Abby Dommer

Frontiers | C-terminus-outward orientation of SARS-CoV-2 envelope proteins on viral capsid enables a novel virus–cell interaction pathway Since the onset of COVID-19, emphasis has been largely placed on spike proteins, while other molecules of severe acute respiratory syndrome coronavirus 2 (SA...

E-protein news!

Cutaway and close-up views of a Martini coarse-grained whole-cell model of JCVI-syn3A, showing the densely packed cytoplasm with proteins, RNA, metabolites, and chromosome inside a lipid membrane with embedded membrane proteins

Our paper on [Bentopy](doi.org/10.1002/pro....) is out in Protein Science! We developed Bentopy to make assembling large-scale MD models more accessible, building on what we learned from trying to simulate whole-cell models. Here's our updated Martini JCVI-syn3A cell model👇

My little outlook on how our lungs 🫁 are like the sea 🌊 is finally out in Central Science. Thanks to the support from incredible mentors @rommieamaro.bsky.social and @kprather.bsky.social !!

i'm super interested in how those organics are enriched/ selectively transferred between lung fluid and aerosol. we really just need some dedicated studies using the right production mechanism and the right lung fluid surrogate!

but what we've learned is that aerosols produced by film bursting are fine, and are enriched in surfactant-like/ surfactant-associated material. other mechanisms produce bigger particles that contain more soluble stuff, more water.

other mechanisms in vocalization, like lips teeth tongue movements produce those larger droplets but i'm not as well versed in those.

but yeah my thoughts are that the composition of these changes based on origin and mechanism. fine particles from film bursting = enriched in surfactant-like stuff

we just submitted an outlook on this (under review) because I think we just don't know! Our hunch, is that these film burst mechanisms are similar to bubble bursting in the ocean producing sea spray, on which we have lots of data, especially wrt organics/virus transfer and aerosol composition, AND:

this is the gajillion dollar question, right!? so many studies use lung surfactant b/c of small airway opening in alveoli, but I've discussed w/ lung cell biologists who say terminal bronchioles also participate, and these can have a whole separate mixture of lung fluid components,

it's my understanding that those submicron particles are more infectious than larger ones generally, having longer airborne lifetimes. I can dig out some literature on this

Upper airways also produce fine aerosols by film bridge rupture in vocal folds! probably these are also loaded up with viral particles and would also be highly infectious. but i'd need to check if those infectivity studies differentiate fine particles from deep lung maneuvers vs. vocalization

Angstrom-resolution imaging of cell-surface glycans Glycobiology is rooted in the study of monosaccharides, Angstrom-sized molecules that are the building blocks of intricate glycosylation patterns. Glycosylated biomolecules form the glycocalyx, a dens...

This is an amazing achievement - angstrom scale imagine of glycan molecules, what a great time for #glycotime. Congrats Leonhard Möckl!

www.biorxiv.org/content/10.1...