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A Langevin equation approach to bridge different timescales of relaxation in protein dynamics.

机译：Langevin方程方法可桥接蛋白质动力学中不同的松弛时间尺度。

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摘要

While dynamics of synthetic macromolecular systems are well described by Langevin Equations (LE), the application of this approach to biological macromolecules presents additional challenges as short and long-range interactions, hydrogen bonding, secondary and tertiary structure, hydrophobic and other effects come into play. In the original LE approach presented here, all these effects are taken into account. In our approach, for the first time hydrophobic effects, through an internal friction coefficient, are included in the description of the protein local dynamics. The input to the theory is provided by atomistically detailed short time (ns) molecular dynamics simulations. The LE is then solved by matrix diagonalization and provides eigenvalues and eigenvectors in which all time correlation functions of interest are expressed. The test of the theory is performed on the signal transduction protein CheY. Without any adjustable parameters, good agreement between bond autocorrelation functions predicted from the theory and calculated directly from the simulation is found in the timescales of nanoseconds (ns). Theoretical predictions of NMR T1, T2, and NOE values are compared with experiments and found to be in close agreement also. In addition, the theory is in agreement with temperature factors as measured in X-ray experiments. A study of the Calcium-binding protein Calmodulin is also presented, in which the relative dynamics of this dumbbell-shaped molecule are discussed. The usefulness of this theory lies in its ability to provide a physical picture of the dynamics of protein in the complete range of timescales of interest. So that other proteins can be studied with this approach, the software package Bridget has been built, which calculates, among other dynamical properties, NMR relaxation parameters. This dissertation includes my co-authored material.
机译：虽然Langevin方程（LE）很好地描述了合成大分子系统的动力学，但这种方法在生物大分子上的应用面临着其他挑战，因为短程和长程相互作用，氢键，二级和三级结构，疏水性和其他效应开始发挥作用。在此处介绍的原始LE方法中，考虑了所有这些影响。在我们的方法中，通过内部摩擦系数的疏水作用首次包括在蛋白质局部动力学的描述中。该理论的输入由原子详细的短时间（ns）分子动力学模拟提供。然后通过矩阵对角化来求解LE，并提供特征值和特征向量，在其中表达所有感兴趣的时间相关函数。对信号转导蛋白CheY进行理论验证。如果没有任何可调整的参数，则在纳秒（ns）的时标中可以找到理论预测的键自相关函数和直接根据仿真计算的键自相关函数之间的良好一致性。将NMR T1，T2和NOE值的理论预测与实验进行了比较，发现它们之间也有密切的一致性。另外，该理论与在X射线实验中测得的温度因子一致。还提出了钙结合蛋白钙调蛋白的研究，其中讨论了该哑铃形分子的相对动力学。该理论的有用之处在于它能够在感兴趣的完整时标范围内提供蛋白质动力学的物理图景。为了使用此方法可以研究其他蛋白质，已构建了Bridget软件包，该软件包除其他动力学性质外，还计算NMR弛豫参数。本文包括我的合著材料。

著录项

  • 作者

    Caballero-Manrique, Esther.;

  • 作者单位

    University of Oregon.;

  • 授予单位 University of Oregon.;
  • 学科 Chemistry Physical.Biophysics General.
  • 学位 Ph.D.
  • 年度 2006
  • 页码 99 p.
  • 总页数 99
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

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