Publications

“The Influence of Ionic Environment on Nucleosome-Mica Interactions Revealed via Molecular Dynamics Simulations” Under Review. Preprint available on bioRxiv.

DOI: 10.1101/2024.06.25.600666

“Modeling Allosteric Mechanisms of Eukaryotic Type II Topoisomerases” Biophys. J. 126, 1620 (2024)

DOI: 10.1016/j.bpj.2024.05.004

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

DOI: 10.1007/s12551-023-01063-8

“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

“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

“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

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

DOI: 10.1038/s41594-022-00758-y

“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

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

DOI: 10.1093/nar/gkab246

“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

“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

“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

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

DOI: 10.1016/j.bpj.2021.01.036

“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

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

DOI: 10.1093/nar/gkaa121

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

DOI: 10.1021/acs.jctc.9b00868

“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

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

DOI: 10.1021/acsinfecdis.9b00066

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

DOI: 10.1016/j.bpj.2019.06.024

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

DOI: 10.1021/acs.biochem.9b00062

“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

“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

“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

“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

“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

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

DOI: 10.1016/bs.apcsb.2017.04.008

“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

“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

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

DOI: h10.1111/cbdd.12962

“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

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

DOI: 10.1016/bs.mie.2016.05.027

“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

“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

“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

“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

“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

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

DOI: 10.1021/bi400499n

“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

“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

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

DOI: 10.1007/s10822-012-9542-5

“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

“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

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

DOI: 10.1002/pro.2024

“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

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

DOI: 10.1017/S0033583511000096

“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

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

DOI: 10.1021/ct100322t

“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

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

DOI: 10.1002/prot.22761

“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

“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

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

DOI: 10.1063/1.2841102

“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

“The Influence of Ionic Environment on Nucleosome-Mica Interactions Revealed via Molecular Dynamics Simulations” Under Review. Preprint available on bioRxiv.

DOI: 10.1101/2024.06.25.600666

“Modeling Allosteric Mechanisms of Eukaryotic Type II Topoisomerases” Biophys. J. 126, 1620 (2024)

DOI: 10.1016/j.bpj.2024.05.004

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

DOI: 10.1007/s12551-023-01063-8

“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

“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

“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

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

DOI: 10.1038/s41594-022-00758-y

“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

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

DOI: 10.1093/nar/gkab246

“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

“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

“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

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

DOI: 10.1016/j.bpj.2021.01.036

“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

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

DOI: 10.1093/nar/gkaa121

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

DOI: 10.1021/acs.jctc.9b00868

“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

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

DOI: 10.1021/acsinfecdis.9b00066

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

DOI: 10.1016/j.bpj.2019.06.024

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

DOI: 10.1021/acs.biochem.9b00062

“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

“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

“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

“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

“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

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

DOI: 10.1016/bs.apcsb.2017.04.008

“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

“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

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

DOI: h10.1111/cbdd.12962

“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

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

DOI: 10.1016/bs.mie.2016.05.027

“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

“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

“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

“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

“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

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

DOI: 10.1021/bi400499n

“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

“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

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

DOI: 10.1007/s10822-012-9542-5

“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

“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

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

DOI: 10.1002/pro.2024

“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

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

DOI: 10.1017/S0033583511000096

“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

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

DOI: 10.1021/ct100322t

“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

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

DOI: 10.1002/prot.22761

“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

“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

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

DOI: 10.1063/1.2841102

“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