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Simulation of steered molecular dynamics on the exploration of the dynamic structure of HIV-1 protease

HIV-1 protease (HIVp) is one of the classic examples of structure-based drug design. And the dynamic structure of protein has become one of the most important characteristics that are directly related to the function of proteins. However, it is still difficult to experimentally track the specific dynamic changes in protein structure. In this work, the combination method of molecular dynamics simulation, steered molecular dynamics simulation and domain analysis was introduced to explore the motion mode of HIVp with external disturbances. It was found that resistance anisotropy and the self-protection function were the two key characteristics of HIVp. Moreover, it was also found that the region in the direction of C was the Achilles heel of the structure of HIVp. These findings with the descriptions of the dynamic structure of HIVp may provide an efficient suggestion for research in drug design and functional protein design.