HARMONICITY AND ANHARMONICITY IN PROTEIN DYNAMICS - A NORMAL-MODE ANALYSIS AND PRINCIPAL COMPONENT ANALYSIS
HARMONICITY AND ANHARMONICITY IN PROTEIN DYNAMICS - A NORMAL-MODE ANALYSIS AND PRINCIPAL COMPONENT ANALYSIS
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DOI：
10.1002/prot.340230207
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发表时间：
1995-10-01
期刊：
影响因子：
--
通讯作者：
GO, N
中科院分区：
文献类型：
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作者：
HAYWARD, S;KITAO, A;GO, N
为了进一步阐明蛋白质动力学中的简谐和非谐方面，比较了牛胰酶抑制剂在真空中200pS分子动力学轨迹的简正模式分析和主成分分析。定义了一个非谐度因子，用来衡量主模或简正模的非谐性程度，结果表明，主模系统自然地分为具有峰值的非谐模。频率低于80厘米(-1)，以及频率高于此值厘米的简谐模式。一般来说，主模的均方涨落越大，其运动的非谐性程度就越大。非谐模式仅占变量总数的12%，但占总均方波动的98%。论证了非简谐运动的过渡性。结果表明，在较大的子空间中，自由能面用多维抛物线近似，该抛物线只是与构象能面单极小值的调和近似相对应的抛物线的重新标度版本。在200ps之后，被称为“正常模式调整系数”的调整系数显然已经收敛到一个值，即子空间内的均方波动大约是正常模式分析预测的两倍。(C)1995年Wiley-Liss公司
A comparison of a normal mode analysis and principal component analysis of a 200-ps molecular dynamics trajectory of bovine pancreatic trypsin inhibitor in vacuum has been made in order to further elucidate the harmonic and anharmonic aspects in the dynamics of proteins. An anharmonicity factor is defined which measures the degree of anharmonicity in the modes, be they principal modes or normal modes, and it is shown that the principal mode system naturally divides into anharmonic modes with peak. frequencies below 80 cm(-1), and harmonic modes with frequencies cm above this value. In general the larger the mean-square fluctuation of a principal mode, the greater the degree of anharmonicity in its motion. The anharmonic modes represent only 12% of the total number of variables, but account for 98% of the total mean-square fluctuation. The transitional nature of the anharmonic motion is demonstrated. The results strongly suggest that in a large subspace, the free energy surface, as probed by the simulation, is approximated by a multi-dimensional parabola which is just a rescaled version of the parabola corresponding to the harmonic approximation to the conformational energy surface at a single minimum. After 200 ps, the rescaling factor, termed the ''normal mode rescaling factor,'' has apparently converged to a value whereby the mean-square fluctuation within the subspace is about twice that predicted by the normal mode analysis. (C) 1995 Wiley-Liss, Inc.