Biology subjects

Kasson, P.

Publications and source records attributed to Kasson, P..

4 recordsLinked to original sources

bioRxiv2021

gmxapi: a Gromacs-native Python interface for molecular dynamics with ensemble and plugin support

Gmxapi provides an integrated, native Python API for both standard and advanced molecular dynamics simulations in GROMACS. The Python interface permits multiple levels of integration with the core GROMACS libraries, and legacy support is provided via an interface that mimics the command-line syntax, so that all GROMACS commands are fully available. Gmxapi has been officially supported since the GROMACS 2019 release and is enabled by default in current versions of the software. Here we describe gmxapi 0.3 and later. Beyond simply wrapping GROMACS library operations, the API permits several advanced operations that are not feasible using the prior command-line interface. First, the API allows custom user plugin code within the molecular dynamics force calculations, so users can execute custom algorithms without modifying the GROMACS source. Second, the Python interface allows tasks to be dynamically defined, so high-level algorithms for molecular dynamics simulation and analysis can be coordinated with loop and conditional operations. Gmxapi makes GROMACS more accessible to custom Python scripting while also providing support for high-level data-flow simulation algorithms that were previously feasible only in external packages. Author SummaryThe gmxapi software provides a Python interface for molecular dynamics simulations in GROMACS. In addition to simply wrapping GROMACS commands, it supports custom user plugin code, ensemble simulation, and data-flow chaining of commands. As such, gmxapi enables the writing and execution of high-level simulation algorithms. The software ships with GROMACS and is freely available under an LGPL2 license.

bioinformatics↗

bioRxiv2021

Single-virus fusion measurements yield an opportunistic model for SARS-CoV-2 fusion

SARS-CoV-2 binds to cell-surface receptors and is activated for membrane fusion and cell entry via proteolytic cleavage. Phenomenological data have shown that SARS-CoV-2 can be activated for entry at either the cell surface or in endosomes, but the relative roles in different cell types and mechanisms of entry have been debated. Here we use single-virus fusion experiments and exogenously controlled proteases to probe activation directly. We find that plasma membrane and an appropriate protease are sufficient to support SARS-CoV-2 pseudovirus fusion. Furthermore, fusion kinetics of SARS-CoV-2 pseudoviruses are indistinguishable no matter which of a broad range of proteases was used to activate the virus. This suggests that fusion mechanism is insensitive to protease identity or even whether activation occurs before or after receptor binding. These data support a model for opportunistic fusion by SARS-CoV-2, where subcellular location of entry likely depends on the differential activity of airway, cell-surface, and endosomal proteases, but all support infection. Inhibiting any single host protease may thus reduce infection in some cells but may be less clinically robust. ImportanceSARS-CoV-2 can use multiple pathways to infect cells, as demonstrated recently when new viral variants switched dominant infection pathways. Here, we use single-virus fusion experiments together with biochemical reconstitution to show that these multiple pathways coexist simultaneously and specifically that the virus can be activated by different proteases in different cellular compartments with mechanistically identical effect. The consequences of this are that the virus is evolutionarily plastic and that therapies targeting viral entry should address multiple pathways at once to achieve optimal clinical effects.

microbiology↗

bioRxiv2020

Precise triggering and chemical control of single-virus fusion within endosomes

Many enveloped viruses infect cells within endocytic compartments. The drop in pH that accompanies endosomal maturation, often in conjunction with proteolytic factors, serves as a trigger for viral fusion proteins to insert into the endosomal membrane and drive fusion. The dynamics of this process has been studied by tracking viruses within living cells, which limits the precision with which fusion can be synchronized and controlled, and by reconstituting viral fusion to synthetic membranes, which introduces non-physiological membrane curvature and composition. To overcome these limitations, we have engineered the chemically controllable triggering of single-virus fusion within endosomes. We isolate influenza virus:endosome conjugates from cells prior to fusion, immobilize them in a microfluidic flow cell, and then rapidly and controllably trigger fusion. This platform demonstrates lipid-mixing kinetics that are grossly similar to influenza fusion with model membranes but display some subtle differences. Because it preserves endosomal membrane asymmetry and protein composition, it also provides a means to test how perturbations to endosomal trafficking and cellular restriction factors affect viral membrane fusion.

biophysics↗

bioRxiv2019

Antibiotic uptake across gram-negative outer membranes: better predictions towards better antibiotics

Crossing the gram-negative bacterial membrane poses a major barrier to antibiotic development, as many small molecules that can biochemically inhibit key bacterial processes are rendered microbiologically ineffective by their poor cellular uptake. The outer membrane is the major permeability barrier for many drug-like molecules, and the chemical properties that enable efficient uptake into mammalian cells fail to predict bacterial uptake. We have developed a computational method for accurate prospective prediction of outer-membrane uptake of drug-like molecules, which we combine with a new medium-throughput experimental assay. Parallel molecular dynamics simulations are used to successfully and quantitatively predict experimental permeabilities. For most polar molecules we test, outer membrane permeability also correlates well with whole-cell uptake. The ability to accurately predict and measure outer-membrane uptake of a wide variety of small molecules will enable simpler determination of which molecular scaffolds and which derivatives are most promising prior to extensive chemical synthesis. It will also assist in formulating a more systematic understanding of the chemical determinants of outer-membrane permeability.

biochemistry↗