Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
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DOI：
10.1016/s1359-0278(97)00024-2
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发表时间：
1997-01-01
期刊：
影响因子：
--
通讯作者：
Erman, B
中科院分区：
文献类型：
--
作者：
Bahar, I;Atilgan, AR;Erman, B
背景资料：提出了一种弹性网络模型，用于描述（小于或等于7.0埃）位于折叠蛋白质中的α-碳对，采用单参数调和势来描述残基在晶体结构中关于其平均位置的波动，该模型基于为蛋白质编写定义残基在空间中的邻近性的Kirchhoff邻接矩阵，Kirchhoff矩阵的逆矩阵的元素直接给出原子涨落的自相关或互相关。结果：准确地预测了从41个残基亚基到633个残基二聚体的12个X射线结构的C-α原子的温度因子。交叉相关性也有效地表征，与正常模式分析加上能量minimization.Conclusions：这里提出的简单的模型和方法提供了一个令人满意的描述原子波动之间的相关性得到的结果密切一致。此外，这是实现计算时间内至少一个数量级短于常用的分子方法。
Background: An elastic network model is proposed for the interactions between closely (less than or equal to 7.0 Angstrom) located alpha-carbon pairs in folded proteins, A single-parameter harmonic potential is adopted for the fluctuations of residues about their mean positions in the crystal structure, The model is based on writing the Kirchhoff adjacency matrix for a protein defining the proximity of residues in space, The elements of the inverse of the Kirchhoff matrix give directly the auto-correlations or cross-correlations of atomic fluctuations.Results: The temperature factors of the C-alpha atoms of 12 X-ray structures, ranging from a 41 residue subunit to a 633 residue dimer, are accurately predicted. Cross-correlations are also efficiently characterized, in close agreement with results obtained with a normal mode analysis coupled with energy minimization.Conclusions: The simple model and method proposed here provide a satisfactory description of the correlations between atomic fluctuations. Furthermore, this is achieved within computation times at least one order of magnitude shorter than commonly used molecular approaches.