New preprint: www.biorxiv.org/content/10.1... We used molecular dynamics simulations and solid-state NMR (@fmp-berlin.de) to look at calcium binding to the pore domain of the calcium-gated K+ channel MthK. @wojciechkopec.bsky.social @compbiophys.bsky.social

New preprint: www.biorxiv.org/content/10.1... We used molecular dynamics simulations and solid-state NMR (@fmp-berlin.de) to look at calcium binding to the pore domain of the calcium-gated K+ channel MthK. @wojciechkopec.bsky.social @compbiophys.bsky.social

Come to my talk on ACS Fall 2025 about K+ channel ECC force field on 19 Aug😏 We also have our new developed GCMC FEP with benchmark.😉 #acsfall2025

MscL channel opens up asymmetrically! Check out our latest story, spearheaded by my brilliant postdoc Olga pubs.acs.org/doi/10.1021/...

Asymmetric Nature of MscL Opening Revealed by Molecular Dynamics Simulations

The bacterial mechanosensitive channel, MscL, opens in response to elevated membrane tension during osmotic shock. Some mutations, like L17A and V21A, can reduce the activation tension threshold, thus...

pubs.acs.org

Excited to share our latest work in @pnas.org! Combining simulations and cryo-ET, we reveal how microtubules decide between growth and shortening. doi.org/10.1073/pnas... @maksimkalutskii.bsky.social @vladimirvolkov.bsky.social @compbiophys.bsky.social @mpi-nat.bsky.social @qmul.ac.uk @dundee.ac.uk.

Bert de Groot, @chenggonghui.bsky.social‬, & colleagues @compbiophys.bsky.social used molecular dynamics simulations to visualize how potassium ions pass through a potassium ion channel at atomic resolution for the first time. This could help understand ion channel regulation and drug interactions.⬇️

Our K+ channel force field paper is now online on PNAS www.pnas.org/doi/epub/10.... It has been a great time working with @reinierdevries.bsky.social @wojciechkopec.bsky.social , Bert de Groot here at @mpi-nat.bsky.social @compbiophys.bsky.social

Happy that this is now out in @pnas.org www.pnas.org/doi/10.1073/...

Reinier de Vries@reinierdevries.bsky.social · 2y ago

Side by side comparison of K+ permeation in MthK using standard Charmm36m and our ECC version.

Very happy that this story found its home at @pnas.org www.pnas.org/doi/10.1073/...

Wojciech Kopec @wojciechkopec.bsky.social · 2y ago

MD simulations of K+ ions permeation through the MthK potassium channel, done at +150 mV. We developed and applied optimized ion parameters within the Electronic Continuum Correction (ECC) framework. The simulated current quantitatively matches the experimental one. www.biorxiv.org/content/10.1...

New preprint: TS2CG version 2, building and simulating membranes with any shape and lateral organisation. We got Martini Globe, Martini Möbius strip and again mitochondrion. www.biorxiv.org/content/10.1... @cg-martini.bsky.social @janstevens.bsky.social @fabianschuhmann.bsky.social

Recharging batteries in Sta Monica with @compbiophys.bsky.social. Come and reach us in #bps2025! (Contributions listed in the comments) @reinierdevries.bsky.social @larsvbock.bsky.social @steschuu.bsky.social @oberend.bsky.social

Poster Session #bps2025 on Sunday, February 16 starting at 1:45 pm in the West Exhibit Hall including posters of Aaron, Sara @saragabrielli.bsky.social, Ole, Bartosz, Chen, Reinier plan.core-apps.com/bpsam2025/ev...

We proudly present a selection of research projects from @compbiophys.bsky.social at this year's #bps2025 meeting in LA! Don't miss the oral presentations or posters being presented and find us in the program biophysics.cld.bz/BPS2025-Full...

An updated version is now available, we added some Kv1.2-2.1 and KcsA simulations (in the SI), because why not :) [IV curves close to experimental ones once again] and expanded the method section quite a bit. Hopefully soon it finds its home!

Wojciech Kopec @wojciechkopec.bsky.social · 2y ago

MD simulations of K+ ions permeation through the MthK potassium channel, done at +150 mV. We developed and applied optimized ion parameters within the Electronic Continuum Correction (ECC) framework. The simulated current quantitatively matches the experimental one. www.biorxiv.org/content/10.1...

New preprint! My postdoc Olga looked in detail into the mechanism, energetics and kinetics of the MscL channel opening! It's asymmetric and harder than you think ;) www.biorxiv.org/content/10.1...

Asymmetric nature of MscL opening revealed by molecular dynamics simulations

We employed all-atom unbiased molecular dynamics to simulate the L17A, V21A mutant of MscL. Under a tension of 30 mN/m, the closed state adopts a funnel-like conformation. Subsequently, five chains of...

biorxiv.org

Side by side comparison of K+ permeation in MthK using standard Charmm36m and our ECC version.

Wojciech Kopec @wojciechkopec.bsky.social · 2y ago

MD simulations of K+ ions permeation through the MthK potassium channel, done at +150 mV. We developed and applied optimized ion parameters within the Electronic Continuum Correction (ECC) framework. The simulated current quantitatively matches the experimental one. www.biorxiv.org/content/10.1...

Side by side comparison of K+ permeation in MthK using standard Charmm36m and our ECC version.

Wojciech Kopec @wojciechkopec.bsky.social · 2y ago

MD simulations of K+ ions permeation through the MthK potassium channel, done at +150 mV. We developed and applied optimized ion parameters within the Electronic Continuum Correction (ECC) framework. The simulated current quantitatively matches the experimental one. www.biorxiv.org/content/10.1...

Happy to be part of the bluesky researcher's community now! Just moved over... Looking forward to the news and views shared here! 😀

cup of TIP3P

MD simulations of K+ ions permeation through the MthK potassium channel, done at +150 mV. We developed and applied optimized ion parameters within the Electronic Continuum Correction (ECC) framework. The simulated current quantitatively matches the experimental one. www.biorxiv.org/content/10.1...