Accurate Calculations of Relative Melting Temperatures of Mutant Proteins by Molecular Dynamics/Free Energy Perturbation Methods
Accurate Calculations of Relative Melting Temperatures of Mutant Proteins by Molecular Dynamics/Free Energy Perturbation Methods
复制标题
利用分子动力学/自由能微扰方法准确计算突变蛋白的相对熔解温度
DOI：
10.1007/978-3-662-04802-3_7
复制
发表时间：
2002
影响因子：
4.4
通讯作者：
M. Saito
中科院分区：
文献类型：
--
作者：
M. Saito
通过改进分子动力学（MD）模拟和自由能微扰计算方法，成功地计算了突变蛋白质的解链温度位移。首先，MD模拟进行明确计算长程库仑相互作用的粒子粒子和粒子细胞（PPPC）的方法，而不截断的相互作用，在传统的截止方法。第二，通过接受比方法（ARM）代替普通的自由能微扰方法（FEPM）来估计野生型蛋白质和突变蛋白质之间的自由能差异。解链温度变化计算的RNaseH1，人溶菌酶，和Myb R2域的14个突变体蛋白与它们的实验值一致，虽然计算方法不包括任何可调的参数或突变体的实验数据。
Melting-temperature shifts of mutant proteins were successfully calculated to high accuracy by improving the methods of molecular dynamics (MD) simulation and free energy perturbation calculations. First, MD simulations were performed by explicitly calculating long-range Coulomb interactions by the Particle—Particle and Particle—Cell (PPPC) method without truncating the interactions as in the conventional cutoff method. Second, free energy differences between the wild-type proteins and mutant proteins were estimated by the Acceptance Ratio Method (ARM) instead of the ordinary free energy perturbation method (FEPM). Melting-temperature shifts calculated for 14 mutant proteins of RNaseHl, human lysozyme, and the Myb R2 domain agreed well with their experimental values, although the calculation methodology does not include any adjustable parameters or experimental data for the mutants.
DOI：
10.1093/protein/10.7.789
发表时间：
1997-07
期刊：
Protein engineering
影响因子：
--
作者：
D. Veenstra;Peter A. Kollman
通讯作者：
D. Veenstra;Peter A. Kollman
影响因子：
56.9
作者：
BASH, PA;SINGH, UC;KOLLMAN, PA
通讯作者：
KOLLMAN, PA
影响因子：
5.6
作者：
ERIKSSON, AE;BAASE, WA;MATTHEWS, BW
通讯作者：
MATTHEWS, BW