不同长度尺度的蛋白质接触网络以及疏水、亲水和带电残基在蛋白质结构组织中的作用
Protein contact networks at different length scales and role of hydrophobic, hydrophilic and charged residues in protein's structural organisation
摘要：
蛋白质的三维结构是其组成氨基酸在三维空间中相互作用的结果。以氨基酸为节点，以氨基酸间的相互作用为边，构建了不同长度尺度的蛋白质接触网络。长、短程相互作用由氨基酸在主链上的位置决定，而接触网络是基于氨基酸的三维空间距离构建的。我们进一步将这些网络分为疏水、亲水和带电残基的子网络。我们的分析表明，一个显着更高的百分比的疏水亚簇的长程疏水网络有助于蛋白质在沟通必要的信息，蛋白质折叠一方面;另一方面，疏水亚基的聚集系数值越高，簇在减缓该过程中起主要作用，使得可以通过氨基酸的内部连接性实现必要的局部和全局稳定性残基此外，更高程度的疏水长程相互作用表明它们在蛋白质折叠和稳定性中的作用更大。小范围全氨基酸网络具有层次结构特征。目前的分析与其他证据表明，在蛋白质的三维构象空间中，连接的增长不是通过优先连接或随机连接进化的;相反，它遵循一个特定的结构必要性为基础的指导原则-其中一些相互作用是主要的，而其他的，作为这些主要相互作用的结果是次要的。
英文摘要：
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed protein contact networks at different length scales, long and short-range. While long and short-range interactions are determined by the positions of amino acids in primary chain, the contact networks are constructed based on the 3D spatial distances of amino acids. We have further divided these networks into sub-networks of hydrophobic, hydrophilic and charged residues. Our analysis reveals that a significantly higher percentage of assortative sub-clusters of long-range hydrophobic networks helps a protein in communicating the necessary information for protein folding in one hand; on the other hand the higher values of clustering coefficients of hydrophobic sub-clusters play a major role in slowing down the process so that necessary local and global stability can be achieved through intra connectivities of the amino acid residues. Further, higher degrees of hydrophobic long-range interactions suggest their greater role in protein folding and stability. The small-range all amino acids networks have signature of hierarchy. The present analysis with other evidences suggest that in a protein's 3D conformational space, the growth of connectivity is not evolved either through preferential attachment or through random connections; rather, it follows a specific structural necessity based guiding principle - where some of the interactions are primary while the others, generated as a consequence of these primary interactions are secondary.
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