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Structure/Function Studies of Metalloenzymes from Thermophilic Microorganisms
The sophistication of modern computational chemistry methods and access to computational resources allow for using in silico approaches to investigate the molecular details of complex biochemical processes. We have developed and validated computational models and methods that provide versatile tools to probe the biochemical machinery of hyperthermophilic archaea at the molecular level. The accuracy of these theoretical simulations is critical; thus we utilize direct structural information from the Lawrence and Peter's groups and spectroscopic results from the Douglas' group to fine tune the virtual chemical models of metalloproteins and metalloenzyme. Our system of interest is the Dps-like protein from Sulfolobus solfataricus (SsDpsL) as a metalloenzymatic model for oxidative stress in hyperthermophilic archaea.
We conduct combined computational and spectroscopic investigations to determine the molecular mechanism of peroxide decomposition as a molecular model for how the chemical functions of acido- and thermophilic organisms are adapted to the high oxidative stress environments. The first target of our research is the structural refinement of holo, apo, and partially loaded SsDpsL metal binding sites. Contrary to other Dps proteins, the catalytically active site is not located at the subunit-subunit interface, but buried in the core of the four-helix bundle in a ferritin-like arrangement. This allows for construction of relatively small virtual chemical models without the need of addressing the undoubtedly complex subunit-subunit interactions and periodicity of the active sites.
From a coordination chemistry perspective, the SsDpsL protein possesses a unique active site, which can be maintained only by a highly organized network of weak interactions, such as hydrogen bonding, dipole, and electrostatic interactions. The crystal structure already at a modest resolution allows for virtual model building. This computational model is being used to refine the active site structure to atomic resolution that is currently not accessible by any means of experimental methods.
In the second target is the probing of two prototypical reaction mechanisms that have been characterized so far for ferritin-like protein cages:
Using the quantum chemically refined active site models and magnetic coupling constant measurements from the Douglas' lab and their collaborators; we constructed a close to 150-atom functional model of the manganese bound SsDpsL active site. This model provided us hypotheses for the molecular mechanism of oxidative stress management that are being probed experimentally in our laboratories.
Current Laboratory Personnel
Dr. Alexios Grigoropoulos, postdoctoral fellow
Mr. Travis Harris, graduate student
Mr. Logan Giles, graduate student
Mr. David Gardenghi, graduate student
Mr. Ethan Edwards, undergraduate student
contact information: computational.chemistry.montana.edu
Celebration of the arrival of a new 16-core Opteron server for virtual chemistry experiments on SsDPS-L
(Robert, Alexios, Travis, David, Ethan, Logan – from front to rear)
Current List of Outside Collaborators
Dr. Britt Hedman (X-ray Absorption Spectroscopy)
Stanford Synchrotron Radiation Lightsource
Stanford University
Dr. Lance Seefelt (Nitrogenase Biochemistry)
Department of Chemistry and Biochemistry
Utah State University
Dr. Mike Frisch (Software Development and Support)
Gaussian Inc, Wallingford, CT
Selected publications
Pandey A.S., Harris T.V., Giles L.J., Peters J.W., Szilagyi R.K.
Dithiomethylether as a Ligand in the Hydrogenase H-Cluster
Journal of the American Chemical Society, 2008, 130(13), 4533-4540
Peters J.W., Szilagyi R.K.: Exploring new frontiers of nitrogenase structure and mechanism Current Opinion in Chemical Biology, 2006, 10(2), 101-108
Rokhsana D., Dooley D.M., Szilagyi R.K.:Systematic development of computational models for the catalytic site in galactose oxidase: impact of outer-sphere residues on the geometric and electronic structures Journal of Biological Inorganic Chemistry, 2008, 13(3), 371-383
Szilagyi R.K., Winslow M.:On the accuracy of density functional theory for iron - sulfur clustersJournal of Computational Chemistry, 2006, 27(12), 1385-1397
Solomon E.I., Hedman B., Hodgson K.O., Dey A., Szilagyi R.K.:Ligand K-edge X-ray absorption spectroscopy: covalency of ligand-metal bonds Coordination Chemistry Reviews, 2005, 249(1-2), 97-129
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