This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The lac repressor protein is of great biochemical interest because regions of the protein fold as the protein binds a specific DNA sequence and bends the DNA (see attached picture). These coupled protein-folding DNA-binding processes, though common in sequence-specific DNA-binding proteins, prove quite challenging to study. Computational science provides a unique approach to studying this problem by allowing researchers to decouple these two processes and study them independently of each other (impossible in traditional biochemical experiments). I am performing molecular dynamics simulations of the lac repressor protein in its folded and unfolded, bound and unbound states. Specifically, in this project I will use the CHARMM package to perform replica exchange simulations to explore the conformational space of the unfolded lac protein bound to non-specific DNA. Although the system is large (61637 atoms, owing to the need to include explicit water and counterions to offset the charge of the DNA), we have developed advanced biasing algorithms to increase the computational efficiency of these simulations. (H. Kamberaj and A. van der Vaart, JCP, 127, 2007) Thermodynamic information about the system will be obtained from these simulations using the Weighted Histogram Analysis Method and will provide insight into the coupling of folding and binding. In addition, covariance matrices of fluctuations will elucidate the coupling of the motion of the unfolded region to the rest of the protein;these results will be compared to the results of the folded protein bound to specific DNA and will shed light on the molecular interactions that may be responsible for driving local folding upon binding the specific DNA operator.
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