Folding a 20 amino acid alpha beta peptide with the diffusion process-controlled Monte Carlo method
Folding a 20 amino acid alpha beta peptide with the diffusion process-controlled Monte Carlo method
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DOI：
10.1063/1.474546
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发表时间：
1997-08-08
影响因子：
4.4
通讯作者：
Derreumaux, P
中科院分区：
文献类型：
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作者：
Derreumaux, P
在这项研究中，我们报告的应用扩散过程控制的蒙特卡罗方法的20个氨基酸的α-β肽（Ac-E-T-Q-A-A-L-L-A-A-Q-K-A-Y-H-P-M-T-M-T-G-Am）。多肽链由一组126个粒子表示，侧链由球体建模，每个氨基酸残基的骨架二面角phi和psi基本上限于一组10个高概率区域，尽管在模拟过程中可以访问整个phi-psi空间。该方法不同于其他非格点蒙特卡罗方法，因为在每次迭代中估计并限制从一个可接受构象到下一个构象的逃逸时间。的构象进行评估的基础上成对的非键合侧链能量来自统计分布的接触在真实的蛋白质和一个简单的主链氢键的潜力。作为从随机扩展构象开始的四次模拟和从与NMR数据一致的结构开始的一次模拟的结果，最低能量构象（即，α β折叠）以类似于10（3）蒙特卡罗步骤的方式检测，尽管获得α β基序的估计概率类似于10（-12）。预测的构象偏离3.0埃均方根与实验结果兼容的模型结构。在这项工作中，提供了进一步的证据，这种方法是有用的，在确定最低能量区的中等大小的多肽链。(C)1997年美国物理研究所。
In this study we report on the application of the diffusion process-controlled Monte Carlo method to a 20 amino acid alpha beta peptide (Ac-E-T-Q-A-A-L-L-A-A-Q-K-A-Y-H-P-M-T-M-T-G-Am). The polypeptide chain is represented by a set of 126 particles, the side chains are modeled by spheres, and the backbone dihedral angles phi and psi of each of the amino acid residue are essentially restricted to a set of ten high probability regions, although the whole phi-psi, space may be visited in the course of the simulation. The method differs from other off-lattice Monte Carlo methods, in that the escape time from one accepted conformation to the next is estimated and limited at each iteration. The conformations are evaluated on the basis of pairwise nonbonded side chain energies derived from statistical distributions of contacts in real proteins and a simple main chain hydrogen bonding potential. As a result of four simulations starting from random extended conformations and one starting from a structure consistent with NMR data, the lowest-energy conformation (i.e., the alpha beta fold) is detected in similar to 10(3) Monte Carlo steps, although the estimated probability of getting the alpha beta motif is similar to 10(-12). The predicted conformations deviate by 3.0 Angstrom rms from a model structure compatible with the experimental results. In this work further evidence is provided that this method is useful in determining the lowest-energy region of medium-size polypeptide chains. (C) 1997 American Institute of Physics.