Exploring the free-energy landscape of a short peptide using an average force -: art. no. 244906
Exploring the free-energy landscape of a short peptide using an average force -: art. no. 244906
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DOI：
10.1063/1.2138694
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发表时间：
2005-12-22
影响因子：
4.4
通讯作者：
Hénin, J
中科院分区：
文献类型：
--
作者：
Chipot, C;Hénin, J
选择十-丙氨酸的可逆折叠作为测试案例，用于表征使用自适应偏置力（ABF）来逃离最小值并克服自由能景观的障碍的方法。这种方法依赖于对偏置力的连续估计，该偏置力产生其中没有平均力沿有序参数xi沿着施加的哈密顿量。优化控制ABF如何应用的参数，该方法被证明是非常有效的，当一个非模棱两可的排序参数可以被定义为探索肽的折叠途径。从β-转角基序开始并将xi限制在从α-螺旋状态延伸到扩展结构系综的构象空间区域，ABF方案成功地将肽链折叠成紧凑的α螺旋。然而，这种构象的采样是边际时，范围内的xi值包括安排更紧凑，从而证明了固有的限制，自由能的方法时，利用模糊的排序参数。(c)2005年美国物理学会。
The reversible folding of deca-alanine is chosen as a test case for characterizing a method that uses an adaptive biasing force (ABF) to escape from the minima and overcome the barriers of the free-energy landscape. This approach relies on the continuous estimation of a biasing force that yields a Hamiltonian in which no average force is exerted along the ordering parameter xi. Optimizing the parameters that control how the ABF is applied, the method is shown to be extremely effective when a nonequivocal ordering parameter can be defined to explore the folding pathway of the peptide. Starting from a beta-turn motif and restraining xi to a region of the conformational space that extends from the alpha-helical state to an ensemble of extended structures, the ABF scheme is successful in folding the peptide chain into a compact alpha helix. Sampling of this conformation is, however, marginal when the range of xi values embraces arrangements of greater compactness, hence demonstrating the inherent limitations of free-energy methods when ambiguous ordering parameters are utilized. (c) 2005 American Institute of Physics.