Computationally Intensive Research Project
Capture and Reduction of Metal Ions out of the Environment by Biomolecular Systems
MSC News
Additional Information
Roberto D. Lins,1 David A. Dixon,2 Marat Valiev,1 Ursula Rothlisberger,3 T. P. Straatsma,2 Brian H. Lower1
1Pacific Northwest National Laboratory, 2University of Alabama, Tuscaloosa EPFL, 3Swiss Federal Institute of Technology
FY07 Allocation - 600,000
Abstract
The use of microbes and/or microbial components has been proven to be an efficient strategy for in situ environmental remediation technologies. The requested allocation of computer time is for computational chemistry approaches focusing on two main areas of bioremediation: i) the capture and ii) the reduction of ionic contaminants by microbial biomolecular systems. The sequestering of metal ions will be investigated by studying immobilization and transport mechanisms. Two carbohydrate-based systems, the lipopolysaccharide (LPS) membrane of Gram-negative bacteria and fungal chitin/chitosan-based polymers, will be used to probe their ability to immobilize metal ions from the environment. Transmembrane transport of metal ions will be investigated via the modeling of synthetic rigid-rod ?-barrel pores. These supramolecules can be immersed into biological membranes and their physico-chemical properties can be tuned by alterations in their peptide chains. Chemical composition will be correlated with structural stability and ion transport. The second part of this proposal involves the electron-transfer pathways of proteins responsible for reducing metal ion contaminants. Focus will be placed on two systems, a small periplasmic tetraheme cytochrome of Shewanella oneidensis MR1, and ii) the [NiFe] hydrogenase of Desulfovibrio fructosovorans. Cytochrome has been experimentally determined to be involved in the electron transport process that ultimately enables the microbe to reduce metals in its environment. The hydrogenase has been shown to efficiently reduce Tc(VII) to Tc(IV) in the periplasmic space. QM/MM calculations and classical multi-configuration thermodynamics integration calculations will be carried out to evaluate the relative free energies of the different redox states of the enzymes. The results can directly relate to the propensity for electrons to move along the molecular wire formed by the redox sites and to titration experiments. These calculations will be performed for homologous enzymes from different microbes to investigate general trends on the enzymatic metal ion reduction mechanism in different organisms. The proposed simulations will be carried out within the NWChem program, a comprehensive suite of advanced computational chemistry software modules tuned for optimal performance on massively parallel computer architectures such as mpp2. The work described in this proposal focuses on molecular modeling strategies to address biogeochemical problems, which are in support of currently DOE-funded as well as recently submitted projects counting with experimental support from EMSL and Ohio State University scientists. Moreover, the proposed work will strengthen the ties among the participating research institutions with a focus on developing a molecular level understanding of biogeochemial phenomena, which can be used to design strategies for biomolecular-based environmental remediation.
