A COMPARISON OF THE RESTRAINED MOLECULAR-DYNAMICS AND DISTANCE GEOMETRY METHODS FOR DETERMINING 3-DIMENSIONAL STRUCTURES OF PROTEINS ON THE BASIS OF INTERPROTON DISTANCES
A COMPARISON OF THE RESTRAINED MOLECULAR-DYNAMICS AND DISTANCE GEOMETRY METHODS FOR DETERMINING 3-DIMENSIONAL STRUCTURES OF PROTEINS ON THE BASIS OF INTERPROTON DISTANCES
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DOI：
10.1016/0014-5793(87)81504-1
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发表时间：
1987-03-23
期刊：
影响因子：
3.5
通讯作者：
GRONENBORN, AM
中科院分区：
文献类型：
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作者：
CLORE, GM;NILGES, M;GRONENBORN, AM
使用 Crambin 作为模型系统，对基于质子间距离确定蛋白质三维结构的度量矩阵距离几何和约束分子动力学方法进行了直接比较。结果表明，两种方法都再现了二级和三级结构（形状和多肽折叠）的整体特征。两种方法生成的会聚结构采样的构象空间区域大小相似，并且在两种情况下，会聚结构都分布在比任何单个结构更接近 X 射线结构的平均结构上。在局部主链构象、侧链位置和非键能方面，受约束的分子动力学结构优于从距离几何获得的结构。
A direct comparison of the metric matrix distance geometry and restrained molecular dynamics methods for determining three‐dimensional structures of proteins on the basis of interproton distances is presented using crambin as a model system. It is shown that both methods reproduce the overall features of the secondary and tertiary structure (shape and polypeptide fold). The region of conformational space sampled by the converged structures generated by the two methods is similar in size, and in both cases the converged structures are distributed about mean structures which are closer to the X‐ray structure than any of the individual structures. The restrained molecular dynamics structures are superior to those obtained from distance geometry as regards local backbone conformation, side chain positions and non‐bonding energies.