CompBioPhys

Braess' Paradox in Enzyme Kinetics: Asymmetry from Population Balance without Direct Cooperativity The ATPase ABCE1, a member of the ubiquitous ATP-Binding Cassette protein superfamily, is essential in eukaryotic and archaeal ribosome recycling. It comprises a pair of homologous nucleotide-binding ...

📝 We proudly present our most recent preprint @biorxiv-biophys.bsky.social about Braess' Paradox in #Enzyme Kinetics: Asymmetry from Population Balance without Direct Cooperativity with Colin and Robert 🤝 #ATPase #ABCE1 #MarkovModel #allostery📜Happy reading: www.biorxiv.org/content/10.1...

🎉

Mechanical principle of allostery Researchers at the MPI-NAT have discovered a previously unknown mechanism that allows mechanical signals to travel across proteins.

👉 Here is also an excellent summary in the corresponding press release www.mpinat.mpg.de/5065934/rn_2...

Allosteric Lever: Toward a Principle of Specific Allosteric Response Allosteric proteins transmit signals through a nonlinear coupling between localized stiffness and soft deformations, revealing a conserved, lever-like mechanism behind long-range molecular communicati...

🎉 New insights on the mechanical principle of #allostery to explain how #signals travel across #proteins now published in @physrevx.bsky.social. Joint paper by our Mathematical bioPhysics and Computational Biomolecular Dynamics groups @mpi-nat.bsky.social in our department 🔗 doi.org/10.1103/wv2k...

😀 Don't miss this excellent #PhD #job opportunity to join the @mpi-nat.bsky.social in #Göttingen, in particular Andreas' new research group @amkueffner.bsky.social #Sustainable #Biocatalysis! 👏

Large scale relative protein ligand binding affinities using non-equilibrium alchemy Ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-physical (alchemical) thermodynamic cycles have shown great promise for structure-based drug design. However, ...

... or check out the study by Gapsys et al. presented in #ChemSci @rsc.org 🔗 pubs.rsc.org/en/content/a... #alchemy #pmx #MD @gromacs.bsky.social

👏 Just in case you missed Sudarshan's intro & #tutorial during the @bioexcelcoe.bsky.social summer school, you have the chance to review it online 🔗bit.ly/45Bcp3V or watch his #webinar 📹 bit.ly/3XjSJxf! @sudars.bsky.social

🎉We proudly present our recent contribution to deciphering the #catalysis mechanism of 👉 #F1-ATPase: Our model reconciles the decade-long bi-site vs. tri-site controversy, clarifying that both pathways contribute depending on #ATP concentration and more... #MarkovModel #Bayes @mpi-nat.bsky.social

A Minimal Chemo-mechanical Markov Model for Rotary Catalysis of F1-ATPase https://www.biorxiv.org/content/10.1101/2025.06.26.661389v1

Indeed! Great so see so many happy faces enjoying the run of our @mpi-nat.bsky.social team at the Altstadtlauf! Congratulations to all of you!! 👍👏🎉

Dynamics and Energetics of Ribosomal Translation

🐦 For the early birds and #ribosome #MD and #ML enthusiasts #EBSA2025: Don't miss 📌 Lars' @larsvbock.bsky.social oral presentation (O-16.1) tomorrow at 8:30 during session 16 in hall 1: "Combining #Simulations and Machine Learning with Experiments to Explore Ribosomal #Translation" 🔗 t1p.de/ccmwk

... and two projects on #IDP #p53 by 📌Jonas (P-3.30) "Guiding the Guardian: How Phosphorylation Shifts the Ensemble of Disordered #p53" and 📌Rajlaxmi (P-3.38) "Protein Concentration Affects Secondary Structure of #p53-TAD" #EBSA2025 Enjoy the congress dinner tonight! 🍹🍽️🥂🕺💃

Bayesian electron density determination from sparse and noisy single-molecule X-ray scattering images Electron densities can be determined from noisy images without orientation determination.

Today's contributions at #EBSA2025 are posters from 📌Johanna (P-3.16) "Influences on C-type Inactivation in Voltage-gated K+ #Channels"; 📌Steffen (P-3.73) "Single-molecule X-ray Scattering at Atomistic Resolution and Without Hit Selection" continuing this story 🔗 www.science.org/doi/10.1126/... ...

📌Carter @carterjwilson.bsky.social‬ is presenting (P-2.44) "A Tale of Two #Aquaporins: Structural Mechanisms of Gating and Inhibition in Aqp3 and Aqp7" and + 📌Florian will explain (P-2.196) "How Loop #Dynamics Control Activity and Selectivity of a Short Chain #Reductase" Happy discussions! 👥

Microtubule dynamics are defined by conformations and stability of clustered protofilaments | PNAS Microtubules are dynamic cytoskeletal polymers that add and lose tubulin dimers at their ends. Microtubule growth, shortening, and transitions betw...

Have a great D2@ #EBSA2025 in Rome🫠! Here are the posters of today's session: 📌Maksim @maksimkalutskii.bsky.social is presenting (P-2.195) his project addressing #Microtubule Dynamics Are Defined by Conformations and Stability of Clustered #Protofilaments 📜🔗 www.pnas.org/doi/10.1073/...

15th EBSA congress, June 30 – July 4, 2025, Rome, Italy – Abstracts - European Biophysics Journal European Biophysics Journal -

Don't miss today's posters: Lisa (P-1.18) "Analysis and Design of Protein Fold Switches Using Physics and Machine Learning Based Methods" & Sara (P-1.186) @saragabrielli.bsky.social "Rest Assured: Programmed Translational Stalling Studied by Means of MD Simulations" #EBSA2025 Abstracts: t1p.de/gqdhx

🎉 We are happy to have many of our dept members from @mpi-nat.bsky.social presenting their research projects at #EBSA2025 in Rome! Tomorrow's (July 1) poster session with Lisa (P-1.18) + Sara (P-1.186) and more to come... 😋 Wish you all an exciting #EBSA #biophysics #congress!!

Many thanks to the PhD representatives for organizing this excellent networking event! 👍It needs to be continued... 😁

🎉🍾 Congratulations to this outstanding honor to both of the awardees! Cai, it's great having you at our department in the #Godec Group! @mpi-nat.bsky.social 🤗

❤️ Many thanks to all of you for visiting our booth during the @ndw-goe.bsky.social last saturday and for many great questions you have asked! 🤗 We were overwhelmed by your immense interest in how proteins work! @mpi-nat.bsky.social!

😍 Lisa's sketch illustrates her passion for #GPCRs: Don't miss her most recent @chemicalscience.rsc.org 📜 publication about "Identification of allosteric sites and ligand-induced modulation in the dopamine receptor through large-scale alchemical mutation scan"🔗 doi.org/10.1039/D4SC... #compchem

Wir freuen uns auf Euch bei der #ndwgoe nächsten Samstag! Trefft uns an Stand #14 am @mpsgoettingen.bsky.social auf Ebene 1 zu Computersimulationen von spannenden "Molekularen Maschinen", an denen man auch zupfen kann oder bastelt Euch eines zum Mitnehmen... @mpi-nat.bsky.social We love proteins! ❤️

😁 We are happy to join the #ndwgoe team @mpi-nat.bsky.social and look forward to meeting you at booth #14 - computer simulations of proteins @mpsgoettingen.bsky.social at the north campus!

📜 Great work by Maksim and Co-authors! Congratulations to this latest #microtubule #publication in @pnas.org 🍾 @maxotubule.bsky.social @maksimkalutskii.bsky.social @vladimirvolkov.bsky.social

😮That's great!

⁉️ How is time #irreversibility connected to #thermodynamic #entropy production in systems observed at coarse resolution? 👉 For a mini- #review on the latest developments in this field, check out our recent #Perspective 📝article in The Journal of Chemical Physics
doi.org/10.1063/5.0251089

Starting from stochastic #equations of motion, we derived thermodynamic bounds on general transport observables. Our results feature 😲surprising practical #advantages, even allowing to address #observables from bulk exp. 📜 out in @physrevlett.bsky.social 🔗 doi.org/10.1103/PhysRevLett.133.067101

🎉Congratulations to all authors to their new K+ #channel force field #paper published in 👉 @pnas.org
@reinierdevries.bsky.social
@wojciechkopec.bsky.social @mpi-nat.bsky.social #FF #MD #compbiophys Read what's new here: www.pnas.org/doi/epub/10....

Review the 📹 video recordings of the excellent past @bioexcelcoe.bsky.social webinars and see you in autumn 🍂 again! #molecularmodelling #molecularsimulations #research #compchem

Don't miss this excellent #job opportunity to join the #GROMACS developement team in Sweden! @gromacs.bsky.social