Folding–unfolding transition in the mini-protein villin headpiece (HP35): An equilibrium study using the Wang–Landau algorithm

Molecular dynamics study of CDC25BR492L mutant causing the activity decrease of CDC25B

Cell division cycle 25B (CDC25B) was responsible for regulating the various stages of cell division in the cell cycle. R492L was one of the common types of CDC25B mutants. Researches showed that compared to CDC25B^WT, CDC25B^R492L mutant had a ∼100-fold reduction in the rate constant for forming phosphatase intermediate (k₂). However, the molecular basis of how the CDC25B^R492L mutant influenced the process of binding between CDC25B and CDK2/CyclinA was not yet known. Therefore, the optimizations of three-dimensional structure of the CDC25B^WT-CDK2/CyclinA system and the CDC25B^R492L-CDK2/CyclinA system were constructed by ZDOCK and RDOCK, and five methods were employed to verify the reasonability of the docking structure. Then the molecular dynamics simulations on the two systems were performed to explore the reason why CDC25B^R492L mutant caused the weak interactions between CDC25B^R492L and CDK2/CyclinA, respectively. The remote docking site (Arg488-Tyr497) and the second active site (Lys538-Arg544) of CDC25B were observed to have high fluctuations in the CDC25B^R492L-CDK2/CyclinA system with post-analysis, where the high fluctuation of these two regions resulted in weak interactions between CD25B and CDK2. In addition, Asp38-Glu42 and Asp206-Asp210 of CDK2 showed the slightly descending fluctuation, and CDK2 revealed an enhanced the self-interaction, which made CDK2 keep a relatively stable state in the CDC25B^R492L-CDK2/CyclinA system. Finally, Leu492 of CDC25B was speculated to be the key residue, which had great effects on the binding between CDC25B^R492L and CDK2 in the CDC25B^R492L-CDK2/CyclinA system. Consequently, overall analyses appeared in this study ultimately offered a helpful understanding of the weak interactions between CDC25B^R492L and CDK2.