蛋白质折叠的方向性控制
Orientational Order Governs Collectivity of Folded Proteins
摘要：
在过去的十年中，我们已经见证了粗粒度蛋白质网络模型的发展和成功，用于预测与集体运动模式相关的许多平衡性质。奇怪的是，结果通常对用于从实验坐标的知识构建残差网络的不同截止距离是鲁棒的。在这项研究中，我们提出了一个系统的研究网络的建设，和他们的预测性能的影响。探测键的取向顺序围绕每个残基，我们提出了一个自然的分区的相互作用成一个基本的和一个残留集。在这幅图中，鲁棒性源于新接触的添加方式，从而建立了不寻常的局部取向顺序。这些残余相互作用对每个残余上的力矢量的影响微乎其微。然后，整体力平衡的稳定性转化为海森函数，表现为慢运动模式的小位移和相应特征向量的不变性。我们介绍了一个重新缩放的版本的海森矩阵，并指出了矩阵Frobenius规范的基础上的频谱稳定性参数之间的联系。处方的最佳选择划分的相互作用成基本和残留成分。蛋白质的生物学相关性质的研究的影响进行了讨论与具体的例子。
英文摘要：
The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the different cutoff distances used for constructing the residue networks from the knowledge of the experimental coordinates. In this study, we present a systematical study of network construction, and their effect on the predicted properties. Probing bond orientational order around each residue, we propose a natural partitioning of the interactions into an essential and a residual set. In this picture the robustness originates from the way with which new contacts are added so that an unusual local orientational order builds up. These residual interactions have a vanishingly small effect on the force vectors on each residue. The stability of the overall force balance then translates into the Hessian as small shifts in the slow modes of motion and an invariance of the corresponding eigenvectors. We introduce a rescaled version of the Hessian matrix and point out a link between the matrix Frobenius norm based on spectral stability arguments. A recipe for the optimal choice of partitioning the interactions into essential and residual components is prescribed. Implications for the study of biologically relevant properties of proteins are discussed with specific examples.
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