Biophysical and computational methods to analyze amino acid interaction networks in proteins

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• 作者：Kathleen F. O'Rourke¹ ; Scott D. Gorman¹ ; David D. Boehr ; ^{ddb12@psu.edu}
• 关键词：Amino acid interaction network ; Allostery ; Graph theory ; CONTACT ; Molecular dynamics ; Elastic network ; NMR ; Coevolution ; Statistical coupling analysis
• 刊名：Computational and Structural Biotechnology Journal
• 出版年：2016
• 出版时间：2016
• 年：2016
• 卷：14
• 期：Complete
• 页码：245-251
• 全文大小：1057 K
• 卷排序：14

文摘

Globular proteins are held together by interacting networks of amino acid residues. A number of different structural and computational methods have been developed to interrogate these amino acid networks. In this review, we describe some of these methods, including analyses of X-ray crystallographic data and structures, computer simulations, NMR data, and covariation among protein sequences, and indicate the critical insights that such methods provide into protein function. This information can be leveraged towards the design of new allosteric drugs, and the engineering of new protein function and protein regulation strategies.