engleski

Manganese binding reduces the available conformational space in the MntR protein from Bacillus subtilis

The MntR protein from Bacillus subtilis is a transcriptional repressor which is activated for DNA binding by manganese ions (Mn2+).[1] There are more than a dozen crystal structures of this protein available in the PDB, both with and without manganese (II) ions, as well as with various other ligands and mutations. However, the differences between the apo- and manganese-bound crystal structures are minor [2] and not sufficient to fully explain the possible allosteric mechanism by which manganese binding modulates the DNA affinity of the MntR protein. Therefore, molecular dynamics (MD) simulations on the μs simulation time scale of different forms of the protein, manganese-bound and apo forms, were conducted. The obtained results suggest that manganese binding doesn't significantly change the structure of the protein, as much as it limits the size of the available conformational space of the protein. The manganese-bound protein adopts a narrow range of conformations with the DNA-binding helices in a relatively fixed orientation. On the other hand, the apo protein, although transiently achieving this conformation, adopts a variety of different conformations. These results are evident from statistical analyses, such as principal component analysis and clustering, and from visualization of the trajectory.

molecular dynamics, transcription factors, MntR

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