Max Planck School Matter to Life

@mattertolife.bsky.social

An international graduate program aiming to understand, simulate and predict life-like processes and systems. Our school connects Germanys leading scientists in the interdisciplinary field of #mattertolife. mattertolife.maxplanckschools.org

🔊 Paper Alert 🗞️ from the group of MtL Fellow @kgoepfrich.bsky.social A Kiss from a Loop! 🌹 These alpha kissing loops greatly expand the repertoire of RNA architectural motifs available for programmable, sequence-defined nanostructure assembly. pubs.acs.org/ancac3/artic...

Programmable Edge-to-Edge Assembly of RNA Nanostructures

Abstract. Building complex RNA nanostructures requires precise molecular connectors for controlled self-assembly. Existing connectors, such as kissing loop

pubs.acs.org

Congratulations to PhD candidates Arsenii Hordeichyk and Kristian Pajanonot for their latest publication. The work was part of the PhD doctoral work of Arsenii and the Master thesis of Kristian in the group of MtL Fellow Andreas Bausch. www.science.org/doi/10.1126/...

Reconstituted nascent adhesion condensates drive actin polymerization on supported lipid bilayers

Adhesion protein condensates with distinct properties differentially shape actin organization.

science.org

Register now at us02web.zoom.us/webinar/regi... and join us next week!

Max Planck School Matter to Life@mattertolife.bsky.social · 4mo ago

It is a pleasure to welcome another new #mattertolife Fellow to our Lecture Series! On 15 April at 3 pm Laura Heinen from DWI-Leibniz Institute for Interactive Materials will join us with an exciting talk on: Synthetic Cells - How to Stay "Alive?" Register now: us02web.zoom.us/webinar/regi...

🧪 Simulating large biomolecules without massive compute costs This new study from the group Frauke Gräter presents a coarse-grained model of chondroitin sulfate A (CSA) using the Martini 3 framework. pubs.acs.org/doi/10.1021/... @mpip-mainz.mpg.de @hitsters.bsky.social

Coarse-Grained Martini 3 Model of Chondroitin Sulfate A

Chondroitin sulfate A (CSA) is a negatively charged linear glycosaminoglycan that plays a vital role in many biological processes. Research on CSA has been challenging due to its size, chemical heterogeneity, and multitude of binding partners. To address these issues, we developed a model of CSA for coarse-grained molecular dynamics simulations based on the Martini 3 force field. We demonstrate that this model is capable of reproducing atomistic properties of the repeating CSA disaccharide unit, including its molecular volume, bonded interactions, and structural polymer properties of CSA chains of different lengths. In particular, for biologically relevant long chains and despite using an explicit solvent, the computational cost is significantly reduced, relative to the cost equivalent atomistic simulations would require. The compatibility of the model with the Martini Go̅ protein model was tested by retrieving the force–response relationship of the CSA–malaria adhesin VAR2CSA complex. Importantly, we explored the influence of electrostatics on CSA aggregation. We show that the default Martini 3 parameters lead to overaggregation. We provide at least three different strategies to alleviate this issue, making use of a bigger bead for sodium cations, reflecting their hydration shell, partial ionic charges as a mean-field resource to take into account electronic polarizability, and, optionally, particle mesh Ewald summation as a more robust treatment of long-range electrostatics. Our model enables predictive modeling of CSA and potentially other chondroitin sulfates with the Martini 3 force field. In addition, this model provides insights for the further development of coarse-grained models of highly charged systems.

pubs.acs.org