Greene Lesley H, Higman Victoria A
Oxford Centre for Molecular Sciences and Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QH, UK.
J Mol Biol. 2003 Dec 5;334(4):781-91. doi: 10.1016/j.jmb.2003.08.061.
Traditionally, proteins have been viewed as a construct based on elements of secondary structure and their arrangement in three-dimensional space. In a departure from this perspective we show that protein structures can be modelled as network systems that exhibit small-world, single-scale, and to some degree, scale-free properties. The phenomenological network concept of degrees of separation is applied to three-dimensional protein structure networks and reveals how amino acid residues can be connected to each other within six degrees of separation. This work also illuminates the unique features of protein networks in comparison to other networks currently studied. Recognising that proteins are networks provides a means of rationalising the robustness in the overall three-dimensional fold of a protein against random mutations and suggests an alternative avenue to investigate the determinants of protein structure, function and folding.
传统上，蛋白质被视为基于二级结构元件及其在三维空间中的排列的一种结构。与这种观点不同，我们表明蛋白质结构可以被建模为具有小世界、单尺度以及在某种程度上无标度特性的网络系统。分离度的现象学网络概念被应用于三维蛋白质结构网络，并揭示了氨基酸残基如何在六个分离度内相互连接。与目前研究的其他网络相比，这项工作还阐明了蛋白质网络的独特特征。认识到蛋白质是网络为合理化蛋白质整体三维折叠对随机突变的稳健性提供了一种方法，并为研究蛋白质结构、功能和折叠的决定因素提出了一条替代途径。
