Justin Lemkul

About

I am currently an Associate Professor in the Department of Biochemistry at Virginia Tech. My research focuses on applying atomistic molecular simulation methods to complex problems in biology and human health, with an emphasis on computer-aided drug design. My postdoctoral work was carried out at the University of Maryland, Baltimore, where I contributed to the development of the Drude polarizable force field for nucleic acids. This cutting-edge polarizable model drives much of our current research.

Work

Virginia Tech
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Associate Professor

US

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Virginia Polytechnic Institute and State University
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Assistant Professor

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University of Maryland Baltimore
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Postdoctoral Fellow

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Virginia Polytechnic Institute and State University
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Research Scientist

US

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Education

Virginia Polytechnic Institute and State University
United States of America

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Ph.D.

Virginia Polytechnic Institute and State University
United States of America

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B.S.

Publications

Weighted ensemble simulations with the Drude polarizable model

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preprint

The pH-Dependent Specificity of Cathepsin S and Its Implications for Inflammatory Communications and Disease

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Biochemistry

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journal-article

Robustness in biomolecular simulations: Addressing challenges in data generation, analysis, and curation

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Cell Reports Physical Science

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journal-article

Interface integrity in septin protofilaments is maintained by an arginine residue conserved from yeast to man

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preprint

Robustness in Biomolecular Simulations: Addressing Challenges in Data Generation, Analysis, and Curation

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preprint

Structural and Electronic Properties of Poly(ethylene terephthalate) (PET) from Polarizable Molecular Dynamics Simulations

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Macromolecules

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journal-article

Running Gaussian-accelerated Molecular Dynamics Simulations in NAMD [Article v1.0]

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Living Journal of Computational Molecular Science

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Balancing Group 1 Monoatomic Ion–Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems

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The Journal of Physical Chemistry B

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Introductory Tutorials for Simulating Protein Dynamics with GROMACS

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The Journal of Physical Chemistry B

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journal-article

Structural and electronic properties of polyethylene terephthalate (PET) from polarizable molecular dynamics simulations

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preprint

Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer

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The Journal of Physical Chemistry B

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journal-article

Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F430 Modifications

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Biochemistry

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journal-article

Pyroglutamylation modulates electronic properties and the conformational ensemble of the amyloid β‐peptide

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Proteins: Structure, Function, and Bioinformatics

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journal-article

Base pair dynamics, electrostatics, and thermodynamics at the LTR-III quadruplex:duplex junction

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Biophysical Journal

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journal-article

Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer

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preprint

Dynamics, Electrostatics, and Thermodynamics of Base Pairing at theLTR-IIIQuadruplex:Duplex Junction

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preprint

Structural dynamics of the methyl-coenzyme M reductase active site are influenced by coenzyme F430modifications

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preprint

Pyroglutamylation Modulates Electronic Properties and the Conformational Ensemble of the Amyloid β -Peptide

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preprint

Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes

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Journal of Chemical Information and Modeling

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journal-article

Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes

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preprint

charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS

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Journal of Chemical Information and Modeling

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journal-article

Anin silicoapproach to determine inter-subunit affinities in human septin complexes

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preprint

Effects of Familial Alzheimer’s Disease Mutations on the Folding Free Energy and Dipole–Dipole Interactions of the Amyloid β-Peptide

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The Journal of Physical Chemistry B

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journal-article

Ion-Dependent Conformational Plasticity of Telomeric G-Hairpins and G-Quadruplexes

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ACS Omega

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Electronic Polarization at the Interface between the p53 Transactivation Domain and Two Binding Partners

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The Journal of Physical Chemistry B

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TUPÃ: Electric field analyses for molecular simulations

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Journal of Computational Chemistry

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journal-article

Effects of Familial Alzheimer’s Disease Mutations on the Folding Free Energy and Dipole-Dipole Interactions of the Amyloid β-Peptide

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preprint

Integration of experimental data and use of automated fitting methods in developing protein force fields

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Communications Chemistry

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journal-article

CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

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Journal of Computational Chemistry

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Impact of Electronic Polarization on Preformed, β-Strand Rich Homogenous and Heterogenous Amyloid Oligomers

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Journal of Computational Biophysics and Chemistry

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Cation competition and recruitment around the c-kit1 G-quadruplex using polarizable simulations

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Biophysical Journal

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Ion Binding Properties and Dynamics of the bcl-2 G-Quadruplex Using a Polarizable Force Field

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Journal of Chemical Information and Modeling

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Polarizable Molecular Dynamics Simulations of Two c-kit Oncogene Promoter G-Quadruplexes: Effect of Primary and Secondary Structure on Loop and Ion Sampling

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Journal of Chemical Theory and Computation

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Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes

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Nucleic Acids Research

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Sequential Bending and Twisting around C–C Single Bonds by Mechanical Lifting of a Pre-Adsorbed Polymer

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Nano Letters

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Molecular Dynamics Simulations of the c-kit1 Promoter G-Quadruplex: Importance of Electronic Polarization on Stability and Cooperative Ion Binding

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The Journal of Physical Chemistry B

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From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package [Article v1.0]

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Living Journal of Computational Molecular Science

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Complete Genome Sequence of Fusobacterium necrophorum subsp. necrophorum ATCC 25286

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Microbiology Resource Announcements

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Small Molecule Thermochemistry: A Tool for Empirical Force Field Development

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Journal of Physical Chemistry A

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Polarizable force field for RNA based on the classical drude oscillator

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Journal of Computational Chemistry

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FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced Fusobacterium Genomes Improves Gene Identification and Characterization

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mSphere

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Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks

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Journal of Computational Chemistry

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HIV-1 Env gp41 Transmembrane Domain Dynamics are Modulated by Lipid, Water, and Ion Interactions

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Biophysical Journal

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Insights into Stabilizing Forces in Amyloid Fibrils of Differing Sizes from Polarizable Molecular Dynamics Simulations

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Journal of Molecular Biology

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Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics

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Journal of Chemical Theory and Computation

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Structure and Dynamics of FosA-Mediated Fosfomycin Resistance in Klebsiella pneumoniae and Escherichia coli

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Antimicrobial Agents and Chemotherapy

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Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA

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Journal of Chemical Theory and Computation

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Parametrization of Halogen Bonds in the CHARMM General Force Field: Improved Treatment of Protein-Ligand Interactions

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Bioorganic & Medicinal Chemistry

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Characterization of Mg2+ Distributions around RNA in Solution

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ACS Omega

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Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model

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Journal of Physical Chemistry B

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An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

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Chemical Reviews

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Phosphorylation of PPARγ Affects the Collective Motions of the PPARγ-RXRα-DNA Complex

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PLoS ONE

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Induced Dipole-Dipole Interactions Influence Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides

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Journal of Physical Chemistry B

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CHARMM-GUI Input Generation for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM Force Fields

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Journal of Chemical Theory and Computation

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DIRECT-ID: An Automated Method to Identify and Quantify Conformational Variations - Application to β2-adrenergic GPCR

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Journal of Computational Chemistry

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Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model

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Journal of Computational Chemistry

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Induced Polarization Influences the Fundamental Forces in DNA Base Flipping

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Journal of Physical Chemistry Letters

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Biophysical and Molecular-Dynamics Studies of Phosphatidic Acid Binding by the Dvl-2 DEP Domain

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Simulations of monomeric amyloid β-peptide (1–40) with varying solution conditions and oxidation state of Met35: Implications for aggregation

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Aggregation of Alzheimer’s Amyloid β-Peptide in Biological Membranes: A Molecular Dynamics Study

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Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer’s amyloid β-peptide

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Aggregation of Alzheimer’s Amyloid β-Peptide in Biological Membranes: A Molecular Dynamics Study

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Biochemistry

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The Role of Molecular Simulations in the Development of Inhibitors of Amyloid β-Peptide Aggregation for the Treatment of Alzheimer’s Disease

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Morin Inhibits the Early Stages of Amyloid β-Peptide Aggregation by Altering Tertiary and Quaternary Interactions to Produce “Off-Pathway” Structures

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Biochemistry

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Morin Inhibits the Early Stages of Amyloid β-Peptide Aggregation by Altering Tertiary and Quaternary Interactions to Produce “Off-Pathway” Structures

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Morin Inhibits the Early Stages of Amyloid β-Peptide Aggregation by Altering Tertiary and Quaternary Interactions to Produce ‘Off-Pathway’ Structures

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Biochemistry

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Lipid composition influences the release of Alzheimer's amyloid β-peptide from membranes

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Characterization of Interactions between PilA from Pseudomonas aeruginosa Strain K and a Model Membrane

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Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations

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Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies

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Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics

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Journal of Physical Chemistry B

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Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics

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Destabilizing Alzheimer’s Aβ42 Protofibrils with Morin: Mechanistic Insights from Molecular Dynamics Simulations

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Biochemistry

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Destabilizing Alzheimer’s Aβ 42 Protofibrils with Morin: Mechanistic Insights from Molecular Dynamics Simulations

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GridMAT-MD: A grid-based membrane analysis tool for use with molecular dynamics

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Perturbation of membranes by the amyloid β-peptide - a molecular dynamics study

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A Comparative Molecular Dynamics Analysis of the Amyloid β-Peptide in a Lipid Bilayer

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Archives of Biochemistry and Biophysics

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A comparative molecular dynamics analysis of the amyloid β-peptide in a lipid bilayer

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