This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.The mechanical manipulation of DNA is central to all aspects of genetic expression in cells [1]. In order to express or repress certain genes, proteins mechanically manipulate DNA away from its equilibrium configuration by introducing bends, loops, twists and supercoils [2] against mechanical strain arising from the DNA. In some cases, this is done to preclude other proteins from binding DNA, e.g., to prevent gene expression. Little is known about how regulatory proteins are able to handle and withstand the forces stemming from DNA. Often, the changes in DNA structure are known to occur, but determination of the structure eludes experimental techniques when the changes are too large or when the DNA becomes disordered. This is the case when regulatory proteins force DNA into loops. The lac repressor (LacI) protein, a paradigm of genetic regulation, controls the function of the lac operon in E. coli, a set of genes involved in lactose catabolism [3] by bending the DNA into a loop. The all-atom structure of LacI bound to its DNA binding sites has been determined, but with the DNA loop missing [4, 5]. It is therefore unclear what are the mechanisms that the protein uses to resist the strain from the connecting DNA loop, which likely changes the structure of LacI. The Resource developed a multiscale method for simulating protein-DNA complexes [6] that combines molecular dynamics simulation with an elastic rod model of DNA. The elastic rod model accounts for the physical properties of DNA to build the structure of the missing DNA loop and computes the forces that this loop exerts on the protein [7, 8, 9, 10]. Molecular dynamics simulation of the protein incorporates these forces using the SMD method [11], revealing the structural dynamics of the protein-DNA interaction. The geometry of the DNA loop and the forces stemming from it are updated and exchanged every 10 ps of MD simulation. The multiscale method was applied to LacI in complex with a 76 base pair elastic loop [6]. The MD part of the simulation encompassed 320,000 atoms, simulated with the NAMD program on 256 processors.
Showing the most recent 10 out of 371 publications
