利用复制相关函数对单分子折叠研究进行分析。
Analysis of single molecule folding studies with replica correlation functions.
作者信息
Lenz Peter, Cho Samuel S, Wolynes Peter G
机构信息
Fachbereich Physik, Philipps-Universität Marburg, D-35032 Marburg, Germany.
出版信息
Chem Phys Lett. 2009 Mar 26;471(4-6):310-314. doi: 10.1016/j.cplett.2009.02.054.
Abstract
Single molecule experiments that can track individual trajectories of biomolecular processes provide a challenge for understanding how these stochastic trajectories relate to the global energy landscape. Using trajectories from a native structure based simulation, we use order parameters that accurately distinguish between protein folding mechanisms that involve a simple, single set of pathways versus a complex one with multiple sets of competing pathways. We show how the folding dynamics can be analyzed with replica correlation functions in a way compatible with single molecule experiments.
摘要
能够追踪生物分子过程中单个轨迹的单分子实验，为理解这些随机轨迹如何与全局能量景观相关联带来了挑战。利用基于天然结构模拟的轨迹，我们使用序参量来准确区分涉及简单单一途径组的蛋白质折叠机制与具有多组竞争途径的复杂机制。我们展示了如何以与单分子实验兼容的方式，用副本相关函数来分析折叠动力学。
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Curr Opin Struct Biol. 2008 Feb;18(1):16-26. doi: 10.1016/j.sbi.2007.12.003. Epub 2008 Jan 24.
2
The experimental survey of protein-folding energy landscapes.蛋白质折叠能量景观的实验研究
Q Rev Biophys. 2005 Aug;38(3):245-88. doi: 10.1017/S0033583506004185. Epub 2006 Jun 19.
3
P versus Q: structural reaction coordinates capture protein folding on smooth landscapes.P 与 Q 的比较：结构反应坐标捕捉平滑能量景观上的蛋白质折叠过程。
Proc Natl Acad Sci U S A. 2006 Jan 17;103(3):586-91. doi: 10.1073/pnas.0509768103. Epub 2006 Jan 9.
4
Theory of protein folding.蛋白质折叠理论
Curr Opin Struct Biol. 2004 Feb;14(1):70-5. doi: 10.1016/j.sbi.2004.01.009.
5
Free energy reconstruction from nonequilibrium single-molecule pulling experiments.从非平衡单分子拉伸实验中重建自由能
Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):3658-61. doi: 10.1073/pnas.071034098.
6
Observing single biomolecules at work with the atomic force microscope.用原子力显微镜观察单个生物分子的工作状态。
Nat Struct Biol. 2000 Sep;7(9):715-8. doi: 10.1038/78929.
7
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J Mol Biol. 2000 May 19;298(5):937-53. doi: 10.1006/jmbi.2000.3693.
8
Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration.用于确定折叠过渡态系综的景观方法：成功与失败取决于受挫程度。
Proc Natl Acad Sci U S A. 2000 Jan 18;97(2):634-9. doi: 10.1073/pnas.97.2.634.
9
Automated analysis of interatomic contacts in proteins.蛋白质中原子间接触的自动化分析。
Bioinformatics. 1999 Apr;15(4):327-32. doi: 10.1093/bioinformatics/15.4.327.
10
Analytical solution of the off-equilibrium dynamics of a long-range spin-glass model.长程自旋玻璃模型非平衡动力学的解析解
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