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David R Bevan - Publications

Affiliations: 
Biochemistry Virginia Polytechnic Institute and State University, Blacksburg, VA, United States 
Area:
Biochemistry, computational chemistry
Website:
https://www.biochem.vt.edu/people/faculty/bevan-david.html
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64 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Pashikanti S, Foster DJ, Kharel Y, Brown AM, Bevan DR, Lynch KR, Santos WL. Sphingosine Kinase 2 Inhibitors: Rigid Aliphatic Tail Derivatives Deliver Potent and Selective Analogues. Acs Bio & Med Chem Au. 2: 469-489. PMID 36281302 DOI: 10.1021/acsbiomedchemau.2c00017  0.643
2022 King KM, Bevan DR, Brown AM. Molecular Dynamics Simulations Indicate Aromaticity as a Key Factor in the Inhibition of IAPP Aggregation. Acs Chemical Neuroscience. 13: 1615-1626. PMID 35587203 DOI: 10.1021/acschemneuro.2c00025  0.669
2022 Kawecki GE, King KM, Cramer NA, Bevan DR, Brown AM. Simulations of cross-amyloid aggregation of amyloid-β and islet amyloid polypeptide fragments. Biophysical Journal. PMID 35538665 DOI: 10.1016/j.bpj.2022.05.007  0.652
2022 Sharp AK, Newman D, Libonate G, Borns-Stern M, Bevan DR, Brown AM, Anandakrishnan R. Biophysical insights into OR2T7: Investigation of a potential prognostic marker for glioblastoma. Biophysical Journal. PMID 35538663 DOI: 10.1016/j.bpj.2022.05.009  0.621
2021 Wu L, Velander P, Brown AM, Wang Y, Liu D, Bevan DR, Zhang S, Xu B. Rosmarinic Acid Potently Detoxifies Amylin Amyloid and Ameliorates Diabetic Pathology in a Transgenic Rat Model of Type 2 Diabetes. Acs Pharmacology & Translational Science. 4: 1322-1337. PMID 34423269 DOI: 10.1021/acsptsci.1c00028  0.615
2020 Congdon M, Fritzemeier RG, Kharel Y, Brown AM, Serbulea V, Bevan DR, Lynch KR, Santos WL. Probing the substitution pattern of indole-based scaffold reveals potent and selective sphingosine kinase 2 inhibitors. European Journal of Medicinal Chemistry. 212: 113121. PMID 33445156 DOI: 10.1016/j.ejmech.2020.113121  0.631
2020 Li H, Sibley CD, Kharel Y, Huang T, Brown AM, Wonilowicz LG, Bevan DR, Lynch KR, Santos WL. Lipophilic tail modifications of 2-(hydroxymethyl)pyrrolidine scaffold reveal dual sphingosine kinase 1 and 2 inhibitors. Bioorganic & Medicinal Chemistry. 30: 115941. PMID 33385956 DOI: 10.1016/j.bmc.2020.115941  0.638
2020 Sibley CD, Morris EA, Kharel Y, Brown AM, Bevan DR, Lynch KR, Santos WL. Discovery of a Small Side Cavity in Sphingosine Kinase 2 that Enhances Inhibitor Potency and Selectivity. Journal of Medicinal Chemistry. PMID 31895563 DOI: 10.1021/Acs.Jmedchem.9B01508  0.651
2019 Hilu KW, Friend SA, Vallanadu V, Brown AM, Hollingsworth LR, Bevan DR. Molecular evolution of genes encoding allergen proteins in the peanuts genus Arachis: Structural and functional implications. Plos One. 14: e0222440. PMID 31675366 DOI: 10.1371/Journal.Pone.0222440  0.627
2019 Worrell BL, Brown AM, Santos WL, Bevan DR. In silico Characterization of Structural Distinctions Between Isoforms of Human and Mouse Sphingosine Kinases for Accelerating Drug Discovery. Journal of Chemical Information and Modeling. PMID 30844267 DOI: 10.1021/Acs.Jcim.8B00931  0.669
2019 Hollingsworth LR, Lemkul JA, Gandour RD, Bevan DR, Brown AM. 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: 46a. DOI: 10.1016/J.Bpj.2018.11.293  0.735
2019 Cramer NA, Kawecki G, Bevan DR, Brown AM. Insight into Amyloid Interactions: Molecular Dynamics Simulations of Model Peptide Fragments Biophysical Journal. 116: 437a. DOI: 10.1016/J.Bpj.2018.11.2353  0.672
2018 Hollingsworth LR, Lemkul JA, Bevan DR, Brown AM. HIV-1 Env gp41 Transmembrane Domain Dynamics Are Modulated by Lipid, Water, and Ion Interactions. Biophysical Journal. 115: 84-94. PMID 29972814 DOI: 10.1016/J.Bpj.2018.05.022  0.75
2018 Hollingsworth LR, Brown AM, Gandour RD, Bevan DR. Computational study of HIV gp120 as a target for polyanionic entry inhibitors: Exploiting the V3 loop region. Plos One. 13: e0190658. PMID 29346393 DOI: 10.1371/Journal.Pone.0190658  0.657
2017 Childress ES, Kharel Y, Brown AM, Bevan DR, Lynch KR, Santos WL. Transforming Sphingosine Kinase 1 Inhibitors into Dual and Sphingosine Kinase 2 Selective Inhibitors: Design, Synthesis, and In Vivo Activity. Journal of Medicinal Chemistry. PMID 28406646 DOI: 10.1021/Acs.Jmedchem.7B00233  0.644
2017 Velander P, Wu L, Henderson F, Zhang S, Bevan DR, Xu B. Natural Product-Based Amyloid Inhibitors. Biochemical Pharmacology. PMID 28390938 DOI: 10.1016/J.Bcp.2017.04.004  0.379
2016 Brown AM, Bevan DR. Influence of sequence and lipid type on membrane perturbation by human and rat amyloid β-peptide (1-42). Archives of Biochemistry and Biophysics. PMID 27884599 DOI: 10.1016/J.Bpj.2014.11.1417  0.677
2016 Brown AM, Bevan DR. Molecular Dynamics Simulations of Amyloid β-Peptide (1-42): Tetramer Formation and Membrane Interactions. Biophysical Journal. 111: 937-49. PMID 27602722 DOI: 10.1016/J.Bpj.2016.08.001  0.696
2016 Brown AM, Lewis SN, Bevan DR. Development of a structured undergraduate research experience: Framework and implications. Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology. PMID 27124101 DOI: 10.1002/Bmb.20975  0.737
2016 Miller DV, Brown AM, Xu H, Bevan DR, White RH. Purine Salvage in Methanocaldococcus jannaschii: Elucidating the Role of a Conserved Cysteine in Adenine Deaminase. Proteins. PMID 26990095 DOI: 10.1002/Prot.25033  0.644
2016 Congdon MD, Kharel Y, Brown AM, Lewis SN, Bevan DR, Lynch KR, Santos WL. Structure-Activity Relationship Studies and Molecular Modeling of Naphthalene-Based Sphingosine Kinase 2 Inhibitors. Acs Medicinal Chemistry Letters. 7: 229-34. PMID 26985306 DOI: 10.1021/Acsmedchemlett.5B00304  0.778
2016 Khandaker MS, Dudek DM, Beers EP, Dillard DA, Bevan DR. Molecular modeling of the elastomeric properties of repeating units and building blocks of resilin, a disordered elastic protein. Journal of the Mechanical Behavior of Biomedical Materials. 61: 110-121. PMID 26851528 DOI: 10.1016/J.Jmbbm.2016.01.017  0.329
2015 Lemkul JA, Lewis SN, Bassaganya-Riera J, Bevan DR. Phosphorylation of PPARγ Affects the Collective Motions of the PPARγ-RXRα-DNA Complex. Plos One. 10: e0123984. PMID 25954810 DOI: 10.1371/Journal.Pone.0123984  0.765
2015 Songtawee N, Bevan DR, Choowongkomon K. Molecular dynamics of the asymmetric dimers of EGFR: simulations on the active and inactive conformations of the kinase domain. Journal of Molecular Graphics & Modelling. 58: 16-29. PMID 25805329 DOI: 10.1016/J.Jmgm.2015.03.002  0.349
2015 Lewis SN, Garcia Z, Hontecillas R, Bassaganya-Riera J, Bevan DR. Pharmacophore modeling improves virtual screening for novel peroxisome proliferator-activated receptor-gamma ligands. Journal of Computer-Aided Molecular Design. 29: 421-39. PMID 25616366 DOI: 10.1007/S10822-015-9831-X  0.7
2015 Zhao X, Xiao S, Berk S, Brown AM, Bevan DR, Armstrong G, Capelluto DG. Structural Basis of Phosphoinositide (PIP) Recognition by the TIRAP PIP-Binding Motif Biophysical Journal. 108: 93a. DOI: 10.1016/J.Bpj.2014.11.539  0.683
2014 Li M, Liu P, Wiley JD, Ojani R, Bevan DR, Li J, Zhu J. A steroid receptor coactivator acts as the DNA-binding partner of the methoprene-tolerant protein in regulating juvenile hormone response genes. Molecular and Cellular Endocrinology. 394: 47-58. PMID 25004255 DOI: 10.1016/J.Mce.2014.06.021  0.308
2014 Capelluto DG, Zhao X, Lucas A, Lemkul JA, Xiao S, Fu X, Sun F, Bevan DR, Finkielstein CV. Biophysical and molecular-dynamics studies of phosphatidic acid binding by the Dvl-2 DEP domain. Biophysical Journal. 106: 1101-11. PMID 24606934 DOI: 10.1016/J.Bpj.2014.01.032  0.655
2014 Allen WJ, Wiley MR, Myles KM, Adelman ZN, Bevan DR. Steered molecular dynamics identifies critical residues of the Nodamura virus B2 suppressor of RNAi Journal of Molecular Modeling. 20: 2092. PMID 24549790 DOI: 10.1007/S00894-014-2092-0  0.303
2014 Brown AM, Lemkul JA, Schaum N, Bevan DR. Simulations of monomeric amyloid β-peptide (1-40) with varying solution conditions and oxidation state of Met35: implications for aggregation. Archives of Biochemistry and Biophysics. 545: 44-52. PMID 24418316 DOI: 10.1016/J.Abb.2014.01.002  0.758
2014 Gerben SR, Lemkul JA, Brown AM, Bevan DR. Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer's amyloid β-peptide. Journal of Biomolecular Structure & Dynamics. 32: 1817-32. PMID 24028075 DOI: 10.1080/07391102.2013.838518  0.765
2013 Lemkul JA, Bevan DR. Aggregation of Alzheimer's amyloid β-peptide in biological membranes: a molecular dynamics study. Biochemistry. 52: 4971-80. PMID 23855340 DOI: 10.1021/Bi400562X  0.674
2012 Lemkul JA, Bevan DR. The role of molecular simulations in the development of inhibitors of amyloid β-peptide aggregation for the treatment of Alzheimer's disease. Acs Chemical Neuroscience. 3: 845-56. PMID 23173066 DOI: 10.1021/Cn300091A  0.679
2012 Badieyan S, Bevan DR, Zhang C. Probing the active site chemistry of β-glucosidases along the hydrolysis reaction pathway. Biochemistry. 51: 8907-18. PMID 23043218 DOI: 10.1021/Bi300675X  0.309
2012 Lemkul JA, Bevan DR. 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. PMID 22762350 DOI: 10.1021/Bi300113X  0.685
2012 Lu P, Hontecillas R, Horne WT, Carbo A, Viladomiu M, Pedragosa M, Bevan DR, Lewis SN, Bassaganya-Riera J. Computational modeling-based discovery of novel classes of anti-inflammatory drugs that target lanthionine synthetase C-like protein 2. Plos One. 7: e34643. PMID 22509338 DOI: 10.1371/Journal.Pone.0034643  0.703
2012 Badieyan S, Bevan DR, Zhang C. A salt-bridge controlled by ligand binding modulates the hydrolysis reaction in a GH5 endoglucanase. Protein Engineering, Design & Selection : Peds. 25: 223-33. PMID 22419828 DOI: 10.1093/Protein/Gzs010  0.327
2012 Badieyan S, Bevan DR, Zhang C. Study and design of stability in GH5 cellulases. Biotechnology and Bioengineering. 109: 31-44. PMID 21809329 DOI: 10.1002/Bit.23280  0.329
2011 Lewis SN, Brannan L, Guri AJ, Lu P, Hontecillas R, Bassaganya-Riera J, Bevan DR. Dietary α-eleostearic acid ameliorates experimental inflammatory bowel disease in mice by activating peroxisome proliferator-activated receptor-γ. Plos One. 6: e24031. PMID 21904603 DOI: 10.1371/Journal.Pone.0024031  0.698
2011 Lemkul JA, Bevan DR. Lipid composition influences the release of Alzheimer's amyloid β-peptide from membranes. Protein Science : a Publication of the Protein Society. 20: 1530-45. PMID 21692120 DOI: 10.1002/Pro.678  0.674
2011 Allen WJ, Bevan DR. Steered molecular dynamics simulations reveal important mechanisms in reversible monoamine oxidase B inhibition Biochemistry. 50: 6441-6454. PMID 21682347 DOI: 10.1021/Bi200446W  0.377
2011 Lemkul JA, Bevan DR. Characterization of interactions between PilA from Pseudomonas aeruginosa strain K and a model membrane. The Journal of Physical Chemistry. B. 115: 8004-8. PMID 21630674 DOI: 10.1021/Jp202217F  0.649
2011 Bassaganya-Riera J, Guri AJ, Lu P, Climent M, Carbo A, Sobral BW, Horne WT, Lewis SN, Bevan DR, Hontecillas R. Abscisic acid regulates inflammation via ligand-binding domain-independent activation of peroxisome proliferator-activated receptor gamma. The Journal of Biological Chemistry. 286: 2504-16. PMID 21088297 DOI: 10.1074/Jbc.M110.160077  0.699
2011 Lu P, Bevan DR, Lewis SN, Hontecillas R, Bassaganya-Riera J. Molecular modeling of lanthionine synthetase component C-like protein 2: a potential target for the discovery of novel type 2 diabetes prophylactics and therapeutics. Journal of Molecular Modeling. 17: 543-53. PMID 20512604 DOI: 10.1007/S00894-010-0748-Y  0.715
2010 Mehere P, Han Q, Lemkul JA, Vavricka CJ, Robinson H, Bevan DR, Li J. Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations. Protein & Cell. 1: 1023-32. PMID 21153519 DOI: 10.1007/S13238-010-0128-5  0.649
2010 Lemkul JA, Allen WJ, Bevan DR. Practical considerations for building GROMOS-compatible small-molecule topologies Journal of Chemical Information and Modeling. 50: 2221-2235. PMID 21117688 DOI: 10.1021/Ci100335W  0.617
2010 Allen WJ, Capelluto DG, Finkielstein CV, Bevan DR. Modeling the relationship between the p53 C-terminal domain and its binding partners using molecular dynamics. The Journal of Physical Chemistry. B. 114: 13201-13. PMID 20873738 DOI: 10.1021/Jp1011445  0.311
2010 Lemkul JA, Bevan DR. Destabilizing Alzheimer's Abeta(42) protofibrils with morin: mechanistic insights from molecular dynamics simulations. Biochemistry. 49: 3935-46. PMID 20369844 DOI: 10.1021/Bi1000855  0.669
2010 Lemkul JA, Bevan DR. Assessing the stability of Alzheimer's amyloid protofibrils using molecular dynamics. The Journal of Physical Chemistry. B. 114: 1652-60. PMID 20055378 DOI: 10.1021/Jp9110794  0.67
2010 Lewis SN, Bassaganya-Riera J, Bevan DR. Virtual Screening as a Technique for PPAR Modulator Discovery. Ppar Research. 2010: 861238. PMID 19746174 DOI: 10.1155/2010/861238  0.695
2009 Lemkul JA, Bevan DR. Perturbation of membranes by the amyloid beta-peptide--a molecular dynamics study. The Febs Journal. 276: 3060-75. PMID 19490108 DOI: 10.1111/J.1742-4658.2009.07024.X  0.663
2009 Yu HY, Kittur FS, Bevan DR, Esen A. Lysine-81 and threonine-82 on maize beta-glucosidase isozyme Glu1 are the key amino acids involved in beta-glucosidase aggregating factor binding. Biochemistry. 48: 2924-32. PMID 19227973 DOI: 10.1021/Bi900012H  0.309
2009 Allen WJ, Lemkul JA, Bevan DR. GridMAT-MD: A grid-based membrane analysis tool for use with molecular dynamics Journal of Computational Chemistry. 30: 1952-1958. PMID 19090582 DOI: 10.1002/Jcc.21172  0.642
2009 Kittur FS, Yu HY, Bevan DR, Esen A. Homolog of the maize beta-glucosidase aggregating factor from sorghum is a jacalin-related GalNAc-specific lectin but lacks protein aggregating activity. Glycobiology. 19: 277-87. PMID 19056785 DOI: 10.1093/Glycob/Cwn132  0.346
2008 Pathange LP, Bevan DR, Zhang C. Quantifying protein microstructure and electrostatic effects on the change in Gibbs free energy of binding in immobilized metal affinity chromatography. Analytical Chemistry. 80: 1628-40. PMID 18229947 DOI: 10.1021/Ac7023188  0.331
2008 Lemkul JA, Bevan DR. A comparative molecular dynamics analysis of the amyloid beta-peptide in a lipid bilayer. Archives of Biochemistry and Biophysics. 470: 54-63. PMID 18053791 DOI: 10.1016/J.Abb.2007.11.004  0.669
2007 Harkcom WT, Bevan DR. Molecular docking of inhibitors into monoamine oxidase B. Biochemical and Biophysical Research Communications. 360: 401-6. PMID 17597580 DOI: 10.1016/J.Bbrc.2007.06.055  0.305
2007 Kittur FS, Lalgondar M, Yu HY, Bevan DR, Esen A. Maize beta-glucosidase-aggregating factor is a polyspecific jacalin-related chimeric lectin, and its lectin domain is responsible for beta-glucosidase aggregation. The Journal of Biological Chemistry. 282: 7299-311. PMID 17210577 DOI: 10.1074/Jbc.M607417200  0.312
2006 Pathange LP, Bevan DR, Larson TJ, Zhang C. Correlation between protein binding strength on immobilized metal affinity chromatography and the histidine-related protein surface structure. Analytical Chemistry. 78: 4443-9. PMID 16808452 DOI: 10.1021/Ac060217X  0.312
2006 Dana CD, Bevan DR, Winkel BS. Molecular modeling of the effects of mutant alleles on chalcone synthase protein structure. Journal of Molecular Modeling. 12: 905-14. PMID 16575575 DOI: 10.1007/S00894-005-0071-1  0.353
2005 Bevan DR, Garst JF, Osborne CK, Sims AM. Application of molecular modeling to analysis of inhibition of kinesin motor proteins of the BimC subfamily by monastrol and related compounds. Chemistry & Biodiversity. 2: 1525-32. PMID 17191952 DOI: 10.1002/Cbdv.200590124  0.371
2003 Verdoucq L, Czjzek M, Moriniere J, Bevan DR, Esen A. Mutational and structural analysis of aglycone specificity in maize and sorghum beta-glucosidases. The Journal of Biological Chemistry. 278: 25055-62. PMID 12684498 DOI: 10.1074/Jbc.M301978200  0.3
2001 Czjzek M, Cicek M, Zamboni V, Burmeister WP, Bevan DR, Henrissat B, Esen A. Crystal structure of a monocotyledon (maize ZMGlu1) beta-glucosidase and a model of its complex with p-nitrophenyl beta-D-thioglucoside. The Biochemical Journal. 354: 37-46. PMID 11171077 DOI: 10.1042/0264-6021:3540037  0.302
2000 Cicek M, Blanchard D, Bevan DR, Esen A. The aglycone specificity-determining sites are different in 2, 4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA)-glucosidase (Maize beta -glucosidase) and dhurrinase (Sorghum beta -glucosidase). The Journal of Biological Chemistry. 275: 20002-11. PMID 10748038 DOI: 10.1074/Jbc.M001609200  0.304
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