咨询与建议

看过本文的还看了

相关文献

该作者的其他文献

文献详情 >Examining Electrostatic Influe... 收藏

Examining Electrostatic Influences on Base-Flipping:A Comparison of TIP3P and GB Solvent Models

检查静电Influenceson的翻转基地:一个比较的TIP3P和GB溶剂模型

作     者:Allyn R.Brice Brian N.Dominy 

作者机构:Department of ChemistryClemson UniversityClemsonSouth Carolina29634USA. 

出 版 物:《Communications in Computational Physics》 (计算物理通讯(英文))

年 卷 期:2013年第13卷第1期

页      面:223-237页

核心收录:

学科分类:081704[工学-应用化学] 07[理学] 08[工学] 0817[工学-化学工程与技术] 070303[理学-有机化学] 0703[理学-化学] 

基  金:supported by National Science Foundation Career Award MCB-0953783(to B.N.D.) 

主  题:TIP3P generalized Born flipping implicit solvation potential of mean force DNA DNA damage 

摘      要:Recently,it was demonstrated that implicit solvent models were capable of generating stable B-form DNA ***,generalized Born(GB)implicit solvent models have improved regarding the solvation of conformational sampling of DNA[1,2].Here,we examine the performance of the GBSW and GBMV models in CHARMM for characterizing base flipping free energy profiles of undamaged and damaged DNA *** sampling of the base flipping process was performed for the bases cytosine,uracil and *** umbrella sampling simulations were carried-out with both explicit(TIP3P)and implicit(GB)solvent in order to establish the impact of the solvent model on base ***,base flipping potential of mean force(PMF)profiles generated with GB solvent resulted in a greater free energy difference of flipping than profiles generated with *** of the significant differences between implicit and explicit solvent models is the approximation of solute-solvent interactions in implicit solvent *** calculated electrostatic interaction energies between explicit water molecules and the base targeted for *** interaction energies were calculated over the base flipping reaction coordinate to illustrate the stabilizing effect of the explicit water molecules on the flipped-out *** is known that nucleic base pair hydrogen bonds also influenced the free energy of flipping since these favorable interactions must be broken in order for a base to flip-out of the *** Watson-Crick base pair hydrogen bond fractions were calculated over the umbrella sampling simulation windows in order to determine the effect of base pair interactions on the base flipping free *** is shown that interaction energies between the flipping base and explicit water molecules are responsible for the lower base flipping free energy difference in the explicit solvent PMF profiles.

读者评论 与其他读者分享你的观点

用户名:未登录
我的评分