David R. Bevan

Professor

Education

Ph.D., Chemistry, Northwestern University, 1978

M.S., Chemistry, Northwestern University, 1975

B.S., Chemistry, Marietta College, 1970

Experience

  • July 2013 – present: Professor, Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg
  • July 1986 – June 2013: Associate Professor, Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg
  • July 1997 – June 1998: Visiting Scientist, Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC
  • August 1990 – December 1990: Visiting Scientist, Department of Biology, University of Virginia, Charlottesville
  • July 1980 – June 1986: Assistant Professor, Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg

Selected Major Awards

  • 2013 – Outstanding Dissertation Advisor, STEM Area, Virginia Tech
  • 2004 - Gamma Sigma Delta (Agriculture Honor Society) Teaching Award of Merit
  • 2000 – Certificate of Teaching Excellence, College of Agriculture and Life Sciences, Virginia Tech

Courses Taught

  • BCHM 4984 – Visualization of Protein Structure
  • BCHM 5024 – Computational Biochemistry for Bioinformatics
  • GBCB 5874 – Problem Solving in Genetics, Bioinformatics, and Computational Biology

Other Teaching and Advising

  • I serve as one of two undergraduate program directors for the undergraduate major in Biochemistry. In this capacity, I oversee advising in the department, meet with prospective high school students, and meet with students who are considering changing their major to biochemistry.
  • Advisor to Biochemistry Club.

Program Focus

The research in my lab involves the application of computational molecular modeling to relate the structure and dynamics of molecular systems to function. Systems currently under investigation include the amyloid beta-peptide that is associated with Alzheimer's disease and peroxisome proliferator-activated receptor that is associated with inflammation, diabetes, and obesity. We also are initiating projects involving G-protein coupled receptors (GPCRs), and irisin, a recently discovered protein with hormone-like properties. Finally, we are using computational methods to design enzymes, with our strategy being to alter the substrate specificity of existing enzymes.

Current Projects

Amyloid Beta-Peptide (A-beta)

The aggregation of A-beta, ultimately forming plaques, is associated with the development of Alzheimer’s disease. We have examined the physicochemical parameters that account for stability of the A-beta aggregates, and we have proposed a mechanism by which a certain class of compounds, the flavonoids, may prevent the aggregation of A-beta into the toxic oligomeric species. We also have performed simulations of A-beta associated with lipid bilayers because disruption of membrane integrity is a proposed mechanism for toxicity of A-beta. We have published 8 papers on this topic over the past 5 years.

Peroxisome Proliferator Activated Receptor (PPAR)

The number of Americans with chronic inflammation-related diseases, including diabetes and obesity, rises significantly each year. The therapeutics used to treat type 2 diabetes, thiazolidinediones (TZDs), often exacerbate the problem by causing side effects, like edema and heart complications. In an attempt to discover more effective and less harmful treatments, our group is working on a combined computational and experimental approach for finding peroxisome proliferator-activated receptor-gamma (PPAR-gamma) agonists. This project involves collaboration with Dr. Josep Bassanganya-Riera of the Virginia Bioinformatics Institute, who guides the wet lab studies with which we correlate our computational studies. The computational work has been carried out primarily by Nikki Lewis, a former graduate student in the GBCB program, who was supported for two years by the Initiative to Maximize Student Development (IMSD) program and then by an NIH F31 grant.

GPCRs and Irisin

GPCRs are the targets for approximately 30% of the drugs that are currently being marketed and thus are important in a variety of diseases. Our interests are primarily in characterizing those GPCRs that are activated by fatty acids. These compounds also activate PPAR-gamma and some of these compounds have the potential to act through both of these receptors, which adds to the complexity when attempting to understand mechanisms of action of these compounds. Our modeling approaches will aid in elucidating the relationship among structure, dynamics, and function.

Irisin is a recently discovered protein hormone that is associated with obesity. It has been shown to stimulate the conversion of white fat cells to brown fat cells, which are much more metabolically active. Very little information is available related to irisin structure, and we are using its sequence relationship to other proteins to predict its structure. We will then apply MD to refine these structures and examine their stability. These projects are being done in collaboration with Dr. Bin Xu in the Department of Biochemistry.

Enzymes as Biocatalysts

We have recently initiated a collaborative project with Dr. Ryan Senger of the Department of Biological Systems Engineering. Dr. Senger has developed an approach to identify metabolic pathways that may lead to the production of novel biofuels and other chemical intermediates using bacterial systems. These systems have the potential to be very specific for the products they produce and environmentally friendly. One of the challenges is that the enzymes that are involved in these pathways may have low activity towards the substrates on which they need to act. We will apply molecular modeling approaches to model structures of the enzymes, examine their dynamics, dock potential substrates, and predict changes in the enzyme that may improve activity towards the substrates.

  • Allen, W.J., Lemkul, J.A., and Bevan, D.R. (2009) GridMAT-MD: A Grid-based Membrane Analysis Tool for use with Molecular Dynamics. J. Comput. Chem. 30: 1952-1958.
  • Yu, H.Y., Kittur, F.S., Bevan, D.R., and Esen, A. (2009) Lysine-81 and Threonine-82 on Maize β-Glucosidase Isozyme Glu1 Are the Key Amino Acids Involved in β-Glucosidase Aggregating Factor Binding. Biochemistry 48: 2924-2932.
  • Lemkul, J.A. and Bevan, D.R. (2009) Perturbation of Membranes by the Amyloid β-Peptide — A Molecular Dynamics Study. FEBS J. 276: 3060-3075.
  • Lewis, S.N., Bassaganya-Riera, J., and Bevan, D.R. (2010) Virtual Screening as a Technique for PPAR Modulator Discovery. PPAR Research 10pp. doi:10.1155/2010/861238.
  • Lemkul, J.A. and Bevan, D.R. (2010) Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics. J. Phys. Chem. B 114: 1652-1660.
  • Lemkul, J.A. and Bevan, D.R. (2010) Destabilizing Alzheimer’s Aβ42 Protofibrils with Morin: Mechanistic Insights from Molecular Dynamics Simulations. Biochemistry 49: 3935-3946.
  • Allen, W.J., Capelluto, D.G.S., Finkielstein, C.V., and Bevan, D.R. (2010) Modeling the Relationship between the p53 C-terminal Domain and its Binding Partners Using Molecular Dynamics. J. Phys. Chem. B 141: 13201-13213.
  • Lee, S., Badieyan, S., Bevan, D.R., Herde, M., Gatz, C., and Tholl, D. (2010) Herbivore-induced and Floral Homoterpene Volatiles are Biosynthesized by a Single CytP450 Enzyme (CYP82G1) in Arabidopsis. Proc. Natl. Acad. Sci. USA 107: 21205-21210.
  • Lemkul, J.A., Allen, W.J., and Bevan, D.R. (2010) Practical Considerations for Building GROMOS- Compatible Small Molecule Topologies. J. Chem. Inf. Model. 50: 2221-2235.
  • Bassaganya-Riera, J., Guri, A.J., Lu, P., Climent, M., Carbo, A., Sobral, B.W., Horne, W.T., Lewis, S.N., Bevan, D.R., and Hontecillas, R. (2011) Abscisic Acid Regulates Inflammation via Ligand Binding Domain-Independent Activation of PPARγ. J. Biol. Chem. 286: 2504-2516.
  • Lu, P., Bevan, D.R., Lewis, S.N., Hontecillas, R., and Bassaganya-Riera, J. (2011) Molecular Modeling of Lanthionine Synthetase Component C-like Protein 2: A Potential Target for the Discovery of Novel Type 2 Diabetes Prophylactics and Therapeutics. J. Mol. Model. 17: 543-553.
  • Lemkul, J.A. and Bevan, D.R. (2011) Characterization of Interactions between PilA from Pseudomonas aeruginosa Strain K and a Model Membrane. J. Phys. Chem. B 115: 8004-8008.
  • Lemkul, J.A. and Bevan, D.R. (2011) Lipid Composition Influences the Release of Alzheimer’s Amyloid β-Peptide from Membranes. Protein Sci. 20: 1530-1545.
  • Allen, W.J. and Bevan, D.R. (2011) Steered Molecular Dynamics Simulations Reveal Important Mechanisms in Reversible Monoamine Oxidase B Inhibition. Biochemistry 50: 6441-6454.
  • Lewis, S.N., Brannan, L., Guri, A.J., Lu, P., Hontecillas, R., Bassaganya-Riera, J., and Bevan, D.R. (2011) Dietary α-Eleostearic Acid Ameliorates Experimental Inflammatory Bowel Disease in Mice by Activating Peroxisome Proliferator-Activated Receptor-γ. PLoS One 6: e24031.
  • Liu, M., Huang, Y., Zhang, L., and Bevan, D.R. (2011) A New Functional Association-Based Pro- tein Complex Prediction. 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2011): 488-494.
  • Badieyan, S., Bevan, D.R., and Zhang, C. (2012) Study and Design of Stability in GH5 Cellulases. Biotechnol. Bioeng. 109: 31-44.
  • Badieyan, S., Bevan, D.R., and Zhang, C. (2012) A Salt-Bridge Controlled by Ligand Binding Modu- lates the Hydrolysis Reaction in a GH5 Endoglucanase. Prot. Eng. Des. Selection 25: 223-233.
  • Zhou, C., Bevan, D.R., Tokuhisa, J., and Esen, A. (2012) Properties of Beta-thioglucoside Hydrolases (TGG1 and TGG2) from Leaves of Arabidopsis thaliana. Plant Sci. 191-192: 82-92.
  • Lu, P., Hontecillas, R., Horne, W.T., Carbo, A., Viladomiu, M., Pedragosa, M., Bevan, D.R., Lewis, S.N., and Bassaganya-Riera, J. (2012) Computational Modeling-based Discovery of Novel Classes of Anti-inflammatory Drugs That Target Lanthionine Synthetase C-like Protein 2. PLoS One 7: e34643.
  • Lemkul, J.A. and Bevan, D.R. (2012) Morin Inhibits the Early Stages of Amyloid β-Peptide Aggregation by Altering Tertiary and Quaternary Interactions to Produce ”Off-Pathway” Structures. Biochemistry 51: 5990-6009.
  • Lemkul, J.A. and Bevan, D.R. (2012) The Role of Molecular Simulations in the Development of In- hibitors or Amyloid β-Peptide Aggregation for the Treatment of Alzheimer’s Disease. ACS Chem. Neurosci. 3: 845-856.
  • Badieyan, S., Bevan, D.R., and Zhang, C. (2012) Probing the Active Site Chemistry of β-Glucosidases along the Hydrolysis Reaction Pathway. Biochemistry 51: 8907-8918.
  • Lemkul, J.A. and Bevan D.R. (2013) Aggregation of Alzheimer’s Amyloid β-Peptide in Biological Membranes: A Molecular Dynamics Study. Biochemistry 52: 4971-4980. 

  • Gerben, S.R., Lemkul, J.A., Brown, A.E., and Bevan, D.R. (2014) Comparing Atomistic Molecular Mechanics Force Fields for a Difficult Target: A Case Study on the Alzheimer’s Amyloid β-Peptide. J. Biomol. Struc. Dynam. 32: 1817-1832. 

  • Brown, A.M., Lemkul, J.A., Schaum, N., and Bevan, D.R. (2014) Simulations of Monomeric Amyloid β-Peptide (1-40) with Varying Solution Conditions and Oxidation State of Met35: Implications for Aggregation. Arch. Biochem. Biophys. 545: 44-52. 

  • Allen, W.J., Wiley, M.R., Myles, K.M, Adelman, Z.N., and Bevan, D.R. (2014) Steered Molecular Dynamics Identifies Critical Residues of the Nodamura Virus B2 Suppressor of RNAi. J. Mol. Model. 20: 2092 

  • Capelluto, D.G.S., Zhao, X., Lucas, A., Lemkul, J.A., Xiao, S., Fu, X., Sun, F., Bevan, D.R., and Finkielstein, C.V. (2014) Biophysical and Molecular Dynamics Studies of Phosphatidic Acid Binding by the Dvl-2 DEP Domain. Biophys. J. 106: 1101-1111. 

  • Li, M., Liu, P., Wiley, J.D., Ojani, R., Bevan, D.R., Li, J., and Zhu, J. (2014) A Steroid Receptor Coactivator Acts as the DNA-binding Partner of the Methoprene-tolerant Protein in Regulating Juvenile Hormone-Responsive Genes. Mol. Cell. Endocrinol. 394: 47-58. 

  • Fisher, A.K., Freedman, B.G., Bevan, D.R., and Senger, R.S. (2014) A Review of Metabolic and Enzymatic Engineering Strategies for Designing and Optimizing Performance of Microbial Cell Factories. Comput. Struct. Biotechnol. J. 11: 91-99. 

  • Yen, J.Y., Tanniche, I., Fisher, A.K., Gillaspy, G.E., Bevan, D.R., and Senger, R.S. (2015) Designing Metabolic Engineering Strategies with Genome-scale Metabolic Flux Modeling. Adv. Genom. Genet. 5, in press. 

  • Lewis, S.N., Garcia, Z., Hontecillas, R., Bassaganya-Riera, J., and Bevan, D.R. (2015) Pharmacophore Modeling Improves Virtual Screening for Novel Peroxisome Proliferator-Activated Receptor-gamma Ligands. J. Comput.-Aided Mol. Des., in press.
  • Lemkul, J.A., Lewis, S.N., Bassaganya-Riera, J., and Bevan, D.R. (2015) Phosphorylation of PPARgamma Affects the Collective Motions of the PPARgamma-RXRalpha-DNA Complex.  PLoS One, in press.