物理化学学报 >> 2012, Vol. 28 >> Issue (07): 1665-1675.doi: 10.3866/PKU.WHXB201204182

理论与计算化学 上一篇    下一篇

残基突变对P53-DNA结合域肽段构象影响的分子动力学模拟

许朝莹1,3, 赵立岭1,2, 曹赞霞1,2, 王吉华1,2   

  1. 1. 山东省功能大分子生物物理重点实验室(德州学院), 山东德州 253023;
    2. 德州学院物理系, 山东德州 253023;
    3. 山东师范大学物理与电子科学学院, 济南 250014
  • 收稿日期:2012-01-10 修回日期:2012-04-14 发布日期:2012-06-07
  • 通讯作者: 王吉华 E-mail:jhwyh@yahoo.com.cn
  • 基金资助:

    国家自然科学基金(30970561, 31000324)和山东省自然科学基金(2009ZRA14027, 2009ZRA14028)资助项目

Effects of the Residue Mutations on the Segment of P53-DNA Binding Region Based on Molecular Dynamics Simulation

XU Zhao-Ying1,3, ZHAO Li-Ling1,2, CAO Zan-Xia1,2, WANG Ji-Hua1,2   

  1. 1. Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics (Dezhou University), Dezhou 253023, Shandong Province, P. R. China;
    2. Department of Physics, Dezhou University, Dezhou 253023, Shandong Province, P. R. China;
    3. College of Physics and Electronics, Shandong Normal University, Jinan 250014, P. R. China
  • Received:2012-01-10 Revised:2012-04-14 Published:2012-06-07
  • Contact: WANG Ji-Hua E-mail:jhwyh@yahoo.com.cn
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (30970561, 31000324) and Natural Science Foundation of Shandong Province, China (2009ZRA14027, 2009ZRA14028).

摘要:

基于分子动力学模拟方法研究了R249S、R248W 和G245S 突变对P53-DNA 结合域肽段(残基230-258)结构的影响. 采用GROMACS 软件包和GROMOS 43A1分子力场, 分别对野生型wtP53肽段、单点突变型P53-R249S肽段、两点突变型P53-R249S/R248W肽段和三点突变型P53-R249S/R248W/G245S肽段进行了4组独立的分子动力学模拟, 每组体系模拟时间为500 ns. 研究结果表明: R249S单残基突变影响肽段残基形成二级结构的情况, 但不改变肽段三维结构的模式, 同时使该肽段结构相对稳定; R249S和R248W两残基同时突变会加剧R249S突变对肽段的影响, 同时导致三维结构发生较大变化, 构象弯曲呈现双turn 结构, 肽段稳定性进一步增大; G245S突变对肽段的影响与R249S和R248W同时突变对其结构的影响相反, 在两残基突变的基础上, G245S突变会使原突变引起的变化减弱甚至消失, 同时使得该肽段结构稳定性减小. 该研究对认识肿瘤致病分子机制和设计新药物有重要意义.

关键词: P53蛋白, 残基突变, 结构变化, 分子动力学模拟, 结构异质性

Abstract:

The structural characteristics of the peptide segment of the P53-DNA binding domain (from residue 230 to 258) were studied using molecular dynamics simulations with different mutations, including R249S, R248W, and G245S. Four independent simulations, including the wild-type segment wtP53, onepoint mutation segment P53-R249S, two-point mutation segment P53-R249S/R248W, and three-point mutation segment P53-R249S/R248W/G245S, were performed using the GROMACS software package and GROMOS 43A1 force field. Each simulation was run for 500 ns. The results indicated that mutation R249S affected the formation of the secondary structure for some residues, but had little impact on the mode of the ternary structure and made the segment more stable than the wild-type segment. In contrast, the R249S/R248W mutation strengthened the effect of R249S on the segment and induced a significant change in the ternary structure, with the structure of the two-point mutation segment R249S/R248W existing as a double-turn motif and becoming more stable. Moreover, the G245S mutation had the opposite effect on the segment, decreasing or eliminating entirely the effects caused by the R249S/R248W mutation on the segment. This study provided important understanding of the molecular mechanism of tumorigenesis and the design of a new drug.

Key words: P53 protein, Residue mutation, Structural change, Molecular dynamics simulation, Structure heterogeneity

MSC2000: 

  • O643