Molecular dynamics studies of a DNA‐binding protein: 1. A comparison of the trp repressor and trp aporepressor aqueous simulations

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Abstract
The results of two 30‐ps molecular dynamics simulations of the trp repressor and trp aporepressor proteins are presented in this paper. The simulations were obtained using the AMBER molecular mechanical force field and in both simulations a 6‐Å shell of TIP3P waters surrounded the proteins. The trp repressor protein is a DNA‐binding regulatory protein and it utilizes a helix‐turn‐helix (D helix‐turn‐E helix) motif to interact with DNA. The trp aporepressor, lacking two molecules of the l‐tryptophan corepressor, cannot bind specifically to DNA. Our simulations show that the N‐ and C‐termini and the residues in and near the helix‐turn‐;helix motifs are the most mobile regions of the proteins, in agreement with the X‐ray crystallographic studies. Our simulations also find increased mobility of the residues in the turn‐D helix‐turn regions of the proteins. We find the average distance separating the DNA‐binding motifs to be larger in the repressor as compared to the aporepressor. In addition to examining the protein residue fluctuations and deviations with respect to X‐ray structures, we have also focused on backbone dihedral angles and corepressor hydrogen‐bonding patterns in this paper.