Maisuradze Gia G, Liwo Adam, Scheraga Harold A
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
Phys Rev Lett. 2009 Jun 12;102(23):238102. doi: 10.1103/PhysRevLett.102.238102.
The molecular dynamics trajectories of protein folding or unfolding, generated with the coarse-grained united-residue force field for the B domain of staphylococcal protein A, were analyzed by principal component analysis (PCA). The folding or unfolding process was examined by using free-energy landscapes (FELs) in PC space. By introducing a novel multidimensional FEL, it was shown that the low-dimensional FELs are not always sufficient for the description of folding or unfolding processes. Similarities between the topographies of FELs along low- and high-indexed principal components were observed.
利用葡萄球菌蛋白A的B结构域的粗粒度联合残基力场生成蛋白质折叠或去折叠的分子动力学轨迹，并通过主成分分析（PCA）进行分析。在主成分（PC）空间中使用自由能景观（FEL）来研究折叠或去折叠过程。通过引入一种新颖的多维FEL，结果表明低维FEL并不总是足以描述折叠或去折叠过程。观察到沿着低索引和高索引主成分的FEL地形之间的相似性。
