Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2

TDA and PIVET successfully identified select residues that are responsible for conformation specific regional fluctuation in the activation cycle of Cyclin Dependent Kinase 2 (CDK2). The detected local changes in protein flexibility have been experimentally confirmed to be essential for the regulation and function of the kinase. The methodologies also highlighted possible errors in previous molecular dynamic simulations that need to be resolved in order to understand this key player in cell cycle regulation. Finally, the use of entropy compensation as a possible allosteric mechanism for protein function is reported for CDK2.The methodologies embodied in TDA and PIVET provide a quick approach to identify local fluctuation change important for protein function and residue contacts that contributes to these changes. Further, these approaches can be used to check for possible errors in protein dynamic simulations and have the potential to facilitate a better understanding of the contribution of entropy to protein allostery and function.The traditional view of allostery has been redefined as a consequence of an observed shift in protein conformational preference [1-3] upon allosteric interaction largely influenced by a select set of key residues. This is evidenced through an examination of dihydrofolate reductase using COREX[4], an ensemble-based computational model that generates all probable conformational states adopted by the protein thus revealing local stabilizing and destabilizing regions that facilitate conformational shifts. In another example, the conformational state preference of guanine nucleotide binding proteins impacts the preference for their corresponding binding partners[5,6]. In both cases, it has been found that a select set of key residues has a large impact on conformational preference.With this expanded view of allostery, the model allows for the consideration of other contributing factors and possible mechanisms such as entropy that was initially