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首页> 外文期刊>Biopolymers: Original Research on Biomolecules and Biomolecular Assemblies >A METHOD FOR CHARACTERIZING TRANSITION CONCERTEDNESS FROM POLYMER DYNAMICS COMPUTER SIMULATIONS
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A METHOD FOR CHARACTERIZING TRANSITION CONCERTEDNESS FROM POLYMER DYNAMICS COMPUTER SIMULATIONS

机译：一种基于聚合物动力学计算机仿真的过渡态导数表征方法

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A statistical method based on classifying the transitions among a set of dihedral angles within an ''energy, transfer window'' is developed, and used to analyze Brownian (BD) and molecular dynamics (MD) simulations of the acyl chains in a lipid bilayer, and MD of neat hexadecane. It is shown for the BD simulation that when a transition of the dihedral angle in the center of the chain occurs, a transition of a particular next nearest neighbor (or angle 2-apart) will follow concertedly with a probability of approximately 0.10 within a time window of approximately 3 ps. The MD bilayer simulations, which are based on a more flexible model of the hydrocarbon chains, yield corresponding concerted transition probabilities of approximately 0.083 and window sizes of 1-2 ps. An analysis of angles 4-apart yields concerted transition probabilities of 0.03 and 0.04 for the ED and MD bilayer simulations, respectively, and window sizes close to those of the corresponding 2-apart cases. Statistical hypothesis testing very strongly rejects the assertion that these follower transitions are occurring at random. Similar analysis reveals marginal ol no evidence of concertedness between 1-apart (nearest neighbor) and between 3-apart dihedral angle transitions. The pattern of concertedness for hexadecane is qualitatively similar to that of the lipid chains, although concertedness is somewhat stronger for the 3-apart transitions and somewhat weaker for those 4-apart. Finally, it is suggested that the diffusion of small solute molecules in membranes is better facilitated by nonconcerted transitions, which are associated with relatively large displacements of the chains, than by concerted transitions, which do little to change the chain shape. (C) 1995 John Wiley & Sons, Inc. [References: 37]
机译：开发了一种统计方法，该方法基于对“能量，传递窗”内的一组二面角之间的过渡进行分类的方法，并用于分析脂质双层中酰基链的布朗（BD）和分子动力学（MD）模拟，和纯十六烷的MD。对于BD仿真显示，当在链的中心发生二面角的过渡时，特定的下一个最近邻（或2分角）的过渡将在一段时间内一致地以大约0.10的概率跟随。约3 ps的窗口。 MD双层模拟基于更灵活的烃链模型，可产生约0.083的对应协调过渡概率和1-2 ps的窗口尺寸。对于ED和MD双层模拟，分别分析4个角度产生的过渡概率分别为0.03和0.04，并且窗口大小接近于相应2个实例的窗口大小。统计假设检验非常强烈地否认了这些跟随者转移是随机发生的断言。相似的分析表明，没有任何证据表明1-part（最近邻）和3-part二面角过渡之间存在协调性。十六烷的一致模式在性质上与脂质链相似，尽管3-部分过渡的协调性较强，而4-部分过渡的则较弱。最后，有人提出，与通过链转移相对较大的非过渡过渡相比，通过无过渡过渡与通过协调过渡几乎不会改变链的形状，该过渡更容易促进膜中小溶质分子的扩散。 （C）1995 John Wiley＆Sons，Inc. [参考：37]

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