Molecular simulation of microbial membrane proteins and protein-DNA complexes
EMSL Project ID
44711
Abstract
Two biochemical systems that are crucial for the integrity of microbial cells in complex environments are studied using molecular dynamics simulations. The first system is the homologous recombination of microbial DNA by RecA, involved in the repair process of damaged DNA. The second process is the transport of ions and small molecules across the outer membrane of Gram-negative microbes, facilitated by specific and non-specific porins. Both of these processes are important to develop a fundamental, molecular-level understanding of the complex dynamic processes involved in the interaction of microbes with contaminants in their environment.This project is investigating the dynamics of the single stranded DNA bound to RecA at atomic resolution and the dynamics of mobile protein loops which are important to stabilize the bound DNA but are only poorly resolved in the X-ray structure. Simulations will include the presence of the dsDNA partner based on a published docking model, in order to refine the docking model and to investigate which regions of the RecA protein contribute to the stabilization of the encounter complex. This will provide the basis for targeted MD simulations starting from the model of an encounter complex between ssDNA-RecA and dsDNA and to use the known final structure after the strand exchange as a simulation target. In such simulation a known target structure is used to introduce a bias or restraint to pull the starting structure towards the target structure.
Extensive free energy simulations are carried out to determine the thermodynamic profiles for ion and ion complexes transport through outer membrane selective and non-selective porins. In addition, such simulations enable the study of the dynamics of the protein conformation upon binding of ion complexes such as ferric citrate in the siderophore binding site of the protein FpvA, and allow correlating these conformational changes with the conformational differences in the reported crystal structures. A second ion tranporter is OprP for phosphate transport. Potential of mean force free energy calculations will be carried out for moving a phosphate along the pore, and the resulting profile will be correlated to the location and interactions with the residue side chains in the pore, in particular the 9-residue arginine ladder internal to the pore from the extracellular pore entrance to the constriction area in the pore. This will provide insight into important questions of porin specificity related to the function of specific residues that have been targeted for mutations in experimental studies.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2011-10-01
End Date
2012-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members