Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.
Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.
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水溶液中 441 个二残基肽的分子动力学模拟：Amber ff99SB-ildn-NMR 力场的构象偏好和邻近残基效应。
DOI：
10.1021/ct5010966
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发表时间：
2015
影响因子：
5.5
通讯作者：
Elcock,Adria
中科院分区：
文献类型：
--
作者：
Li,Shuxiang;Andrews,CaseyT;Frembgen-Kesner,Tamara;Miller,MarkS;Siemonsma,StephenL;Collingsworth,TimothyD;Rockafellow,IsaacT;Ngo,NguyetAnh;Campbell,BradyA;Brown,ReidF;Guo,Chengxuan;Schrodt,Michael;Liu,Yu-Tsan;Elcock,Adria
了解氨基酸固有的构象偏好以及它们被邻近残基调节的程度是建立蛋白质折叠和稳定性预测模型的关键问题。在这里，我们展示了441个独立的显式溶剂MD模拟的结果，这些模拟包含了20种标准氨基酸的所有可能的双残基肽，并以组氨酸的中性和质子化状态为模型。MD模拟计算的3jhnh α偶联常数和δ h α化学位移与最近发表的相应双残基肽的实验测量结果具有很好的相关性。邻残效应（NREs）对邻残平均3jhnh α和δ h α值的影响也得到了较好的再现，特别是芳香族残所产生的较大的邻残效应被准确捕获。计算了邻近氨基酸二级结构偏好的NREs，并与线圈库中观察到的相应效应进行了比较，并确定了所有氨基酸类型的平均β-转偏好。最后，组氨酸的固有构象偏好及其对相邻残基构象偏好的NREs都受到咪唑环质子化状态的强烈影响。
Understanding the intrinsic conformational preferences of amino acids and the extent to which they are modulated by neighboring residues is a key issue for developing predictive models of protein folding and stability. Here we present the results of 441 independent explicit-solvent MD simulations of all possible two-residue peptides that contain the 20 standard amino acids with histidine modeled in both its neutral and protonated states.3JHNHαcoupling constants and δHαchemical shifts calculated from the MD simulations correlate quite well with recently published experimental measurements for a corresponding set of two-residue peptides. Neighboring residue effects (NREs) on the average3JHNHαand δHαvalues of adjacent residues are also reasonably well reproduced, with the large NREs exerted experimentally by aromatic residues, in particular, being accurately captured. NREs on the secondary structure preferences of adjacent amino acids have been computed and compared with corresponding effects observed in a coil library and the average β-turn preferences of all amino acid types have been determined. Finally, the intrinsic conformational preferences of histidine, and its NREs on the conformational preferences of adjacent residues, are both shown to be strongly affected by the protonation state of the imidazole ring.
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来自蛋白质局部和远程相互作用的基于知识的构象概率的计算基础
DOI：
--
发表时间：
2006
期刊：
Proteins: Structure, Function, and Bioinformatics
影响因子：
--
作者：
L. Ormeci;A. Gursoy;Guzin Tunca;B. Erman
通讯作者：
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影响因子：
5.6
作者：
S. Griffiths;G. Sharman;A. J. Maynard;M. Searle
通讯作者：
M. Searle
影响因子：
3
作者：
Duan, Y;Wu, C;Kollman, P
通讯作者：
Kollman, P
影响因子：
2
作者：
Jung, Young-Sang;Oh, Kwang-Im;Cho, Minhaeng
通讯作者：
Cho, Minhaeng
重新审视蛋白质中的β-和γ-转角：一组新的氨基酸转角类型依赖的位置偏好和潜力。
影响因子：
2.9
作者：
K. Guruprasad;S. Rajkumar
通讯作者：
S. Rajkumar