J. A. McCammon

Dilated cardiomyopathy mutation in beta-cardiac myosin enhances actin activation of the power stroke and phosphate release

This paper investigates how the E525K mutation in beta-cardiac myosin affects actin activation, power stroke, and phosphate release, revealing structural and kinetic changes linked to dilated cardiomyopathy.

Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome bd Oxidase

This study identifies six new cytochrome bd inhibitor scaffolds through computational screening and validates their activity against Mycobacterium tuberculosis.

CO2 Response Screen in Grass Brachypodium Reveals Key Role of a MAP-Kinase in CO2-Triggered Stomatal Closure

This study identifies a MAP-kinase, BdMPK5, as critical for CO2-induced stomatal closure in Brachypodium, using forward genetics and structural modeling.

Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics

This study examines how glycosylation and membrane crowding affect the stability and dynamics of influenza neuraminidase through computational simulations of three different systems.

Capturing differences in the regulation of LRRK2 dynamics and conformational states by small molecule kinase inhibitors

This study uses simulations and HDX-MS to analyze how two LRRK2 inhibitors affect the protein's conformational dynamics and kinase activity.

Integrating comparative modeling and accelerated simulations reveals conformational and energetic basis of actomyosin force generation

This study uses comparative modeling and accelerated simulations to reveal how ATP-hydrolysis product release correlates with force generation in the actomyosin complex.

PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period

This study shows that PER phosphorylation inhibits CK1 activity, stabilizing PER and extending circadian period through feedback inhibition.

Architecture and self-assembly of the jumbo bacteriophage nuclear shell

The paper identifies chimallin as the primary protein forming the bacteriophage nuclear shell and characterizes its self-assembly into closed compartments.

Elucidation of cryptic and allosteric pockets within the SARS-CoV-2 protease

The paper identifies cryptic and allosteric pockets in the SARS-CoV-2 main protease using enhanced sampling methods and assesses their druggability for potential inhibitor development.

A glycan gate controls opening of the SARS-CoV-2 spike protein

This study identifies a glycan gate and key residues that facilitate SARS-CoV-2 spike protein RBD opening through simulations and experimental validation.

Multiscale simulations examining glycan shield effects on drug binding to influenza neuraminidase

This study uses multiscale simulations to show glycans reduce drug binding to influenza neuraminidase by sterically blocking the primary binding site.

Structural and Dynamic Basis of Molecular Recognition between Acyltransferase and Carrier Protein in E. coli Fatty Acid Synthesis

This study determines the structure and dynamics of ACP-AT interactions in E. coli FAS using crystallography, MD simulations, and biochemical analyses, revealing flexible conformations and subdomain motions critical for catalysis.

An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries

The paper introduces GAMer 2, a mesh generation tool for converting structural biology data into geometric meshes suitable for biophysical modeling.

Gating Mechanism of β-Ketoacyl-ACP Synthases

The paper investigates the gating mechanism in β-ketoacyl-ACP synthases using structural and dynamic analyses to reveal how substrate discrimination occurs during catalytic reactions.

Molecular mechanism of off-target effects in CRISPR-Cas9

This paper uses molecular dynamics simulations to uncover the molecular mechanism of off-target effects in CRISPR-Cas9, identifying how DNA mismatches affect HNH domain activation and cleavage.

Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package

The paper introduces a GPU-accelerated implementation of thermodynamic integration in AMBER for faster and more efficient alchemical free energy calculations.