Denys Biriukov

A big thanks also to my long-time collaborator and friend @denysbiriukov.bsky.social, who served as an internal peer-reviewer for the simulation part of the work ☺️

The work became possible thanks to
@iocbprague.bsky.social, @ceitec.eu, and collaborators from #EPFL and Gdansk.

Transient Formation of Supramolecular Complexes Between Hyaluronan and Oligopeptides at Submicromolar Concentration Charged polymer interactions govern critical biological and technological processes by altering the structure and dynamics of the surrounding aqueous environment. However, studying these interactions ...

While NMR was limited to higher concentrations, SHS proved ideal for probing these subtle interactions, and MD simulations offered crucial mechanistic insight. Check the preprint for more details!
www.biorxiv.org/content/10.1...

Even at ultra-low concentrations, hyaluronan engages in multivalent, dynamic, and selective interactions—precisely the kind of behavior expected of the glycocalyx, largely shaped by hyaluronan.

🚨 Preprint alert! 🚨
We showed the transient binding and supramolecular complexation between hyaluronan and polypeptides using a suite of techniques (NMR, SHS, DLS, and MD) across a broad concentration range, including *for the first time* the submicromolar regime.

🇺🇦

I’m intentionally not including links or names. Instead, I challenge you to reflect on what might unfold in Europe and its neighboring regions in the near future.

If you usually avoid political discussions and only follow global events passively (or not at all) I still encourage you to catch up on recent developments, especially those of the past few weeks and today. Share your thoughts with friends, colleagues, or anyone in your circle.

Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions Glycosaminoglycans (GAGs) are negatively charged polysaccharides found on cell surfaces, where they regulate transport pathways of foreign molecules toward the cell. The structural and functional dive...

If you're interested in recent work we've been doing, take a look at these:
doi.org/10.1021/acs....
doi.org/10.1021/acs....
doi.org/10.1016/j.ca...

🚨 All right, since this is a place of sanity now, let’s kick things off with an open PhD position in my team to work on simulating glycans and their interactions. If you’re passionate about computational biophysics and glycobiology, go ahead and apply! Any shares would be greatly appreciated. 🙃

Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations Understanding the molecular mechanisms of pore formation is crucial for elucidating fundamental biological processes and developing therapeutic strategies, such as the design of drug delivery systems and antimicrobial agents. Although experimental methods can provide valuable information, they often lack the temporal and spatial resolution necessary to fully capture the dynamic stages of pore formation. In this study, we present two novel collective variables (CVs) designed to characterize membrane pore behavior, particularly its energetics, through molecular dynamics (MD) simulations. The first CV─termed Full-Path─effectively tracks both the nucleation and expansion phases of pore formation. The second CV─called Rapid─is tailored to accurately assess pore expansion in the limit of large pores, providing quick and reliable method for evaluating membrane line tension under various conditions. Our results clearly demonstrate that the line tension predictions from both our CVs are in excellent agreement. Moreover, these predictions align qualitatively with available experimental data. Specifically, they reflect higher line tension of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes containing 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS) lipids compared to pure POPC, the decrease in line tension of POPC vesicles as the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) content increases, and higher line tension when ionic concentration is increased. Notably, these experimental trends are accurately captured only by the all-atom CHARMM36 and prosECCo75 force fields. In contrast, the all-atom Slipids force field, along with the coarse-grained Martini 2.2, Martini 2.2 polarizable, and Martini 3 models, show varying degrees of agreement with experiments. Our developed CVs can be adapted to various MD simulation engines for studying pore formation, with potential implications in membrane biophysics. They are also applicable to simulations involving external agents, offering an efficient alternative to existing methodologies.

Third, Tim and @denysbiriukov.bsky.social presented new collective variables to study the energetics of lipid membrane pores.
pubs.acs.org/doi/10.1021/...

Good job!