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Protein Conformational Change Based on a Two-dimensional Generalized Langevin Equation
Ying-xi Wang,Shuang-mu Linguang,Nan-rong Zhao*,Yi-jing Yan
Author NameAffiliationE-mail
Ying-xi Wang College of Chemistry, Sichuan University, Chengdu 610064, China  
Shuang-mu Linguang College of Chemistry, Sichuan University, Chengdu 610064, China  
Nan-rong Zhao* College of Chemistry, Sichuan University, Chengdu 610064, China zhaonanr@scu.edu.cn 
Yi-jing Yan Department of Chemistry, Hong Kong University of Science and Technology, Kowloon, Hong KongHefei National Laboratory for Physical Sciences at the Microscale, University of Science and Tech-nology of China, Hefei 230026, China  
Abstract:
A two-dimensional generalized Langevin equation is proposed to describe the protein con-formational change, compatible to the electron transfer process governed by atomic packing density model. We assume a fractional Gaussian noise and a white noise through bond and through space coordinates respectively, and introduce the coupling effect coming from both fluctuations and equilibrium variances. The general expressions for autocorrelation functions of distance fluctuation and fluorescence lifetime variation are derived, based on which the exact conformational change dynamics can be evaluated with the aid of numerical Laplace inversion technique. We explicitly elaborate the short time and long time approximations. The relationship between the two-dimensional description and the one-dimensional theory is also discussed.
Key words:  Protein conformational fluctuation, Two-dimensional generalized Langevin equation, Atomic packing density model, Fractional Gaussian noise
FundProject:
蛋白质构型变化的二维广义郎之万方程描述
王莹希,林广双木,赵南蓉*,严以京
摘要:
采用二维广义郎之万方程描述蛋白质构型的随机变化,并与电子输运过程的原子密度填充模型相协调. 假设通过键和通过空间的两类电子输运路径分别受到高斯分数噪声和高斯白噪声的影响. 推导了电子转移给体-受体距离涨落和荧光寿命涨落自相关函数的一般表达式. 采用数值拉普拉斯反变换计算了蛋白质构型涨落动力学,并详尽讨论了长时间和短时间行为的渐近解析. 最后,明确了基于二维广义郎之万方程的蛋白质构型描述与一维描述之间的关系.
关键词:  蛋白质构型涨落,二维广义郎之万方程,原子密度填充模型,高斯分数噪声
DOI:10.1088/1674-0068/24/05/597-603
分类号: