2016

  1. Brown, A.M., Lewis, S.N., and Bevan, D.R. (2016) "Development of a Structure Undergraduate Research Experience: Framework and Implications". Biochem. Mol. Biol. Educ. Revision accepted.

  2. 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

  3. 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]


  4. ACS Med Chem Letters, March 2016 issue
    2014

  5. 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]

  6. 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]

  7. 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]

  8. 2013

  9. 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]

  10. 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]

  11. 2012

  12. 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]

  13. 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]

  14. 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]

  15. 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]

  16. 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]

  17. 2011

  18. 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]

  19. 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]

  20. 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].

  21. 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].

  22. 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]

  23. 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]

  24. 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]

  25. 2010

  26. 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]

  27. 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]

  28. 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]

  29. 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]

  30. 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]

  31. 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]

  32. 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]

  33. 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]

  34. 2009

  35. 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]

  36. 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]

  37. 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]

  38. 2008

  39. 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]

  40. 2007

  41. 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]

  42. 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]

  43. 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]

  44. 2006

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

  46. 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.

  47. 2005

  48. 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]

  49. 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]

  50. 2004

  51. 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.

  52. 2003

  53. 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]

  54. 2000

  55. 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]

  56. 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]

  57. 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]

  58. 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]

  59. 1999

  60. 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]