Deb Dhruba, Vishveshwara Saraswathi, Vishveshwara Smitha
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
Biophys J. 2009 Sep 16;97(6):1787-94. doi: 10.1016/j.bpj.2009.07.016.
Underlying the unique structures and diverse functions of proteins are a vast range of amino-acid sequences and a highly limited number of folds taken up by the polypeptide backbone. By investigating the role of noncovalent connections at the backbone level and at the detailed side-chain level, we show that these unique structures emerge from interplay between random and selected features. Primarily, the protein structure network formed by these connections shows simple (bond) and higher order (clique) percolation behavior distinctly reminiscent of random network models. However, the clique percolation specific to the side-chain interaction network bears signatures unique to proteins characterized by a larger degree of connectivity than in random networks. These studies reflect some salient features of the manner in which amino acid sequences select the unique structure of proteins from the pool of a limited number of available folds.
蛋白质独特的结构和多样的功能是由大量的氨基酸序列以及多肽主链所采用的数量极为有限的折叠方式所决定的。通过研究主链层面和详细侧链层面非共价连接的作用，我们发现这些独特的结构源自随机特征与特定特征之间的相互作用。首先，由这些连接形成的蛋白质结构网络呈现出简单（键）和高阶（团）渗流行为，这明显让人联想到随机网络模型。然而，侧链相互作用网络特有的团渗流具有蛋白质所特有的特征，其连接程度比随机网络更大。这些研究反映了氨基酸序列从有限数量的可用折叠库中选择蛋白质独特结构的方式的一些显著特征。
