Margaret E. Johnson
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View article: A membrane-driven biochemical oscillator tunable by the volume to surface area ratio
A membrane-driven biochemical oscillator tunable by the volume to surface area ratio Open
Oscillations are ubiquitous features of biological organisms, playing crucial roles in processes from circadian rhythms to developmental patterning. Protein-based biochemical oscillators have particular applications in synthetic biology be…
View article: Membrane bending energy selects for compact growth of protein assemblies
Membrane bending energy selects for compact growth of protein assemblies Open
Remodeling of cell membranes into vesicles is essential for receptor transport into cells and viral escape from infected cells. Membranes must be forced into these highly curved vesicles, and this is primarily driven through a structured a…
View article: Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization
Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization Open
Successful DNA transcription demands coordination between proteins that bind DNA while simultaneously binding to one another to form dimers or higher-order complexes. For proteins with numerous DNA targets throughout the genome, measuremen…
View article: Binding affinities for 2D protein dimerization benefit from enthalpic stabilization
Binding affinities for 2D protein dimerization benefit from enthalpic stabilization Open
Dimerization underpins all macromolecular assembly processes both on and off the membrane. While the strength of dimerization, K_D, is commonly quantified in solution (3D), many proteins like the soluble BAR domain-containing proteins also…
View article: The PH domain in the ArfGAP ASAP1 drives catalytic activation through an unprecedented allosteric mechanism
The PH domain in the ArfGAP ASAP1 drives catalytic activation through an unprecedented allosteric mechanism Open
ASAP1 is a multidomain Arf GTPase-activating protein (ArfGAP) that catalyzes GTP hydrolysis on the small GTPase Arf1 and is implicated in cancer progression. The PH domain of ASAP1 enhances its activity greater than 7 orders of magnitude b…
View article: Parallelization of particle-based reaction-diffusion simulations using MPI
Parallelization of particle-based reaction-diffusion simulations using MPI Open
Particle-based reaction-diffusion models offer a high-resolution alternative to the continuum reaction-diffusion approach, capturing the discrete and volume-excluding nature of molecules undergoing stochastic dynamics. These methods are th…
View article: Dynamin1 long- and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters
Dynamin1 long- and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters Open
Endocytosis requires a coordinated framework of molecular interactions that ultimately lead to the fission of nascent endocytic structures. How cytosolic proteins such as dynamin concentrate at discrete sites that are sparsely distributed …
View article: Discovering optimal kinetic pathways for self-assembly using automatic differentiation
Discovering optimal kinetic pathways for self-assembly using automatic differentiation Open
Macromolecular complexes are often composed of diverse subunits. The self-assembly of these subunits is inherently nonequilibrium and must avoid kinetic traps to achieve high yield over feasible timescales. We show how the kinetics of self…
View article: Predicting protein curvature sensing across membrane compositions with a bilayer continuum model
Predicting protein curvature sensing across membrane compositions with a bilayer continuum model Open
Cytoplasmic proteins must recruit to membranes to function in processes such as endocytosis and cell division. Many of these proteins recognize not only the chemical structure of the membrane lipids, but the curvature of the surface, bindi…
View article: Discovering optimal kinetic pathways for self-assembly using automatic differentiation
Discovering optimal kinetic pathways for self-assembly using automatic differentiation Open
During self-assembly of macromolecules ranging from ribosomes to viral capsids, the formation of long-lived intermediates or kinetic traps can dramatically reduce yield of the functional products. Understanding biological mechanisms for av…
View article: Secretion‐Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface
Secretion‐Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface Open
Protein‐based biomaterials have played a key role in tissue engineering, and additional exciting applications as self‐healing materials and sustainable polymers are emerging. Over the past few decades, recombinant expression and production…
View article: Secretion‐Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface
Secretion‐Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface Open
Protein‐based biomaterials have played a key role in tissue engineering, and additional exciting applications as self‐healing materials and sustainable polymers are emerging. Over the past few decades, recombinant expression and production…
View article: GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion
GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion Open
To elucidate how eukaryotic sequence-specific transcription factors (TFs) search for gene targets on chromatin, we used multi-color smFRET and single-particle imaging to track the diffusion of purified GAGA-Associated Factor (GAF) on DNA a…
View article: Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions
Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions Open
For HIV virions to become infectious, the immature lattice of Gag polyproteins attached to the virion membrane must be cleaved. Cleavage cannot initiate without the protease formed by the homo-dimerization of domains linked to Gag. However…
View article: Dynamin1 long- and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters
Dynamin1 long- and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters Open
Endocytosis requires a coordinated framework of molecular interactions that ultimately lead to the fission of nascent endosomes. How cytosolic proteins, such as dynamin, timely concentrate at discrete sites that are sparsely distributed ac…
View article: Temporal control by co-factors prevents kinetic trapping in retroviral Gag lattice assembly
Temporal control by co-factors prevents kinetic trapping in retroviral Gag lattice assembly Open
For retroviruses like HIV to proliferate, they must form virions shaped by the self-assembly of Gag polyproteins into a rigid lattice. This immature Gag lattice has been structurally characterized and reconstituted in vitro , revealing the…
View article: Title IX and "Menstruation or Related Conditions"
Title IX and "Menstruation or Related Conditions" Open
itle IX of the Education Amendments Act of 1972 (“Title IX”) prohibits sex discrimination in educational programs or activities receiving federal financial assistance. Neither the statute nor its implementing regulations explicitly define …
View article: Defects in the HIV immature lattice support essential lattice remodeling within budded virions
Defects in the HIV immature lattice support essential lattice remodeling within budded virions Open
For HIV virions to become infectious, the immature lattice of Gag polyproteins attached to the virion membrane must be cleaved. Cleavage cannot initiate without the protease formed by the homo-dimerization of domains linked to Gag. However…