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In recent years, the earlier view of proteins as relatively rigid structures has been replaced by a dynamic model in which the internal motions and resulting conformational changes play an essential role in their function. In this context, molecular dynamics (MD) simulations have become an important computational tool for understanding the physical basis of the structure and function of biological...
Molecular dynamics simulations on the tetracycline-repressor (TetR) protein, both in the absence of an inducer and complexed with the inducers tetracycline and 5a,6-anhydrotetracycline, show significant differences in the structures and dynamics of the induced and non-induced forms of the protein. C α -density-difference plots, low-frequency normal vibrations and inter-residue interaction...
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