Publications – Wereszczynski Lab

[52] S. Evoli, N. L. Kariyawasam, K. C. Nitiss, J. L. Nitiss, J. Wereszczynski

“Modeling Allosteric Mechanisms of Eukaryotic Type II Topoisomerases” Preprint Available on bioRxiv

DOI: 10.1101/2023.08.02.551689

[51] E. Akbari, E.J. Park, A. K. Singh, V. Vinayak, R. K. A. Virk, J. Wereszczynski, and C. A. Musselman

“Multiscale genome organization symposium—annual biophysical society meeting 2023” Biophys. Rev., 15, 313, (2023)

[50] L. Baweja and J. Wereszczynski

“Conformational and Thermodynamic Differences Underlying Wild-type and Mutant YEATS Domain Specificity for Epigenetic Marks” J Chem Inf Model, 63, 1229 (2023)

DOI: 10.1021/acs.jcim.2c01660

[49] H. Kohestani and J. Wereszczynski

“The Effects of RNA.DNA-DNA Triple Helices on Nucleosome Structures and Dynamics” Biophys. J. 122, 1229 (2023)

DOI: 10.1016/j.bpj.2023.02.013

[48] J. Clayton, K. Ellis-Guardiola, B. Mahoney, J. Soule, R. T. Clubb, Jeff Wereszczynski

“Directed inter-domain motions enable the IsdH Staphylococcus aureus receptor to rapidly extract heme from human hemoglobin” J. Molec Biol. 434, 167623 (2022)

DOI: 10.1016/j.jmb.2022.167623

[47] K. Zhou, M. Gebala, D. C. Woods, K. Sundararajan, G. Edwards, D. Krzizike, J. Wereszczynski, A. F. Straight, K. Luger

“CENP-N promotes the compaction of centromeric chromatin” Nat. Struct. Mol. Biol. 29, 403 (2022)PDF

DOI: 10.1038/s41594-022-00758-y

[46] J. Clayton, L. Baweja, J. Wereszczynski

“Peptide Dynamics and Metadynamics: Leveraging Enhanced Sampling Molecular Dynamics to Robustly Model Long-Timescale Transitions” Simonson T. (eds) Computational Peptide Science. Methods in Molecular Biology, vol 2405. Humana, New York, NY

DOI: 10.1007/978-1-0716-1855-4_8

[45] E. A. Morrison, L. Baweja, M. G. Poirier, J. Wereszczynski, C. A. Musselman

“Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility” Nucleic Acids Res. 49 4750 (2021)PDF

DOI: 10.1093/nar/gkab246

[44] D. C. Woods, F. Rodríguez-Ropero, J. Wereszczynski

“The Dynamic Influence of Linker Histone Saturation within the Poly-Nucleosome Array” J. Molec. Biol. 433, 16902 (2021)

DOI: 10.1016/j.jmb.2021.166902

[43] S. Bowerman, J. Wereszczynski, K. Luger

“Archaeal chromatin ‘slinkies’ are inherently dynamic complexes with deflected DNA wrapping pathways” eLife 10:e65587, (2021). Highlighted in WIRED PDF

DOI: 10.7554/eLife.65587

[42] Z. Sierzega, J. Wereszczynski, C. Prior

“WASP: A software package for correctly characterizing the topological development of ribbon structures” Sci. Rep. 11, 1527 (2021)PDF

DOI: 10.1038/s41598-020-80851-8

[41] H. Kohestani and J. Wereszczynski

“Effects of H2A.B incorporation on nucleosome structures and dynamics” Biophys. J. 120, 1498 (2021).

DOI: 10.1016/j.bpj.2021.01.036

[40] J. C. Sanchez, L. Zhang*, S. Evoli*, N. J. Schnicker, M. Nunez-Hernandez, K. Yu, J. Wereszczynski, M. A. Pufall, C. A. Musselman

“The Molecular Basis of Specific DNA Binding by the BRG1 AT-hook and Bromodomain” BBA-Gene. Regul. Mech, 1863, 194566 (2020)PDF

DOI: 10.1016/j.bbagrm.2020.194566

[39] D. C. Woods and J. Wereszczynski

“Elucidating the Influence of Linker Histone Variants on Chromatosome Dynamics and Energetics” Nucleic Acids Res. 48, 3591 (2020)PDF

DOI: 10.1093/nar/gkaa121

[38] A. Rice, M. Rooney, A. I. Greenwood, M. L. Cotten, J. Wereszczynski

“Lipopolysaccharide Simulations are Sensitive to Phosphate Charge and Ion Parameterization” J. Chem. Theory Comput. 16, 1806 (2020)

DOI: 10.1021/acs.jctc.9b00868

[37] K. Ellis-Guardio*, J. Clayton* ,C. Phama, B. Mahoney, J. Wereszczynski, R. T. Clubb

“The Staphylococcus aureus IsdH receptor forms a dynamic complex with human hemoglobin that triggers heme release via two distinct hot spots” J. Mol. Biol., 432, 1064 (2020)

DOI: 10.1016/j.jmb.2019.12.023

[36] M. W. Martynowycz*, A. Rice* , K. Andreev, T. M. Nobre, I. Kuzmenko, J. Wereszczynski, D. Gidalevitz

“Salmonella Membrane Structural Remodeling Increases Resistance to Antimicrobial Peptide LL-37” ACS Infect. Dis., 5, 1214 (2019)

DOI: 10.1021/acsinfecdis.9b00066

[35] S. Bowerman, J. E. Curtis, J. Clayton, E. H. Brookes, J. Wereszczynski

“BEES: Bayesian Ensemble Estimation from SAS” Biophys. J., 117, 399 (2019)

DOI: 10.1016/j.bpj.2019.06.024

[34] K. Ma, E. Thomas, J. Wereszczynski, and N. Menhart

“Empirical and Computational Comparison of Alternative Therapeutic Exon Skip Repairs for Duchenne Muscular Dystrophy” Biochemistry, 58, 2061 (2019)

DOI: 10.1021/acs.biochem.9b00062

[33] S. Bowerman, R. J. Hickock, and J. Wereszczynski

“Unique Dynamics in Asymmetric macroH2A-H2A Hybrid Nucleosomes Result in Increased Complex Stability” Young Scientists Special Issue, J. Phys. Chem. B, 123, 419

DOI: 10.1021/acs.jpcb.8b10668

[32] E. A. Morrison, S. Bowerman, K. L Sylvers, J. Wereszczynski, C. A Musselman

“The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome” eLife, 7, e31481 (2018)PDF

DOI: 10.7554/eLife.31481

[31] A. Rice and J. Wereszczynski

“Atomistic Scale Effects of Lipopolysaccharide Modifications on Bacterial Outer Membrane Defenses” Biophys. J., 113, 1389 (2018)PDF

DOI: 10.1016/j.bpj.2018.02.006

[30] M. Sjodt, R. Macdonald, J. Marshall, J. Clayton, J. Olson, M. Phillips, D. Gell, J. Wereszczynski, R. T. Clubb

“The Energetics Underlying Hemin Extraction from the α-subunit of Human Hemoglobin by Staphylococcus aureus” J. Biol. Chem. 293, 6942 (2018)PDF

DOI: 10.1074/jbc.RA117.000803

[29] E. B. Naziga and J. Wereszczynski

“Molecular Mechanisms of the Binding and Specificity of Streptococcus Pneumoniae Sortase C Enzymes for Pilin Subunits” Sci. Rep. 7, 13119 (2017)PDF

DOI: 10.1038/s41598-017-13135-3

[28] A. W. Jacobitz, M. D. Kattke, J. Wereszczynski, R. T. Clubb

“Sortase Transpeptidases: Structural Biology and Catalytic Mechanism” Adv. Protein Chem. 109, 233 (2017)

DOI: 10.1016/bs.apcsb.2017.04.008

[27] A. Rice and J. Wereszczynski

“Probing the disparate effects of arginine and lysine residues on antimicrobial peptide/bilayer association” BBA Biomemb. 1859, 1941 (2017)PDF

DOI: 10.1016/j.bbamem.2017.06.002

[26] S. Bowerman*, A. Rana*, A. Rice, G. Pham, E. Strieter, J. Wereszczynski

“Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations” J. Chem. Theory Comput., 13, 2418 (2017)

DOI: 10.1021/acs.jctc.7b00059

[25] A. H. Chan, S. W. Yi, E. M. Weiner, B. R. Amer, C. K. Sue, J. Wereszczynski, C. A. Dillen, S. Senese, J. Z. Torres, J. A. McCammon, L. S. Miller, M. E. Jung and R. T. Clubb

“NMR structure-based optimization of Staphylococcus aureus sortase A pyridazinone inhibitors” Chem. Bio. Drug. Des. 90, 327 (2017)

DOI: h10.1111/cbdd.12962

[24] M. Alwarawrah and J. Wereszczynski

“Investigation of the Effects of Bilayer Composition on PKCα-C2 Docking Using Molecular Dynamics Simulation” J. Phys. Chem. B., 121, 78 (2017)

DOI: 10.1021/acs.jpcb.6b10188

[23] S. Bowerman and J. Wereszczynski

“Detecting Allosteric Networks using Molecular Dynamics Simulation” Method Enzymol., 578, 429 (2016)

DOI: 10.1016/bs.mie.2016.05.027

[22] P. Shrestha and J. Wereszczynski

“Discerning the Catalytic Mechanism of Staphylococcus aureus Sortase A with QM/MM Free Energy Calculations” J Mol Graph Model., 67, 33 (2016)

DOI: 10.1016/j.jmgm.2016.04.006

[21] A. W. Jacobitz*, E. B. Naziga*, S. W. Yi, S. A. McConnell, R. Peterson, M. E. Jung, R. T. Clubb, J. Wereszczynski

“The ‘lid’ in the Streptococcus pneumoniae SrtC1 sortase adopts a rigid structure that regulates substrate access to the active site” J. Phys. Chem. B., 120, 8302 (2016)

DOI: 10.1021/acs.jpcb.6b01930

[20] S. Bowerman and J. Wereszczynski

“Effects of macroH2A and H2A.Z on nucleosome structure and dynamics as elucidated by molecular dynamics simulations” Biophys. J., 110, 317 (2016)PDF

DOI: 10.1016/j.bpj.2015.12.015

[19] A. Mentes, A.M. Florescu, E. Brunk, J. Wereszczynski, M. Joyeux, and I. Andricioaei

“Free-energy landscape and characteristic forces for the initiation of DNA unzipping” Biophys. J., 108, 1727 (2015)PDF

DOI: 10.1016/j.bpj.2015.01.025

[18] A. Jacobitz, J. Wereszczynski, S. W. Yi, B. R. Amer, G.L. Huang, A. V. Nguyen, M.R. Sawaya, M.E. Jung, J. A. McCammon, and R. T. Clubb

“Structural and Computational Studies of the Staphylococcus aureus Sortase B-Substrate Complex Reveal a Substrate-stabilized Oxyanion Hole” J. Biol. Chem., 289, 8891 (2014)PDF

DOI: 10.1074/jbc.M113.509273

[17] I. Tikhonva, B. Selvam, A.D. Ivetac, J. Wereszczynski, and J. A. McCammon

“Simulations of biased agonists in the β2 adrenergic receptor with accelerated molecular dynamics” Biochemistry, 52, 5593 (2013)PDF

DOI: 10.1021/bi400499n

[16] A. Chan, J. Wereszczynski, B. Amer, S. W. Yi, M. E. Jung, J A. McCammon, R. T. Clubb

“Discovery of Staphylococcus aureus Sortase A Inhibitors Using Virtual Screening and the Relaxed Complex Scheme” Chem. Bio. Drug Des., 82, 418 (2013) PDF

DOI: 10.1111/cbdd.12167

[15] K. Kappel, J. Wereszczynski, R. Clubb, and J. A. McCammon

“The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations” Prot. Sci., 21, 1858 (2012)PDF

DOI: 10.1002/pro.2168

[14] M. Lawrenz, J. Wereszczynski, J. M. Ortiz-Sánchez, S. E. Nichols, and J. A. McCammon

“Thermodynamic Integration to Predict Host-Guest Binding Affinities” J. Comput.-Aided Mol. Des., 26, 569 (2012)

DOI: 10.1007/s10822-012-9542-5

[13] J. Wereszczynski and J. A. McCammon

“Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations” Proc. Natl. Acad. Sci. U.S.A., 109, 7759 (2012)PDF

DOI: 10.1073/pnas.1117441109

[12] B. Selvam, J. Wereszczynski, and I. Tikhonva

“Comparison of dynamics of extracellular access to the β1 and β2 adrenoreceptors binding sites uncovers the potential of kinetics-basis of antagonist selectivity” Chem. Biol. Drug. Des., 80, 215 (2012)PDF

DOI: 10.1111/j.1747-0285.2012.01390.x

[11] J. Wereszczynski and J. A. McCammon

“Simulations of the p97 Complex Suggest Novel Conformational States of Hydrolysis Intermediates” Prot. Sci., 21, 475 (2012)PDF

DOI: 10.1002/pro.2024

[10] J. Wereszczynski and J. A. McCammon

“Accelerated Molecular Dynamics in Computational Drug Design” Computational Drug Discovery and Design (Riccardo Baron, editor), Humana Press, New York (2012)

DOI: 10.1007/978-1-61779-465-0_30

[9] J. Wereszczynski and J. A. McCammon

“Statistical Mechanics and Molecular Dynamics in Evaluating Thermodynamic Properties of Biomolecular Recognition” Quart. Rev. Biophys., 45, 1 (2012)

DOI: 10.1017/S0033583511000096

[8] T. Lillian, M. Taranova, J. Wereszczynski, I. Andricioaei, and N. Perkins

“A Multiscale Dynamic Model of DNA Supercoil Relaxation by Topoisomerase IB” Biophys J., 100, 2016 (2011)PDF

DOI: 10.1016/j.bpj.2011.03.003

[7] J. Wereszczynski and J. A. McCammon

“Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations” J. Chem. Theory Comput., 6, 3285 (2010)PDF

DOI: 10.1021/ct100322t

[6] J. Wereszczynski and I. Andricioaei

“Free Energy Calculations Reveal Rotating-Ratchet Mechanism for DNA Supercoil Relaxation by Topoisomerase IB and its Inhibition” Biophys J., 99, 869 (2010)PDF

DOI: 10.1016/j.bpj.2010.04.077

[5] M. Lawrenz, J. Wereszczynski, R. Amaro, R. Walker, A. Roitberg, and J. A. McCammon

“Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy” Proteins, 78, 2523 (2010)PDF

DOI: 10.1002/prot.22761

[4] J. Wereszczynski and I. Andricioaei

“Conformational and Solvent Entropy Contributions to the Thermal Response of Nucleic Acid-Based Nanothermometers” J. Phys. Chem. B, 114, 2076 (2010)

DOI: 10.1021/jp911681n

[3] C. Kelly, P. Leroueil, E. Nett, J. Wereszczynski, J. Baker, B. Orr, M. Holl, and I. Andricioaei

“Poly(amidoamine) dendrimers on lipid bilayers I: Free energy and conformation of binding” J. Phys. Chem. B 112, 9337-9345 (2008)

DOI: 10.1021/jp801377a

[2] J. MacFadyen, J. Wereszczynski, and I. Andricioaei

“Directionally Negative Friction: A Method for Enhanced Sampling of Rare Event Kinetics” J. Chem. Phys., 128, 114112 (2008)

DOI: 10.1063/1.2841102

[1] J. Wereszczynski, Ioan Andricioaei

“On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension” Proc. Natl. Acad. Sci. U.S.A. 103, 16200 (2006)PDF

DOI: 10.1073/pnas.0603850103

[12] S. Evoli, N. L. Kariyawasam, K. C. Nitiss, J. L. Nitiss, J. Wereszczynski

“Modeling Allosteric Mechanisms of Eukaryotic Type II Topoisomerases” Preprint Available on bioRxiv

DOI: 10.1101/2023.08.02.551689

[11] E. Akbari, E.J. Park, A. K. Singh, V. Vinayak, R. K. A. Virk, J. Wereszczynski, and C. A. Musselman

“Multiscale genome organization symposium—annual biophysical society meeting 2023” Biophys. Rev., 15, 313, (2023)

DOI: 10.1007/s12551-023-01063-8

[10] L. Baweja and J. Wereszczynski

“Conformational and Thermodynamic Differences Underlying Wild-type and Mutant YEATS Domain Specificity for Epigenetic Marks” J Chem Inf Model, 63, 1229 (2023)

DOI: 10.1021/acs.jcim.2c01660

[9] H. Kohestani and J. Wereszczynski

“The Effects of RNA.DNA-DNA Triple Helices on Nucleosome Structures and Dynamics” Biophys. J. 122, 1229 (2023)

DOI: 10.1016/j.bpj.2023.02.013

[8] J. Clayton, K. Ellis-Guardiola, B. Mahoney, J. Soule, R. T. Clubb, Jeff Wereszczynski

“Directed inter-domain motions enable the IsdH Staphylococcus aureus receptor to rapidly extract heme from human hemoglobin” J. Molec Biol. 434, 167623 (2022)

DOI: 10.1016/j.jmb.2022.167623

[7] K. Zhou, M. Gebala, D. C. Woods, K. Sundararajan, G. Edwards, D. Krzizike, J. Wereszczynski, A. F. Straight, K. Luger

“CENP-N promotes the compaction of centromeric chromatin” Nat. Struct. Mol. Biol. 29, 403 (2022)PDF

DOI: 10.1038/s41594-022-00758-y

[6] J. Clayton, L. Baweja, J. Wereszczynski

DOI: 10.1007/978-1-0716-1855-4_8

[5] E. A. Morrison, L. Baweja, M. G. Poirier, J. Wereszczynski, C. A. Musselman

“Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility” Nucleic Acids Res. 49 4750 (2021)PDF

DOI: 10.1093/nar/gkab246

[4] D. C. Woods, F. Rodríguez-Ropero, J. Wereszczynski

“The Dynamic Influence of Linker Histone Saturation within the Poly-Nucleosome Array” J. Molec. Biol. 433, 16902 (2021)

DOI: 10.1016/j.jmb.2021.166902

[3] S. Bowerman, J. Wereszczynski, K. Luger

“Archaeal chromatin ‘slinkies’ are inherently dynamic complexes with deflected DNA wrapping pathways” eLife 10:e65587, (2021). Highlighted in WIRED PDF

DOI: 10.7554/eLife.65587

[2] Z. Sierzega, J. Wereszczynski, C. Prior

“WASP: A software package for correctly characterizing the topological development of ribbon structures” Sci. Rep. 11, 1527 (2021)PDF

DOI: 10.1038/s41598-020-80851-8

[1] H. Kohestani and J. Wereszczynski

“Effects of H2A.B incorporation on nucleosome structures and dynamics” Biophys. J. 120, 1498 (2021).

DOI: 10.1016/j.bpj.2021.01.036

[21] J. C. Sanchez, L. Zhang*, S. Evoli*, N. J. Schnicker, M. Nunez-Hernandez, K. Yu, J. Wereszczynski, M. A. Pufall, C. A. Musselman

“The Molecular Basis of Specific DNA Binding by the BRG1 AT-hook and Bromodomain” BBA-Gene. Regul. Mech, 1863, 194566 (2020)PDF

DOI: 10.1016/j.bbagrm.2020.194566

[20] D. C. Woods and J. Wereszczynski

“Elucidating the Influence of Linker Histone Variants on Chromatosome Dynamics and Energetics” Nucleic Acids Res. 48, 3591 (2020)PDF

DOI: 10.1093/nar/gkaa121

[19] A. Rice, M. Rooney, A. I. Greenwood, M. L. Cotten, J. Wereszczynski

“Lipopolysaccharide Simulations are Sensitive to Phosphate Charge and Ion Parameterization” J. Chem. Theory Comput. 16, 1806 (2020)

DOI: 10.1021/acs.jctc.9b00868

[18] K. Ellis-Guardio*, J. Clayton* ,C. Phama, B. Mahoney, J. Wereszczynski, R. T. Clubb

“The Staphylococcus aureus IsdH receptor forms a dynamic complex with human hemoglobin that triggers heme release via two distinct hot spots” J. Mol. Biol., 432, 1064 (2020)

DOI: 10.1016/j.jmb.2019.12.023

[17] M. W. Martynowycz*, A. Rice* , K. Andreev, T. M. Nobre, I. Kuzmenko, J. Wereszczynski, D. Gidalevitz

“Salmonella Membrane Structural Remodeling Increases Resistance to Antimicrobial Peptide LL-37” ACS Infect. Dis., 5, 1214 (2019)

DOI: 10.1021/acsinfecdis.9b00066

[16] S. Bowerman, J. E. Curtis, J. Clayton, E. H. Brookes, J. Wereszczynski

“BEES: Bayesian Ensemble Estimation from SAS” Biophys. J., 117, 399 (2019)

DOI: 10.1016/j.bpj.2019.06.024

[15] K. Ma, E. Thomas, J. Wereszczynski, and N. Menhart

“Empirical and Computational Comparison of Alternative Therapeutic Exon Skip Repairs for Duchenne Muscular Dystrophy” Biochemistry, 58, 2061 (2019)

DOI: 10.1021/acs.biochem.9b00062

[14] S. Bowerman, R. J. Hickock, and J. Wereszczynski

“Unique Dynamics in Asymmetric macroH2A-H2A Hybrid Nucleosomes Result in Increased Complex Stability” Young Scientists Special Issue, J. Phys. Chem. B, 123, 419

DOI: 10.1021/acs.jpcb.8b10668

[13] E. A. Morrison, S. Bowerman, K. L Sylvers, J. Wereszczynski, C. A Musselman

“The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome” eLife, 7, e31481 (2018)PDF

DOI: 10.7554/eLife.31481

[12] A. Rice and J. Wereszczynski

“Atomistic Scale Effects of Lipopolysaccharide Modifications on Bacterial Outer Membrane Defenses” Biophys. J., 113, 1389 (2018)PDF

DOI: 10.1016/j.bpj.2018.02.006

[11] M. Sjodt, R. Macdonald, J. Marshall, J. Clayton, J. Olson, M. Phillips, D. Gell, J. Wereszczynski, R. T. Clubb

“The Energetics Underlying Hemin Extraction from the α-subunit of Human Hemoglobin by Staphylococcus aureus” J. Biol. Chem. 293, 6942 (2018)PDF

DOI: 10.1074/jbc.RA117.000803

[10] E. B. Naziga and J. Wereszczynski

“Molecular Mechanisms of the Binding and Specificity of Streptococcus Pneumoniae Sortase C Enzymes for Pilin Subunits” Sci. Rep. 7, 13119 (2017)PDF

DOI: 10.1038/s41598-017-13135-3

[9] A. W. Jacobitz, M. D. Kattke, J. Wereszczynski, R. T. Clubb

“Sortase Transpeptidases: Structural Biology and Catalytic Mechanism” Adv. Protein Chem. 109, 233 (2017)

DOI: 10.1016/bs.apcsb.2017.04.008

[8] A. Rice and J. Wereszczynski

“Probing the disparate effects of arginine and lysine residues on antimicrobial peptide/bilayer association” BBA Biomemb. 1859, 1941 (2017)PDF

DOI: 10.1016/j.bbamem.2017.06.002

[7] S. Bowerman*, A. Rana*, A. Rice, G. Pham, E. Strieter, J. Wereszczynski

“Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations” J. Chem. Theory Comput., 13, 2418 (2017)

DOI: 10.1021/acs.jctc.7b00059

[6] A. H. Chan, S. W. Yi, E. M. Weiner, B. R. Amer, C. K. Sue, J. Wereszczynski, C. A. Dillen, S. Senese, J. Z. Torres, J. A. McCammon, L. S. Miller, M. E. Jung and R. T. Clubb

“NMR structure-based optimization of Staphylococcus aureus sortase A pyridazinone inhibitors” Chem. Bio. Drug. Des. 90, 327 (2017)

DOI: h10.1111/cbdd.12962

[5] M. Alwarawrah and J. Wereszczynski

“Investigation of the Effects of Bilayer Composition on PKCα-C2 Docking Using Molecular Dynamics Simulation” J. Phys. Chem. B., 121, 78 (2017)

DOI: 10.1021/acs.jpcb.6b10188

[4] S. Bowerman and J. Wereszczynski

“Detecting Allosteric Networks using Molecular Dynamics Simulation” Method Enzymol., 578, 429 (2016)

DOI: 10.1016/bs.mie.2016.05.027

[3] P. Shrestha and J. Wereszczynski

“Discerning the Catalytic Mechanism of Staphylococcus aureus Sortase A with QM/MM Free Energy Calculations” J Mol Graph Model., 67, 33 (2016)

DOI: 10.1016/j.jmgm.2016.04.006

[2] A. W. Jacobitz*, E. B. Naziga*, S. W. Yi, S. A. McConnell, R. Peterson, M. E. Jung, R. T. Clubb, J. Wereszczynski

“The ‘lid’ in the Streptococcus pneumoniae SrtC1 sortase adopts a rigid structure that regulates substrate access to the active site” J. Phys. Chem. B., 120, 8302 (2016)

DOI: 10.1021/acs.jpcb.6b01930

[1] S. Bowerman and J. Wereszczynski

“Effects of macroH2A and H2A.Z on nucleosome structure and dynamics as elucidated by molecular dynamics simulations” Biophys. J., 110, 317 (2016)PDF

DOI: 10.1016/j.bpj.2015.12.015

[12] A. Mentes, A.M. Florescu, E. Brunk, J. Wereszczynski, M. Joyeux, and I. Andricioaei

“Free-energy landscape and characteristic forces for the initiation of DNA unzipping” Biophys. J., 108, 1727 (2015)PDF

DOI: 10.1016/j.bpj.2015.01.025

[11] A. Jacobitz, J. Wereszczynski, S. W. Yi, B. R. Amer, G.L. Huang, A. V. Nguyen, M.R. Sawaya, M.E. Jung, J. A. McCammon, and R. T. Clubb

“Structural and Computational Studies of the Staphylococcus aureus Sortase B-Substrate Complex Reveal a Substrate-stabilized Oxyanion Hole” J. Biol. Chem., 289, 8891 (2014)PDF

DOI: 10.1074/jbc.M113.509273

[10] I. Tikhonva, B. Selvam, A.D. Ivetac, J. Wereszczynski, and J. A. McCammon

“Simulations of biased agonists in the β2 adrenergic receptor with accelerated molecular dynamics” Biochemistry, 52, 5593 (2013)PDF

DOI: 10.1021/bi400499n

[9] A. Chan, J. Wereszczynski, B. Amer, S. W. Yi, M. E. Jung, J A. McCammon, R. T. Clubb

“Discovery of Staphylococcus aureus Sortase A Inhibitors Using Virtual Screening and the Relaxed Complex Scheme” Chem. Bio. Drug Des., 82, 418 (2013) PDF

DOI: 10.1111/cbdd.12167

[8] K. Kappel, J. Wereszczynski, R. Clubb, and J. A. McCammon

“The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations” Prot. Sci., 21, 1858 (2012)PDF

DOI: 10.1002/pro.2168

[7] M. Lawrenz, J. Wereszczynski, J. M. Ortiz-Sánchez, S. E. Nichols, and J. A. McCammon

“Thermodynamic Integration to Predict Host-Guest Binding Affinities” J. Comput.-Aided Mol. Des., 26, 569 (2012)

DOI: 10.1007/s10822-012-9542-5

[6] J. Wereszczynski and J. A. McCammon

“Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations” Proc. Natl. Acad. Sci. U.S.A., 109, 7759 (2012)PDF

DOI: 10.1073/pnas.1117441109

[5] B. Selvam, J. Wereszczynski, and I. Tikhonva

DOI: 10.1111/j.1747-0285.2012.01390.x

[4] J. Wereszczynski and J. A. McCammon

“Simulations of the p97 Complex Suggest Novel Conformational States of Hydrolysis Intermediates” Prot. Sci., 21, 475 (2012)PDF

DOI: 10.1002/pro.2024

[3] J. Wereszczynski and J. A. McCammon

“Accelerated Molecular Dynamics in Computational Drug Design” Computational Drug Discovery and Design (Riccardo Baron, editor), Humana Press, New York (2012)

DOI: 10.1007/978-1-61779-465-0_30

[2] J. Wereszczynski and J. A. McCammon

“Statistical Mechanics and Molecular Dynamics in Evaluating Thermodynamic Properties of Biomolecular Recognition” Quart. Rev. Biophys., 45, 1 (2012)

DOI: 10.1017/S0033583511000096

[1] T. Lillian, M. Taranova, J. Wereszczynski, I. Andricioaei, and N. Perkins

“A Multiscale Dynamic Model of DNA Supercoil Relaxation by Topoisomerase IB” Biophys J., 100, 2016 (2011)PDF

DOI: 10.1016/j.bpj.2011.03.003

[7] J. Wereszczynski and J. A. McCammon

“Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations” J. Chem. Theory Comput., 6, 3285 (2010)PDF

DOI: 10.1021/ct100322t

[6] J. Wereszczynski and I. Andricioaei

“Free Energy Calculations Reveal Rotating-Ratchet Mechanism for DNA Supercoil Relaxation by Topoisomerase IB and its Inhibition” Biophys J., 99, 869 (2010)PDF

DOI: 10.1016/j.bpj.2010.04.077

[5] M. Lawrenz, J. Wereszczynski, R. Amaro, R. Walker, A. Roitberg, and J. A. McCammon

“Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy” Proteins, 78, 2523 (2010)PDF

DOI: 10.1002/prot.22761

[4] J. Wereszczynski and I. Andricioaei

“Conformational and Solvent Entropy Contributions to the Thermal Response of Nucleic Acid-Based Nanothermometers” J. Phys. Chem. B, 114, 2076 (2010)

DOI: 10.1021/jp911681n

[3] C. Kelly, P. Leroueil, E. Nett, J. Wereszczynski, J. Baker, B. Orr, M. Holl, and I. Andricioaei

“Poly(amidoamine) dendrimers on lipid bilayers I: Free energy and conformation of binding” J. Phys. Chem. B 112, 9337-9345 (2008)

DOI: 10.1021/jp801377a

[2] J. MacFadyen, J. Wereszczynski, and I. Andricioaei

“Directionally Negative Friction: A Method for Enhanced Sampling of Rare Event Kinetics” J. Chem. Phys., 128, 114112 (2008)

DOI: 10.1063/1.2841102

[1] J. Wereszczynski, Ioan Andricioaei

“On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension” Proc. Natl. Acad. Sci. U.S.A. 103, 16200 (2006)PDF

DOI: 10.1073/pnas.0603850103