Distinguishing among structural ensembles of the GB1 peptide: REMD simulations and NMR experiments.
Distinguishing among structural ensembles of the GB1 peptide: REMD simulations and NMR experiments.
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区分 GB1 肽的结构整体：REMD 模拟和 NMR 实验。
DOI：
10.1021/ja0677517
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发表时间：
2007
影响因子：
15
通讯作者：
Baum,Jean
中科院分区：
文献类型：
--
作者：
Weinstock,DanielS;Narayanan,Chitra;Felts,AnthonyK;Andrec,Michael;Levy,RonaldM;Wu,Kuen-Phon;Baum,Jean
利用副本交换分子动力学模拟方法，在270~690K之间为G肽产生了20个结构系综，对应于蛋白质G B1结构域的41−56残基，然后将每个结构系综与我们记录的实验核磁共振化学位移、J偶联和NOE数据进行了比较。我们表明，在模拟温度范围的中部的多肽系综提供了与低温(278K)实验核磁共振数据的最佳拟合，从而提供了一组模型来可视化实验系综中存在的大量结构异质性，并提供了可用于帮助校准用于多肽建模的有效势的信息。
Replica exchange molecular dynamics simulations are used to generate a set of 20 structural ensembles between 270 and 690 K for the G peptide corresponding to residues 41−56 of the B1 domain of protein G. Each of the structural ensembles is then compared with experimental NMR chemical shift,J-coupling, and NOE data we recorded for the peptide. We show that the peptide ensembles in the middle of the simulation temperature range provide the best fit to the low temperature (278 K) experimental NMR data, thereby providing a set of models for visualizing the large amount of structural heterogeneity present in the experimental ensemble and also providing information that can be used to help calibrate effective potentials employed for peptide modeling.