM’s suitability to study the solvation properties of an interesting encounter complex, barnase–barstar. The promising results suggest that coarse-graining the protein with the MARTINI force field is indeed a valuable step to broaden VISM’s and MARTINI’s applications in the near future.
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影响因子：
5.5
作者：
Cheng, Li-Tien;Xie, Yang;Dzubiella, Joachim;McCammon, J. Andrew;Che, Jianwei;Li, Bo
通讯作者：
Li, Bo
影响因子：
5.5
作者：
de Jong, Djurre H.;Singh, Gurpreet;Marrink, Siewert J.
通讯作者：
Marrink, Siewert J.
DOI：
10.1038/nsb1001-848
发表时间：
2001-10-01
期刊：
NATURE STRUCTURAL BIOLOGY
影响因子：
--
作者：
Lim, D;Park, HU;Strynadka, NCJ
通讯作者：
Strynadka, NCJ
影响因子：
4.4
作者：
Huang, Q;Ding, SW;Chen, CL
通讯作者：
Chen, CL
影响因子：
3.4
作者：
Dong, F;Vijayakumar, M;Zhou, HX
通讯作者：
Zhou, HX