Bahar I, Atilgan A R, Erman B
Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey.
Fold Des. 1997;2(3):173-81. doi: 10.1016/S1359-0278(97)00024-2.
An elastic network model is proposed for the interactions between closely (< or = 7.0 A) 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.
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.
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.
提出了一种弹性网络模型，用于描述折叠蛋白质中紧密相邻（距离小于或等于7.0埃）的α-碳原子对之间的相互作用。采用单参数谐振子势来描述残基围绕其在晶体结构中的平均位置的波动。该模型基于为蛋白质编写基尔霍夫邻接矩阵，该矩阵定义了残基在空间中的接近程度。基尔霍夫矩阵的逆矩阵元素直接给出原子波动的自相关或互相关。
准确预测了12个X射线结构的Cα原子的温度因子，这些结构从一个41个残基的亚基到一个633个残基的二聚体不等。互相关也得到了有效表征，与通过结合能量最小化的正常模式分析获得的结果非常一致。
这里提出的简单模型和方法对原子波动之间的相关性提供了令人满意的描述。此外，这是在比常用分子方法至少短一个数量级的计算时间内实现的。
