Bevan & Brown Lab
Bevan & Brown Lab

Publications

What We Have Published

2018

  1. 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]
  2. Hollingsworth, L. R., Lemkul, J., Bevan, D. R., & Brown, A. M. (2018). HIV-1 Env gp41 Transmembrane Domain Dynamics are Modulated by Lipid, Water, and Ion Interactions. BioRxiv. doi:10.1101/292326 [Abstract]
  3. Liu, J., Zou, X., Gotoh, T., Brown, A. M., Jiang, L., Kim, J. K., & Finkielstein, C. V. (2018). Distinct control of PERIOD2 degradation and circadian rhythms by the oncoprotein MDM2. BioRxiv. doi:10.1101/286708

2017 

  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 Chemistry60(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 Relationships15(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]

2016 

  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 Journal31(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]

2015

  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 Journal108(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] 

2014 

  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] 

2013 

  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]

2012 

  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] 

2011 

  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]

2010 

  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 ArabidopsisProc. 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]

2009 

  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]

2008 

  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] 

2007 

  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] 

2006 

  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.

2005 

  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] 

2004 

  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.

2003 

  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] 

2000 

  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] 

1999 

  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]