蛋白质的慢正常模式在不同平台上精确复制
Slow Normal Modes of Proteins are Accurately Reproduced across Different Platforms
摘要：
蛋白质数据库（PDB）包含超过105个生物分子的原子结构，分辨率优于2.8 A。组成每个大分子的原子的身份和坐标的列表允许分析这些大系统对微小扰动的慢时间振动响应。个别振荡模式的3D视频动画演示了区域如何交错以创建有凝聚力的集体运动，为整个3D架构提供了全面的框架和熟悉度。此外，最软、最慢变形坐标的分离和表示为酶功能的机械模型的发展提供了机会。因此，特征向量分解必须准确、可靠、快速，才能得到广泛报道。我们得到的本征模的1.2A 34 kDa PDB条目使用无论是专门的重原子或部分或完全约化的原子集;笛卡尔或内部坐标;原子间的力场从一个完整的笛卡尔势，约化的原子势或高斯距离依赖的潜力;和独立开发的软件。这些不同的技术是相似的，因为每一种都通过使用二面角自由度来保持适当的立体化学，二面角自由度冻结键长和键角，或者通过使用包括实际键长和角度限制的全原子势来保持适当的立体化学。我们发现，最慢的本征向量的形状几乎是相同的，而不仅仅是相似。
英文摘要：
The Protein Data Bank (PDB) contains the atomic structures of over 105 biomolecules with better than 2.8A resolution. The listing of the identities and coordinates of the atoms comprising each macromolecule permits an analysis of the slow-time vibrational response of these large systems to minor perturbations. 3D video animations of individual modes of oscillation demonstrate how regions interdigitate to create cohesive collective motions, providing a comprehensive framework for and familiarity with the overall 3D architecture. Furthermore, the isolation and representation of the softest, slowest deformation coordinates provide opportunities for the development of me- chanical models of enzyme function. The eigenvector decomposition, therefore, must be accurate, reliable as well as rapid to be generally reported upon. We obtain the eigenmodes of a 1.2A 34kDa PDB entry using either exclusively heavy atoms or partly or fully reduced atomic sets; Cartesian or internal coordinates; interatomic force fields derived either from a full Cartesian potential, a reduced atomic potential or a Gaussian distance-dependent potential; and independently devel- oped software. These varied technologies are similar in that each maintains proper stereochemistry either by use of dihedral degrees of freedom which freezes bond lengths and bond angles, or by use of a full atomic potential that includes realistic bond length and angle restraints. We find that the shapes of the slowest eigenvectors are nearly identical, not merely similar.
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