Capture and Reduction of Metal Ions out of the
Environment by Biomolecular Systems
EMSL Project ID
20892
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 β-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.
Project Details
Project type
Grand Challenge
Start Date
2006-10-01
End Date
2009-11-19
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Boily JF, and RD Lins. 2009. "Electrostatic Cooperativity of Hydroxyl Groups at Metal Oxide Surfaces." Journal of Physical Chemistry C 113(38):16568-16570. doi:10.1021/jp906124a
Bose, S, M. F. Hochella Jr., Y. A. Gorby, D. W. Kennedy, D. E. McCready, A. S. Madden, and B. H. Lower. 2009. "Bioreduction of hematite nanoparticles by the dissimilatory iron reducing bacterium Shewanella oneidensis MR-1." Geochimica et Cosmochimica Acta 73: 962-976.
Franca ED, RD Lins, LC Freitas, and TP Straatsma. 2008. "Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution." Journal of Chemical Theory and Computation 4(12):2141-2149. doi:10.1021/ct8002964
Gutowski KE, VA Cocalia, ST Griffin, NJ Bridges, DA Dixon, and RD Rogers. 2007. "Interactions of 1-Methylimidazole with UO₂(CH₃CO₂)₂ and UO₂(NO₃)₂: Structural, Spectroscopic, and Theoretical Evidence for Imidazole Binding to the Uranyl Ion." Journal of the American Chemical Society 129(3):526-536.
Lins RD, ER Vorpagel, M Guglielmi, and TP Straatsma. 2008. "Computer Simulation of Uranyl Uptake by the Rough Lipopolysaccharide Membrane of Pseudomonas aeruginosa." Biomacromolecules 9(1):29-35. doi:10.1021/bm700609r.
Li Z, MH Matus, HA Velazquez, DA Dixon, and CJ Cassady. 2007. "Gas-phase Acidities of Aspartic Acid, Glutamic Acid, and their Amino Acid Amides." International Journal of Mass Spectrometry 265(2-3):213-223.
Lower BH, RD Lins, ZW Oestreicher, TP Straatsma, MF Hochella Jr., L Shi, and SK Lower. 2008. "In Vitro Evolution of a Peptide with a Hematite Binding Motif That May Constitute a Natural Metal-Oxide Binding Archetype ." Environmental Science & Technology 42(10):3821-3827. doi:10.1021/es702688c.
Oliveira OV, LC Freitas, TP Straatsma, and RD Lins. 2009. "Interaction between the CBM of Cel9A from Thermobifida fusca and Cellulose Fibers." Journal of Molecular Recognition 22(1):38-45.
Soares TA, TP Straatsma, and RD Lins. 2008. "Influence of the B-band O-antigen chain in the Structure and Electrostatics of the Lipopolysaccharide Membrane of Pseudomonas aeruginosa." Journal of the Brazilian Chemical Society 19(2):312-320.