Böde Csaba, Kovács István A, Szalay Máté S, Palotai Robin, Korcsmáros Tamás, Csermely Péter
Department of Biophysics and Radiation Biology, Semmelweis University, Puskin Street 9, H-1088 Budapest, Hungary.
FEBS Lett. 2007 Jun 19;581(15):2776-82. doi: 10.1016/j.febslet.2007.05.021. Epub 2007 May 21.
The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here, we review the results of the topological analysis of protein structures as molecular networks describing their small-world character, and the role of hubs and central network elements in governing enzyme activity, allosteric regulation, protein motor function, signal transduction and protein stability. We summarize available data how central network elements are enriched in active centers and ligand binding sites directing the dynamics of the entire protein. We assess the feasibility of conformational and energy networks to simplify the vast complexity of rugged energy landscapes and to predict protein folding and dynamics. Finally, we suggest that modular analysis, novel centrality measures, hierarchical representation of networks and the analysis of network dynamics will soon lead to an expansion of this field.
网络范式越来越多地用于描述复杂系统的拓扑结构和动态特性。在此，我们回顾了将蛋白质结构作为分子网络进行拓扑分析的结果，这些网络描述了它们的小世界特征，以及枢纽和核心网络元件在调控酶活性、变构调节、蛋白质运动功能、信号转导和蛋白质稳定性方面的作用。我们总结了现有数据，即核心网络元件如何在活性中心和配体结合位点富集，从而指导整个蛋白质的动态变化。我们评估了构象网络和能量网络在简化崎岖能量景观的巨大复杂性以及预测蛋白质折叠和动态方面的可行性。最后，我们认为模块化分析、新颖的中心性度量、网络的层次表示以及网络动态分析将很快推动该领域的扩展。
