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Siewert-Jan Marrink

@cg-martini.bsky.social

Martini lover. Shaken, stirred, or self-assembled. https://cgmartini.nl/

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Siewert-Jan Marrink@cg-martini.bsky.social · 4mo ago

Another interesting paper from Liguo Wang, now online at JACS:

Condensates as Conformation Editors of Disordered Client Proteins

Biomolecular condensates organize cellular biochemistry not only by passive concentration modulation of molecules but also by potentially remodeling client protein conformations. However, the systematic principles governing such conformational editing are unknown. Here, we use coarse-grained simulations to demonstrate that diverse condensate environments remodel disordered client proteins in a scaffold-specific manner. Additionally, we explore the factors of this remodeling, establishing that the linear patterning of scaffold interaction motifs along sequence (sticker clustering) plays an important role, whereas an increased scaffold chain length primarily slows client dynamics while leaving their sequence-specific intrachain contact patterns largely preserved. This conformational remodeling is mediated by varied and nonuniform client–condensate interaction maps that are not solely encoded by primary sequence grammar but are cooperatively shaped by the emergent condensate architecture. Our work reveals that condensates function as sophisticated regulators of recruited disordered client conformation, with broad implications for cellular regulation and therapeutic intervention.

pubs.acs.org

Siewert-Jan Marrink@cg-martini.bsky.social · 4mo ago

Proudly presenting work from my student Liguo Wang, who systematically compared condensates formed by full-length MDPs to IDR-only systems.

Folded domains impose structural heterogeneity and attenuated dynamics in biomolecular condensates - Nature Communications

Unlike simplified IDR-only models, natural condensates with folded domains exhibit pronounced structural heterogeneity and attenuated dynamics, revealing folded domains as architectural keystones in n...

doi.org

Jan Stevens@janstevens.bsky.social · 6mo ago

Building realistic models of cells means fitting proteins, RNA, and metabolites at experimental concentrations inside complex cellular architectures. Here's a movie showing how we pack the cytoplasmic space of the JCVI-Syn3A cell:

Siewert-Jan Marrink@cg-martini.bsky.social · 7mo ago

Let's safe the planet and get rid of PFAS! A good start is to perform simulations, now possible with:

Martini 3 coarse-grain model for linear PerFluoroAlkyl Substances | ChemRxiv

PerFluoroAlkyl Substances (PFAS) are a family of over seven million chemicals found in a vast number of industrial and consumer applications. Often referred to as the "forever chemicals", they gained increasing attention due to their environmental and ...

chemrxiv.org