M. E. Johnson

Predicting protein curvature sensing across membrane compositions with a bilayer continuum model

The paper develops a bilayer continuum model to predict how lipid composition affects protein curvature sensing in membranes.

Discovering optimal kinetic pathways for self-assembly using automatic differentiation

This paper uses automatic differentiation to optimize kinetic pathways for self-assembly, identifying strategies to avoid kinetic traps and improve assembly yield in multi-subunit complexes.

GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion

This study tracks GAF's chromatin search mechanism using smFRET and imaging, showing 1D-3D diffusion enables efficient target finding despite nucleosome barriers.

Defects in the HIV immature lattice support essential lattice remodeling within budded virions

This paper uses reaction-diffusion simulations to show that incomplete HIV immature lattice dynamics enable rapid Gag-Pol dimerization, essential for viral maturation.

Discovery and characterization of highly potent and selective covalent inhibitors of SARS-CoV-2 PLpro

This study identifies and characterizes two covalent PLpro inhibitors, HUP0109 and DX-027, as potential treatments for SARS-CoV-2.

Surveillance of Vermont wildlife in 2021-2022 reveals no detected SARS-CoV-2 viral RNA

The study tested 739 Vermont wildlife samples for SARS-CoV-2 and found no viral RNA, contrasting with findings in other North American deer populations.

Temporal control by co-factors prevents kinetic trapping in retroviral Gag lattice assembly

This study uses a reaction-diffusion model to show that co-factors like IP6 delay Gag lattice assembly, preventing kinetic trapping and enabling productive lattice formation.

Quantitative single-cell transcriptome-based ranking of engineered AAVs in human retinal explants

This study ranks engineered AAVs in human retinal explants using single-cell RNA-Seq, identifying top-performing serotypes for retinal gene therapy.

The bitter end: T2R bitter receptor agonists elevate nuclear calcium and induce apoptosis in non-ciliated airway epithelial cells

This study shows T2R agonists induce apoptosis in non-ciliated airway cells through nuclear calcium and mitochondrial pathways, potentially as a defense against infection or a risk in disease.

A continuum membrane model predicts curvature sensing by helix insertion

The paper develops a continuum membrane model to predict how helix insertion affects curvature sensing in membranes, showing it lowers energy for small vesicles but destabilizes larger ones.

Nascent clathrin lattices spontaneously disassemble without sufficient adaptor proteins

This paper quantifies the conditions necessary for stable clathrin assembly on membranes, showing that sufficient adaptor proteins are required to prevent spontaneous disassembly.

Speed limits of protein assembly with reversible membrane localization

The paper derives a model for protein assembly on membranes, showing how reduced dimensionality can significantly speed up complex formation.

Integrative genomics identifies lncRNA regulatory networks across 1,044 pediatric leukemias and extra-cranial solid tumors

The paper identifies lncRNA regulatory networks in pediatric cancers using integrated genomics data from 1,044 samples, revealing their roles in proliferation, metabolism, and DNA damage.

Thermodynamics and free energy landscape of BAR-domain dimerization from molecular simulations

This study uses molecular simulations to analyze the thermodynamics and free energy landscape of BAR-domain dimerization, revealing stable specific and nonspecific dimers and their roles in membrane interactions.

scAAVengr: Single-cell transcriptome-based quantification of engineered AAVs in non-human primate retina

The paper develops scAAVengr, a single-cell pipeline to quantify AAV gene expression efficiency in non-human primate retina, demonstrating its utility with a top-performing AAV variant.

The identity of human tissue-emigrant CD8+ T cells

The paper characterizes tissue-emigrant CD8+ T cells in humans and non-human primates, revealing distinct migratory behaviors and clonal dynamics.

NERDSS: a non-equilibrium simulator for multibody self-assembly at the cellular scale

NERDSS simulates multibody self-assembly processes by integrating reaction-diffusion with rule-based models, enabling comparison with experimental data on clathrin-mediated endocytosis and viral lattice assembly.

An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology

This paper introduces an implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology, showing agreement with explicit lipid models and enabling stable multi-protein complex formation.

Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis

The paper shows that protein copy numbers in yeast endocytosis networks are balanced relative to their binding partners, and this balance affects functional outcomes like complex formation.

Cytosolic proteins can exploit membrane localization to trigger functional assembly

The paper quantifies how membrane localization enhances protein-protein interactions by reducing search space, showing significant increases in effective affinity for endocytic proteins.