蛋白质L9 N端结构域的多正则分子动力学模拟
Multicanonical Molecular Dynamics Simulations of the N-terminal Domain of Protein L9.
作者信息
Yaşar Fatih, Jiang Ping, Hansmann Ulrich H E
机构信息
Department of Physics Engineering, Hacettepe University, Ankara, 06800, TURKEY.
Department of Chemistry & Biochemistry, University of Oklahoma, Norman, OK 73019-5251, USA.
出版信息
Europhys Lett. 2014 Feb 1;105(3):30008. doi: 10.1209/0295-5075/105/30008.
Abstract
We describe multicanonical molecular dynamic simulations of the N-terminal domain of the protein L9. Analyzing free energy landscapes and thermal ordering, we propose a possible folding mechanism for the protein. By comparing our results with that of molecular dynamics runs of the protein at constant temperature, we find that multicanonical molecular dynamics leads to orders of magnitude higher sampling of folding transitions.
摘要
我们描述了蛋白质L9 N端结构域的多规范分子动力学模拟。通过分析自由能景观和热有序性，我们提出了该蛋白质可能的折叠机制。通过将我们的结果与该蛋白质在恒温下的分子动力学模拟结果进行比较，我们发现多规范分子动力学导致折叠转变的采样数量提高了几个数量级。
相似文献
1
Multicanonical Molecular Dynamics Simulations of the N-terminal Domain of Protein L9.蛋白质L9 N端结构域的多正则分子动力学模拟
Europhys Lett. 2014 Feb 1;105(3):30008. doi: 10.1209/0295-5075/105/30008.
2
Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics.蛋白质折叠转变的采样：多正则与副本交换分子动力学
J Chem Theory Comput. 2013 Aug 13;9(8). doi: 10.1021/ct400312d.
3
Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes.用于蛋白质分子系统自由能景观的增强且有效的构象采样。
Biophys Rev. 2012 Mar;4(1):27-44. doi: 10.1007/s12551-011-0063-6. Epub 2012 Jan 11.
4
Investigating the folding mechanism of the N-terminal domain of ribosomal protein L9.研究核糖体蛋白 L9 的 N 端结构域的折叠机制。
Proteins. 2021 Jul;89(7):832-844. doi: 10.1002/prot.26062. Epub 2021 Feb 23.
5
Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.用于分子动力学和蒙特卡罗模拟的部分多正则算法
J Chem Phys. 2008 Sep 28;129(12):124116. doi: 10.1063/1.2970883.
6
Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction.用于构建蛋白质-伴侣底物相互作用自由能景观的增强采样模拟。
Biophys Rev. 2016 Mar;8(1):45-62. doi: 10.1007/s12551-015-0189-z. Epub 2016 Jan 11.
7
Simple and effective application of the Wang-Landau method for multicanonical molecular dynamics simulation.Wang-Landau 方法在多正则系综分子动力学模拟中的简单有效应用。
J Chem Phys. 2011 Jan 14;134(2):024109. doi: 10.1063/1.3517105.
8
Statistical temperature molecular dynamics: application to coarse-grained beta-barrel-forming protein models.统计温度分子动力学：在粗粒度β-桶状形成蛋白模型中的应用。
J Chem Phys. 2007 Apr 7;126(13):135101. doi: 10.1063/1.2711812.
9
Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm.通过多正则-多重重叠算法在小肽的构象空间中进行有效采样。
Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Aug;76(2 Pt 2):026705. doi: 10.1103/PhysRevE.76.026705. Epub 2007 Aug 22.
10
Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level.使用多正则分子动力学的动态对接：在原子水平模拟复合物形成
Methods Mol Biol. 2021;2266:187-202. doi: 10.1007/978-1-0716-1209-5_11.
本文引用的文献
1
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.GROMACS 4：高效、负载均衡和可扩展的分子模拟算法。
J Chem Theory Comput. 2008 Mar;4(3):435-47. doi: 10.1021/ct700301q.
2
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation.P-LINCS：一种用于分子模拟的并行线性约束求解器。
J Chem Theory Comput. 2008 Jan;4(1):116-22. doi: 10.1021/ct700200b.
3
Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics.蛋白质折叠转变的采样：多正则与副本交换分子动力学
J Chem Theory Comput. 2013 Aug 13;9(8). doi: 10.1021/ct400312d.
4
Modeling Structural Flexibility of Proteins with Go-Models.使用Go模型对蛋白质的结构灵活性进行建模。
J Chem Theory Comput. 2012 Jun 12;8(6):2127-2133. doi: 10.1021/ct3000469.
5
Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes.用于蛋白质分子系统自由能景观的增强且有效的构象采样。
Biophys Rev. 2012 Mar;4(1):27-44. doi: 10.1007/s12551-011-0063-6. Epub 2012 Jan 11.
6
Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39).从头算蛋白质折叠的分子模拟研究 NTL9(1-39)毫秒折叠体。
J Am Chem Soc. 2010 Feb 10;132(5):1526-8. doi: 10.1021/ja9090353.
7
Interpretation of p-cyanophenylalanine fluorescence in proteins in terms of solvent exposure and contribution of side-chain quenchers: a combined fluorescence, IR and molecular dynamics study.从溶剂暴露和侧链猝灭剂的作用角度解读蛋白质中对氰基苯丙氨酸荧光：荧光、红外和分子动力学联合研究
Biochemistry. 2009 Sep 29;48(38):9040-6. doi: 10.1021/bi900938z.
8
Long-timescale molecular dynamics simulations of protein structure and function.蛋白质结构与功能的长时间尺度分子动力学模拟
Curr Opin Struct Biol. 2009 Apr;19(2):120-7. doi: 10.1016/j.sbi.2009.03.004. Epub 2009 Apr 8.
9
Optimizing the ensemble for equilibration in broad-histogram Monte Carlo simulations.在宽直方图蒙特卡罗模拟中优化系综以实现平衡
Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Oct;70(4 Pt 2):046701. doi: 10.1103/PhysRevE.70.046701. Epub 2004 Oct 4.
10
Exploring protein native states and large-scale conformational changes with a modified generalized born model.使用改进的广义玻恩模型探索蛋白质天然状态和大规模构象变化。
Proteins. 2004 May 1;55(2):383-94. doi: 10.1002/prot.20033.
Zotero 插件