Gaining Insights into Protein Flexibility, Dynamics and Stability using Network Models
Abstract: Knowledge about the dynamics and motions of proteins are required in order to understand and control the mechanisms of protein function. Graph-based network models of proteins provide an efficient means to characterize the differential motions and stabilities of regions within proteins. With the rapid growth of structural data available, we show how the construction of elastic network models and constraint-based rigidity models to represent all possible conformations of similar structures yields insight into the functionally relevant motions and fluctuations of these molecules. Variations observed between similar (homologous) proteins are used to identify key stabilizing interactions and shown to reflect thermodynamic stability. Analysis from these models is compared to various experimental data to construct a better understanding of protein functions and interactions.
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