Bevan & Brown Lab
Bevan & Brown Lab


What We Have Published


  1. Worrell, B. L.; Brown, A. M.; Santos, W. L.; Bevan, D. R., In silico Characterization of Structural Distinctions Between Isoforms of Human and Mouse Sphingosine Kinases for Accelerating Drug Discovery. Journal of Chemical Information and Modeling. [Abstract]

  2. Cramer, N. A.; Kawecki, G.; Bevan, D. R.; Brown, A. M., Insight into Amyloid Interactions: Molecular Dynamics Simulations of Model Peptide Fragments. Biophysical Journal, 116 (3), 437a. [Abstract]

  3. Capelluto, D. G.; Xiong, W.; Littleton, E.; Jiang, L.; Brown, A. M.; Finkielstein, C., Autoinhibition Mechanism for Phosphoinositide Binding by the Endosomal Trafficking Protein Tom1. Biophysical Journal, 116 (3), 369a. [Abstract]

  4. Hollingsworth, L. R. I. V.; Lemkul, J. A.; Gandour, R. D.; Bevan, D. R.; Brown, A. M., Molecular Dynamics Simulations of gp120 and gp41 of HIV Env Provide Insights into Strain Specificity and the Role of the Membrane Environment. Biophysical Journal, 116 (3), 46a. [Abstract]


  1. Shrestha, M., Compton, K. K., Mancl, J. M., Webb, B. A., Brown, A. M., Scharf, B. E., & Schubot, F. D. (2018) Structure of the sensory domain of McpX from Sinorhizobium meliloti, the first known bacterial chemotactic sensor for quaternary ammonium compounds. Biochemical Journal, 475 (24), 3949. [Abstract]

  2. Liu, J. J., Zou, X., Gotoh, T., Brown, A. M., Jiang, L., Wisdom, E. L., Kim, J. K., & Finkielstein, C. V. (2018) Distinct control of PERIOD2 degradation and circadian rhythms by the oncoprotein and ubiquitin ligase MDM2. Science Signaling, 11 (556), eaau0715. [Abstract]

  3. Davidson, D. S., Brown, A. M., & Lemkul, J. A. (2018) Insights into Stabilizing Forces in Amyloid Fibrils of Differing Sizes from Polarizable Molecular Dynamics Simulations. Journal of Molecular Biology, 430 (20). 3819-3834. [Abstract]

  4. Ogier, A. L., Brown, A. M., Petters, J. L., Hilal, A. E., & Porter, N. D. (2018) Enhancing Collaboration Across the Research Ecosystem: Using Libraries as Hubs for Discipline-Specific Data Experts. Proceedings of the Practice and Experience on Advanced Research Computing, ACM: Pittsburgh, PA, USA; pp 1-6. [Abstract]

  5. Ricketts, H. R., Salsbury, A. M., Bevan, D. R, & Brown, A. M. (2018) Using Immersive Visualization Environments to Engage Students in Hands-On Learning. Proceedings of the Practice and Experience on Advanced Research Computing, ACM: Pittsburgh, PA, USA; pp 1-5. [Abstract]

  6. Hollingsworth, L. R., Brown, A. M., Gandour, R. D., & Bevan, D. R. (2018). Computational study of HIV gp120 as a target for polyanionic entry inhibitors: Exploiting the V3 loop region. Plos One, 13(1). doi:10.1371/journal.pone.0190658 [Abstract]

  7. Hollingsworth, L. R., Lemkul, J. A., Bevan, D. R., & Brown, A. M. (2018). HIV-1 Env gp41 Transmembrane Domain Dynamics are Modulated by Lipid, Water, and Ion Interactions. Biophysical Journal, 115 (1), 84-94. [Abstract]


  1. Hollingsworth IV, L. R., Brown, A. M., & Bevan, D. R. (2017, July). Utilizing Computational Techniques to Accelerate Discovery in Peanut Allergenicity: A Case Study. In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact (p. 73). ACM. [Abstract]

  2. Brown, A. M., & Bevan, D. R. (2017, July). Introducing Protein 3-D Visualization Software to Freshman Undergraduate Students: Making Connections and Building Skills. In Proceedings of the Practice and Experience in Advanced Research Computing 2017 on Sustainability, Success and Impact (p. 51). ACM. [Abstract]

  3. Childress, E. S., Kharel, Y., Brown, A. M., Bevan, D. R., Lynch, K. R., & Santos, W. L. (2017). Transforming Sphingosine Kinase 1 Inhibitors into Dual and Sphingosine Kinase 2 Selective Inhibitors: Design, Synthesis, and in Vivo Activity. Journal of Medicinal Chemistry, 60(9), 3933-3957. [Abstract]

  4. Turner, S. G., Brown, A. M., & Jarrott, S. E. (2017). For Students, By Students: Service-Learner Involvement in the Development of Visiting Kits to Facilitate Student Interactions with Old Adults. Journal of Intergenerational Relationships, 15(2), 181-187. [Abstract]

  5. Brown, A. M., & Bevan, D. R. (2017). Influence of Sequence and Lipid Type on Membrane Perturbation by Human and Rat Amyloid β-Peptide (1-42). Biophysical Journal, 108(2). doi:10.1016/j.bpj.2014.11.1417

  6. Velander, P., Wu, L., Henderson, F., Zhang, S., Bevan, D.R., and Xu, B. (2017) Natural Product-Based Amyloid Inhibitors. Biochem. Pharmacol. 139: 40-55. [Abstract]


  1. Wu, L., Velander, P., Ray, K., Brown, A., Helm, R., Bevan, D., & Xu, B. (2016, October). Discovery and Mechanisms of Small Molecule Inhibitors against Amylin Amyloidosis in the pancreas and the brain. In Protein Science (Vol. 25, pp. 18-18). Wiley-Blackwell.

  2. Velander, P. W., Wu, L., Ray, K., Zhang, S., Helm, R., Bevan, D., & Xu, B. (2017). Rosmarinic acid, a catechol-containing natural product, potently inhibits amylin amyloidosis. The FASEB Journal, 31(1 Supplement), 914-5. [Abstract]

  3. Brown, A., & Bevan, D. (2016). Molecular Dynamics Simulations of Amyloid β -Peptide (1-42): Tetramer Formation and Membrane Interactions. Biophysical Journal, 111(5), 937-949. doi:10.1016/j.bpj.2016.08.001 [Abstract]

  4. Brown, A. M., Lewis, S. N., & Bevan, D. R. (2016). Development of a structured undergraduate research experience: Framework and implications. Biochemistry and Molecular Biology Education, 44(5), 463-474. [Abstract]

  5. Brown, A., Polys, N., Bevan, D., & Mohammed, A. (2016, July). Insights into Alzheimer's Disease: Molecular Dynamics (MD) Simulations of Peptide-Membrane Interactions. In Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale (p. 59). ACM. [Abstract]

  6. Miller, D. V., Brown, A. M., Xu, H., Bevan, D. R., & White, R. H. (2016). Purine salvage in Methanocaldococcus jannaschii: Elucidating the role of a conserved cysteine in adenine deaminase. Proteins: Structure, Function, and Bioinformatics, 84(6), 828-840. doi:10.1002/prot.25033 [Abstract]

  7. Brown, A. M. (2016). Insights into Mechanisms of Amyloid Toxicity: Molecular Dynamics Simulations of the Amyloid andbeta-peptide (Aandbeta) and Islet Amyloid Polypeptide (IAPP) (Doctoral dissertation, Virginia Tech). [Abstract]

  8. Miller, D.V., Brown, A.M., Xu, H., Bevan, D.R., and White, R.H. (2016) "Elucidating the Role of a Conserved Cysteine in Adenine Deaminase." Proteins. In press. doi: 10.1002/prot.25033

  9. Congdon, M.D., Kharel, Y., Brown, A.M., Lewis, S.N., Thorpe, S.B., Bevan, D.R., Lynch, K.R., and Santos, W. L. (2016) "Structure-activity relationship studies and molecular modeling of naphthalene-based sphingosine kinase 2 inhibitors" J. Med. Chem. Letters. 7 (3), 229-234. (Cover Art for March 2016)[Abstract]

  10. Khandaker, M.S.K., Dudek, D.M., Dillard, D.A., Beers, E.P., and Bevan, D.R. (2016) Molecular Modeling of the Elastomeric Properties of Repeating Units and Building Blocks of Resilin, a Disordered Elastic Protein. J. Mech. Behav. Biomed. Mat. 61: 110-121. [Abstract]


  1. Zhao, X., Xiao, S., Berk, S., Brown, A. M., Bevan, D. R., Armstrong, G., & Capelluto, D. G. (2015). Structural Basis of Phosphoinositide (PIP) Recognition by the TIRAP PIP-Binding Motif. Biophysical Journal, 108(2), 93a. [Abstract]

  2. Lemkul, J.A., Lewis, S.N., Bassaganya-Riera, J., and Bevan, D.R. (2015) Phosphorylation of PPARγ Affects the Collective Motions of the PPARγ-RXRα-DNA Complex. PLoS One May 8;10(5):e0123984. [Abstract]

  3. Songtawee, N., Bevan, D.R., and Choowongkomon, K. (2015) Molecular Dynamics of the Asymmetric Dimers of EGFR: Simulations on the Active and Inactive Conformations of the Kinase Domain. J. Mol. Graph. Model. 58: 16-29. [Abstract]

  4. 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. 29: 421-439. [Abstract]

  5. 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: 93-105. [Abstract]


  1. 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. [Abstract]

  2. 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 [Abstract]

  3. 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. [Abstract]

  4. 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. [Abstract]

  5. 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. [Abstract]


  1. Gerben, S.R., Lemkul, J.A., Brown, A.M., and Bevan, D.R. (2013) Comparing Atomistic Molecular Mechanics Force Fields for a Difficult Target: A Case Study on the Alzheimer's Amyloid β-Peptide. J. Biomol. Struct. Dyn. 1-16. [Abstract]

  2. Lemkul, J.A. and Bevan, D.R. (2013) Aggregation of Alzheimer's Amyloid β-Peptide in Biological Membranes: A Molecular Dynamics Study. Biochemistry 52 (29): 4971-4980. [Abstract]


  1. Lemkul, J.A. and Bevan, D.R. (2012) The Role of Molecular Simulations in the Development of Inhibitors of Amyloid β-Peptide Aggregation for the Treatment of Alzheimer's Disease. ACS Chem. Neurosci. 3 (11): 845-856. [Abstract] [Cover Art]

  2. Badieyan, S., Bevan, D.R., and Zhang, C. (2012) Probing the Active Site Chemistry of β-Glucosidases along the Hydrolysis Reaction Pathway. Biochemistry 51 (44): 8907-8918. [Abstract]

  3. 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 (30): 5990-6009. [Abstract]

  4. Badieyan, S., Bevan, D.R., and Zhang, C.M. (2012) A salt-bridge controlled by ligand binding modulates the hydrolysis reaction in a GH5 endoglucanase. Protein Eng. Des. Sel.25 (5): 223-233. [Abstract]

  5. Badieyan, S., Bevan, D.R., and Zhang, C.M. (2012) Study and design of stability in GH5 cellulases. Biotechnol. Bioeng. 102 (1): 31-44. [Abstract]

  6. 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. [Abstract]

  7. 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. [Abstract]


  1. 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 (8): e24031. [Open Access Full Text]

  2. Lemkul, J.A. and Bevan, D.R. (2011) Lipid composition influences the release of Alzheimer's amyloid β-peptide from membranes. Protein Sci. 20 (9): 1530-1545. [Abstract]

  3. Allen, W.J. and Bevan, D.R. (2011) Steered Molecular Dynamics Simulations Reveal Important Mechanisms in Reversible Monoamine Oxidase B Inhibition. Biochemistry 50 (29): 6441-6454. [Abstract].

  4. 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 (24): 8004-8008. [Abstract].

  5. Grimm, M.L., Allen, W.J., Finn, M., Castagnoli, Jr., N., and Tanko, J.M. (2011) Reaction of benzophenone triplet with aliphatic amines. What a potent neurotoxin can tell us about the reaction mechanism. Bioorg. Med. Chem. 19 (4): 1458-1463. [Abstract]

  6. 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 (3): 543-553. [Abstract]

  7. Bassaganya-Riera, J., Guri, A.J., Lu, P., Climent, M., Carbo, A., Sobral, B.W., Evans, C., Horne, W.T., Lewis, S.N., Bevan, D.R., and Hontecillas, R. (2011) Abscisic acid Regulates Inflammation via Ligand-Binding Domain-Independent Activation of PPAR-γ. J. Biol. Chem. 286 (4): 2504-2516. [Abstract]


  1. 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 (12): 2221-2235. [Abstract]

  2. 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 P450 enzyme (CYP82G1) in Arabidopsis. Proc. Natl. Acad. Sci. USA 107 (49): 21205-21210. [Abstract]

  3. Mehere, P., Han, Q., Lemkul, J.A., Vavricka, C.J., Robinson, H., Bevan, D.R., and Li, J. (2010) Tyrosine Aminotransferase: biochemical and structural properties and molecular dynamics simulations. Protein & Cell 1 (11): 1023-1032. [Abstract]

  4. 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 114 (41): 13201-13213. [Abstract]

  5. Lemkul, J.A. and Bevan, D.R. (2010) Destabilizing Alzheimer's Aβ42 Protofibrils with Morin: Mechanistic Insights from Molecular Dynamics Simulations. Biochemistry 49 (18): 3935-3946. [Abstract]

  6. Kittur, F.S., Yu, H.Y., Bevan, D.R., and Esen, A. (2010) Deletion of the N-terminal dirigent domain in maize β-glucosidase aggregating factor and its homolog sorghum lectin dramatically alters the sugar-specificities of their lectin domains. Plant Physiol. Biochem. 48 (8): 731-734. [Abstract]

  7. Lemkul, J.A. and Bevan, D.R. (2010) Assessing the Stability of Alzheimer's Amyloid Protofibrils Using Molecular Dynamics. J. Phys. Chem. B 114 (4): 1652-1660. [Abstract]

  8. Lewis, S.N., Bassaganya-Riera, J., and Bevan, D.R. (2010) Virtual screening as a technique for PPAR modulator discovery. PPAR Research 2010, Article ID 861238: 10 pp. [Open Access Full Text]


  1. 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 (12): 1952-1958. [Abstract]

  2. Lemkul, J.A. and Bevan, D.R. (2009) Perturbation of membranes by the amyloid β-peptide - a molecular dynamics study. FEBS J. 276 (11): 3060-3075. [Abstract]

  3. 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 (13): 2924-2932. [Abstract]


  1. Lemkul, J.A. and Bevan, D.R. (2008) A Comparative Molecular Dynamics Analysis of the Amyloid β-Peptide in a Lipid Bilayer. Arch. Biochem. Biophys. 470 (1): 54-63. [Abstract]


  1. Harkcom, W.T. and Bevan, D.R. (2007) Molecular docking of inhibitors into monoamine oxidase B. Biochem. Biophys. Res. Commun. 360 (2): 401-406. [Abstract]

  2. Ahn, Y.O., Zheng, M., Winkel, B., Bevan, D. R., Esen, A., Shin-Han, S., Benson, J., Peng, H., Miller, J.T., Cheng, C., Poulton, J.E., and Shih, M. (2007) Functional genomic analysis of Arabidopsis thaliana Glycoside Hydrolase Family 35. Phytochem. 68 (11): 1510-1520. [Abstract]

  3. Kittur, F.S., Lalgondar, M., Yu, H.Y., Bevan, D.R., and Esen, A. (2007) Maize β-glucosidase-aggregating factor is a polyspecific jacalin-related chimeric lectin, and its lectin domain is responsible for β-glucosidase aggregation. J. Biol. Chem. 282 (10): 7299-7311. [Abstract]


  1. Ruscio, J.Z. and Onufriev, A. (2006) A computational study of nucleosomal DNA flexibility. Biophys. J. 91: 4121-4132. [Abstract]

  2. Dana, C.D., Bevan, D.R., and Winkel, B.S.J. (2006) Molecular Modeling of the Effects of Mutant Alleles on Chalcone Synthase Protein Structure. J. Mol. Model. 12 (6): 905-914.


  1. Bevan, D.R., Garst, J.F., Osborne, C.K., and Sims, A.M. (2005) Application of Molecular Modeling to Analysis of Inhibition of Kinesin Motor Proteins of the BimC Subfamilty by Monastrol and Related Compounds. Chem. Biodiversity 2 (11): 1525-1532. [Abstract]

  2. Verdoucq, L., Moriniere, J., Bevan, D.R., Esen, A., Vasella, A., Henrissat, B., and Czjzek, M. (2004) Structural determinants of substrate specificity in family 1 β-glucosidases: Novel insights from the crystal structure of sorghum dhurrinase-1, a plant β-glucosidase with strict specificity, in complex with its natural substrate. J. Biol. Chem. 279 (30): 31796-31803. [Abstract]


  1. Xu, Z., Escamilla-Trevino, L.L., Zeng, L., Lalgondar, M., Bevan, D.R., Winkel, B.S.J., Mohamed, A., Cheng, C.-L., Shih, M.-C., Poulton, J.E., and Esen, A. (2004) Functional Genomic Analysis of Arabidopsis thaliana Glycoside Hydrolase Family 1. Plant Mol. Biol. 55 (3): 343-367.


  1. Verdoucq, L., Czjzek, M., Moriniere, J., Bevan, D.R., and Esen, A. (2003) Mutational and Structural Analysis of Aglycone Specificity in Maize and Sorghum β-Glucosidases. J. Biol. Chem. 278 (27): 25055-25062. [Abstract]


  1. Bevan, D.R., Li, L., Pedersen, L.G., and Darden, T.A. (2000) Molecular Dynamics Simulations of the d(CCAACGTTGG)2 Decamer. Influence of the Crystal Environment. Biophys. J. 78: 668-682. [Abstract]

  2. Yeh, D.C., Thorsteinsson, M.V., Bevan, D.R., Potts, M., and La Mar, G.N. (2000) Solution 1H NMR Study of the Heme Cavity and Folding Topology of the Abbreviated Chain 118-Residue Globin from the Cyanobacterium Nostoc commune. Biochemistry 39: 1389-1399. [Abstract]

  3. Cicek, M., Blanchard, D.J., Bevan, D.R., and Esen, A. (2000) The Aglycone Specificity Determining Sites are Different in 2,4-Dihydroxy-7-Methoxy-1,4-Benzoxzin-3-One (DIMBOA)-Glucosidase (Maize β-Glucosidase) and dhurrinase (Sorghum β-Glucosidase). J. Biol. Chem. 275: 20002-20011. [Abstract]

  4. Czjzek, M., Cicek, M., Zamboni. V., Bevan, D.R., Henrissat, B., and Esen, A. (2000) The Mechanism of Substrate (Aglycone) specificity in β-Glucosidase is Revealed by Crystal Structures of Mutant Maize β-Glucosidase-DIMBOA, -DIMBOAGlc, and -Dhurrin Complexes. Proc. Natl. Acad. Sci. USA 97: 13555-13560. [Abstract]


  1. Thorsteinsson, M.V., Bevan, D.R., Potts, M., Dou, Y., Eich, R.F., Hargrove, M.S., Gibson, Q.H., and Olson, J.S. (1999) A cyanobacterial hemoglobin with unusual ligand binding kinetics and stability properties. Biochemistry 38: 2117-2126. [Abstract]