MOLECULAR DYNAMICS SIMULATIONS OF PROTEIN-DNA SLIDING

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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. Recognition and binding of specific sites on DNA by proteins is central for regulation of gene expression, recombination, replication and other processes. To bind its specific site on DNA a protein first has to locate the site among a very large number of alternative sequences that are present in the same DNA molecule. To find the right site in a short time, the protein alternates between 3D diffusion, and 1D sliding along DNA. The rate of 1D sliding determines the rate of the overall search process, and thus can important for timing of gene expression. How fast can a protein slide along DNA? Recent studies by NMR spectroscopy solved the structure of dimeric lactose repressor (LacI) bond to a non-specific region of DNA. It was suggested that a protein is capable of sliding when bound to non-specific DNA in this conformation. We aim at using Molecular Dynamic to study how fast a protein can slide along DNA. Specifically, we would like to address the following questions about protein-DNA sliding. (1) Learning whether a protein that diffuses along DNA goes straight or along the major grove in a spiral motion; (2) Estimating the height of the free energy barrier for diffusion and using this estimate it to calculate the rate of diffusion; (3) Testing whether the barriers are sequence-dependent. First, using NAMD, well examine whether the protein (LacI, pdb:1OSL) is capable of moving along DNA under external force. We will examine two possibilities: (1) straight motion along DNA and (2) in spiral motion along DNA major grove. To compare these two possibilities (straight vs spiral) we will set up simulations in which an identical force is applied to the protein in straight or spiral direction, and measure the rate of protein displacement. Second, we will estimate the minimal force needed to make the protein move and hence calculate the height of the barrier for two possible scenarios. Third, we will change the sequence of DNA and measure the barriers and rates of diffusion as a function of sequence using techniques described above. In order to reach these goals, different simulation techniques implemented in NAMD program will be used. These include Constant velocity simulations, Constant force simulations, and Adaptive biasing force simulations. The amount of computer time needed for the pilot part of this project is estimated to be 30,000 SUs.