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PUBLICATIONS

​Peer-Reviewed Journal Articles

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  1. H.M. Michel and J.A. Lemkul (2024) “Base Pair Dynamics, Electrostatics, and Thermodynamics at the LTR-III Quadruplex:Duplex Junction” Biophys. J. In Press. [DOI]
     

  2. D.S. Davidson and J.A. Lemkul (2024) “Pyroglutamylation Modulates Electronic Properties and the Conformational Ensemble of the Amyloid β-Peptide.” Proteins: Structure, Function & Bioinformatics. In Press. [DOI]
     

  3. M.D. Polêto and J.A. Lemkul (2023) “Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes.” J. Chem. Inf. Model. 63 (21) 6851-6862. (PMC10841373) [DOI]
     

  4. A.F. Wacha and J.A. Lemkul (2023) “charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS.” J. Chem. Inf. Model. 63 (14) 4246-4252. (PMC109369483) [DOI]
     

  5. N. Giacon, E. Lo Cascio, D.S. Davidson, M.D. Polêto, J.A. Lemkul, V. Pennacchietti, L. Pagano, C. Zamparelli, A. Toto, and A. Arcovito (2023) “Structural and functional insights on the interaction between SARS-CoV-2 E protein and ZO1-PDZ2.” Comput. Struct. Biotechnol. J. 21: 3259-3271. (PMC10210826) [DOI]
     

  6. B. Grupp, J.A. Lemkul, and T. Gronemeyer (2023) “An in silico approach to determine inter-subunit affinities in human septin complexes.” Cytoskeleton 80 (7-8): 141-152. [DOI]
     

  7. D.S. Davidson, J.A. Kraus, J.M. Montgomery, and J.A. Lemkul (2022) “Effects of Familial Alzheimer’s Disease Mutations on the Folding Free Energy and Dipole-Dipole Interactions of the Amyloid β-Peptide” J. Phys. Chem. B 126 (39): 7552-7566. (PMC9547858) [DOI]
     

  8. A.M. Salsbury, H.M. Michel, and J.A. Lemkul (2022) "Ion-Dependent Conformational Plasticity of Telomeric G-Hairpins and G-Quadruplexes" ACS Omega 7 (27): 23368-23379. (PMC9280957) [DOI]
     

  9. A.N. Corrigan and J.A. Lemkul (2022) “Electronic Polarization at the Interface Between the p53 Transactivation Domain and Two Binding Partners” J. Phys. Chem. B 126 (26): 4814-4827. (PMC9267131) [DOI]
     

  10. K.M. King, A.K. Sharp, D.S. Davidson, A.M. Brown, and J.A. Lemkul (2022) “Impact of Electronic Polarization on Preformed, β-Sheet Rich Homogenous and Heterogenous Amyloid Oligomers” J. Comput. Biophys. Chem. 21 (4): 449-460. (PMC9216210) [DOI]
     

  11. M.D. Polêto and J.A. Lemkul (2022) "TUPÃ: Electric field analyses for molecular simulations" J. Comput. Chem. 43 (16): 1113-1119.  (PMC9098685) [DOI]
     

  12. M.D. Polêto and J.A. Lemkul (2022) "Integration of experimental data and use of automated fitting methods in developing protein force fields" Comms. Chem. 5: 38. (PMC8979544) [DOI]
     

  13. A.A. Kognole, J. Lee, S.-J. Park, S. Jo, P. Chatterjee, J.A. Lemkul, J. Huang, A.D. MacKerell Jr., and W. Im (2022) “CHARMM-GUI Drude Prepper for Molecular Dynamics Simulation Using the Classical Drude Polarizable Force Field” J. Comput. Chem. 43 (5): 359-375. (PMC8741736) [DOI]
     

  14. A.M. Salsbury and J.A. Lemkul (2021) "Cation Competition and Recruitment around the c-kit1 G-Quadruplex Using Polarizable Simulations." Biophys. J. 120 (11): 2249-2261. (PMC8390831) [DOI]
     

  15. A.M. Salsbury and J.A. Lemkul (2021) "Recent Developments in Empirical Atomistic Force Fields for Nucleic Acids and Applications to Studies of Folding and Dynamics." Curr. Opin. Struct. Biol. 67: 9-17. (PMC7965779) [DOI]
     

  16. B.D. Ratnasinghe, A.M. Salsbury, and J.A. Lemkul (2020) “Ion Binding Properties and Dynamics of the bcl-2 G-Quadruplex Using a Polarizable Force Field.” J. Chem. Inf. Model. 60 (12): 6476-6488. (PMC7775346) [DOI]
     

  17. A.M. Salsbury, T.J. Dean, and J.A. Lemkul (2020) “Polarizable Molecular Dynamics Simulations of Two c-kit Promoter G-Quadruplexes: Effect of Primary and Secondary Structure on Loop and Ion Sampling.” J.Chem. Theory Comput. 16 (5): 3430-3444. (PMC7221321) [DOI]
     

  18. J.A. Lemkul (2020) “Same Fold, Different Properties: Polarizable Molecular Dynamics Simulations of Telomeric and TERRA G-Quadruplexes” Nucleic Acids Res. 48 (2): 561-575. (PMC6954416) [DOI] 
     

  19. R. Pawlak, J.G. Vilhena, P. D’Astolfo, X. Liu, G. Prampolini, T. Meier, T. Glatzel, J.A. Lemkul, R. Häner, S. Decurtins, A. Baratoff, R. Pérez, S.-X. Liu, and E. Meyer (2020) “Sequential Bending and Twisting of C-C Bonds by Mechanical Lifting of a Pre-Adsorbed Polymer” Nano Lett. 20 (1): 652-657. [DOI]
     

  20. A.M. Salsbury, A.M. Brown, and J.A. Lemkul (2019) “Integrating Scientific Programming in Communities of Practice for Students in the Life Sciences.” Proceedings of Practice & Experience in Advanced Research Computing (PEARC19), 6 pp. (Honorable Mention in “Workforce Development and Diversity” paper category)
     

  21. A. Umana, J.A. Lemkul, and D.J. Slade (2019) "Complete genome of Fusobacterium necrophurm subsp. necrophorum ATCC 25286." Microbiol. Resour. Announc. 8 (8): e00025-19. [DOI]
     

  22. A.M. Salsbury and J.A. Lemkul (2019) "Molecular Dynamics Simulations of the c-kit1 Promoter G-Quadruplex: Importance of Electronic Polarization on Stability and Ion Cooperativity." J. Phys. Chem. B 123 (1): 148-159. [DOI]
     

  23. J.A. Lemkul (2019) "From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package [Article v1.0]." Living J. Comp. Mol. Sci. 1 (1): 5068. [DOI]
     

  24. D. van der Spoel, M.M. Ghahremanpour, and J.A. Lemkul (2018) "Small Molecule Thermochemistry: A Tool for Empirical Force Field Development." J. Phys. Chem. A 122 (45): 8982-8988. [DOI]
     

  25. J.A. Lemkul and A.D. MacKerell, Jr. (2018) "Polarizable Force Field for RNA Based on the Classical Drude Oscillator." J. Comput. Chem. 39 (32): 2624-2646. (PMC6284239) [DOI]
     

  26. D.S. Davidson, A.M. Brown, and J.A. Lemkul (2018) "Insights into Stabilizing Forces in Amyloid Fibrils of Differing Sizes from Polarizable Molecular Dynamics Simulations." J. Mol. Biol. 430 (20): 3819-3834. [DOI] (F1000 Prime recommended article)
     

  27. B.E. Sanders, A. Umana, J.A. Lemkul, and D.J. Slade (2018) “FusoPortal: An interactive repository of hybrid MinION-sequenced Fusobacterium genomes improves gene identification and characterization.” mSphere. 3: e00228-18. [DOI]
     

  28. J. Huang, J.A. Lemkul, P.K. Eastman, and A.D. MacKerell, Jr. (2018) "Molecular Dynamics Simulations Using the Drude Polarizable Force Field on GPUs with OpenMM: Implementation, Validation, and Benchmarks." J. Comput. Chem. 39 (21) 1682-1689. [DOI]
     

  29. L. R. Hollingsworth, J.A. Lemkul, D.R. Bevan, and A.M. Brown (2018) "HIV-1 Env Transmembrane Domain Dynamics Are Modulated by Lipid, Water, and Ion Interactions." Biophys. J. 115 (1): 84-94. [DOI]
     

  30. E.H. Klontz, A.D. Tomich, S. Günther, J.A. Lemkul, D. Deredge, Z. Silverstein, J.F. Shaw, C. McElheny, Y. Doi, P. Wintrode, A.D. MacKerell, Jr., N. Sluis-Cremer, and E.J. Sundberg (2017) “Structure and dynamics of FosA-mediated fosfomycin resistance in Klebsiella pneumonia and Escherichia coli.” Antimicrob. Agents and Chemother. 61 (11): e01572-17. (PMC5655077) [DOI]
     

  31. J.A. Lemkul and A.D. MacKerell, Jr. (2017) “Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.” J. Chem. Theory Comput. 13 (5): 2053-2071. (PMC5484419) [DOI]
     

  32. J.A. Lemkul and A.D. MacKerell, Jr. (2017) “Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA.” J. Chem. Theory Comput. 13 (5): 2072-2085. (PMC5485260) [DOI]
     

  33. J.A. Lemkul and A.D. MacKerell, Jr. (2016) “Balancing Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model.” J. Phys. Chem. B 120 (44): 11436-11448. (PMC5148688) [DOI]
     

  34. J.A. Lemkul, S.K. Lakkaraju, and A.D. MacKerell, Jr. (2016) “Characterization of Mg2+ Distributions around RNA in Solution.” ACS Omega 1 (4): 680-688. (PMC5088455) [DOI]
     

  35. I. Soteras, F.-Y. Lin, K. Vanommeslaeghe, J.A. Lemkul, K. A. Armacost, C.L. Brooks III, and A.D. MacKerell, Jr. (2016) “Parametrization of Halogen Bonds in the CHARMM General Force Field: Improved Treatment of Ligand-Protein Interactions.” Bioorg. Med. Chem. 24 (20): 4812-4825. (PMC5053860) [DOI]
     

  36. J.A. Lemkul, J. Huang, B. Roux, and A.D. MacKerell, Jr. (2016) “An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.” Chem. Rev. 116 (9): 4983-5013. (PMC4865892) [DOI]
     

  37. J. Lee, X. Cheng, J. Swails, M.S. Yeom, P. Eastman, J.A. Lemkul, S. Wei, J. Buckner, J.C. Jeong, Y. Qi, S. Jo, V. Pande, D.A. Case, C.L. Brooks III, A.D. MacKerell, Jr., J.B. Klauda, and W. Im (2016) “CHARMM-GUI Input Generation for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM Force Fields.” J. Chem. Theory Comput. 12 (1): 405-413. (PMC4712441) [DOI]
     

  38. S.K. Lakkaraju, J.A. Lemkul, J. Huang, and A.D. MacKerell, Jr. (2016) “DIRECT-ID: An Automated Method to Identify and Quantify Conformational Variations - Application to β2-adrenergic GPCR.” J. Comput. Chem. 37 (4): 416-425. (PMC4756637) [DOI]
     

  39. J.A. Lemkul, J. Huang, and A.D. MacKerell, Jr. (2015) “Induced Dipole-Dipole Interactions Influence Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides.” J. Phys Chem. B 119 (51): 15574-15582. (PMC4690896) [DOI]
     

  40. J.A. Lemkul, B. Roux, D. van der Spoel, and A.D. MacKerell, Jr. (2015) “Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model.” J. Comput. Chem. 36 (19): 1473-1479. (PMC4481176) [DOI]
     

  41. J.A. Lemkul, S.N. Lewis, J. Bassaganya-Riera, and D.R. Bevan (2015) “Phosphorylation of PPARγ Affects Collective Motions of the PPARγ-RXRα-DNA Complex.” PLOS ONE. 10 (5): e0123984. [DOI]
     

  42. S.R. Gerben, J.A. Lemkul, A.M. Brown, and D.R. Bevan (2014) “Comparing Atomistic Molecular Mechanics Force Fields for a Difficult Target: A Case Study of the Amyloid β-Peptide.” J. Biomol. Struct. Dyn. 32 (11): 1817-1832. [DOI]
     

  43. J.A. Lemkul, A. Savelyev, and A.D. MacKerell, Jr. (2014) “Induced Polarization Influences the Fundamental Forces in DNA Base Flipping.” J. Phys. Chem. Lett. 5 (12): 2077-2083. (PMC4064933) [DOI] [ACS LiveSlides]
     

  44. D.G.S. Capelluto, X. Zhao, A. Lucas, J.A. Lemkul, S. Xiao, X. Fu, F. Sun, D.R. Bevan, and C.V. Finkielstein (2014) “Biophysical and molecular dynamics studies of phosphatidic acid binding to the Dvl-2 DEP domain.” Biophys. J. 106 (5): 1101-1111. [DOI]
     

  45. A.M. Brown, J.A. Lemkul, N. Schaum, and D.R. Bevan (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 (1): 44-62. [DOI]
     

  46. J.A. Lemkul and D.R. Bevan (2013) “Aggregation of Alzheimer’s Amyloid β-Peptide in Biological Membranes: A Molecular Dynamics Study.” Biochemistry. 52 (29): 4971-4980. [DOI]
     

  47. J.A. Lemkul and D.R. Bevan (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. [DOI] [Cover Art]
     

  48. J.A. Lemkul and D.R. Bevan (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. [DOI]
     

  49. J.A. Lemkul and D.R. Bevan (2011) “Lipid Composition Influences the Release of Alzheimer’s Amyloid β-Peptide from Membranes.” Protein Sci. 20 (9): 1530-1545. [DOI]
     

  50. J.A. Lemkul and D.R. Bevan (2011) “Characterization of Interactions Between PilA from Pseudomonas aeruginosa Strain K and a Model Membrane.” J. Phys. Chem. B 115 (24): 8004-8008. [DOI]
     

  51. J.A. Lemkul, W.J. Allen, and D.R. Bevan (2010) “Practical Considerations for Building GROMOS-Compatible Small Molecule Topologies.” J. Chem. Inf. Model. 50 (12): 2221-2235. [DOI]
     

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

  53. J.A. Lemkul and D.R. Bevan (2010) “Destabilizing Alzheimer’s Aβ42 Protofibrils with Morin: Mechanistic Insights from Molecular Dynamics Simulations.” Biochemistry. 49 (18): 3935-3946. [DOI]
     

  54. J.A. Lemkul and D.R. Bevan (2010) “Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics” J. Phys. Chem. B 114 (4): 1652-1660. [DOI]
     

  55. W.J. Allen, J.A. Lemkul, and D.R. Bevan (2009) “GridMAT-MD: A Grid-based Membrane Analysis Tool for Use With Molecular Dynamics.”  J. Comput. Chem. 30 (12): 1952-1958. [DOI]
     

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

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

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​Book Chapters

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  1. J.A. Lemkul (2021) "Preparing and Analyzing Polarizable Molecular Dynamics Simulations with the Classical Drude Oscillator Model" In Methods in Molecular Biology. J. Mourão, I. Moreira, and M. Machuquiero, Eds. 2315: 219-240. [DOI]
     

  2. J.A. Lemkul (2020) "Pairwise-additive and polarizable atomistic force fields for molecular dynamics simulations of proteins" Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly. In Progress in Molecular Biology and Translational Science. B. Strodel and B. Barz, Eds. 170: 1-71. [DOI]

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