GPCR-arrestin complex formation

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Last Updated: Thursday, 23 December 2021 09:02

toc2.pngMartini-based simulations capture the spontaneous binding of beta-arrestin2 to beta2-adrenergic receptor in a similar pose as the crystallographically resolved structure of rhodopsin/arresin-1. Cool !

See the paper from Pluhackova et al.: https://doi.org/10.3389/fcell.2021.807913

The complex formation is found to be dependent on specific lipids, as well as on phosphorylation state. Parameters for phosphorylated serine and threonine in the framework of Martini 2/2P are provided in the SI.

Cell-scale membrane envelope

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Last Updated: Monday, 20 December 2021 11:55

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From the lab of Tajkhorshid: a protocol for setting up simulations of cell-scale membrane envelopes, using Martini.

Paving the way for whole cell simulations !

See Vermaas et al., JCIM, online, for details.

Deep eutectic solvents

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Last Updated: Thursday, 16 December 2021 13:10

sc1c06521_0010.gifDeep eutectic solvents (DESs) are a more environmentally friendly, cost-effective, and recyclable alternative for ionic liquids. Since the number of possible deep eutectic solvents is very large, there are needs for effective methods to predict the physicochemical nature of possible new deep eutectic solvents that are not met by the currently available models.

To meet this challenge, we parameterized and validated a first set of DESs compatible with Martini 3, and showed its application in simulating liquid-liquid extraction processes.

For details, check Vainikka et al., ACS Sust. Chem. Engin., online.

Martini 3 versus force matching

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Last Updated: Monday, 29 November 2021 08:17

An interesting study from the Wilson lab shows how Martini 3 can reproduce complex chromonic self-assembly, whereas specifically parameterized CG models obtained with force matching (FM) cannot. To see the details and the underlying reasons for the failure of FM, see: Yu & Wilson, J. Mol. Liq., online.

Self-assembling fibers

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Last Updated: Wednesday, 24 November 2021 07:55

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The challenge for modern day force fields to correctly describe self-assembling supramolecular polymers is nicely illustrated in a paper from Piskorz et al., JCIM, online. Most atomistic force fields, as well as standard Martini, are not capable of maintaining the fibrous structure of the compound 1,3,5-trisamidocyclohexane. Only Charmm-Drude and GAFF perform well, along with ..... polarizable Martini !

Nanopore for protein sequencing

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Last Updated: Friday, 19 November 2021 07:12

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Components from all three domains of life are used by the Maglia group to fabricate an integrated multiprotein complex that controls the unfolding and threading of individual proteins across a nanopore.

Multiscale models including Martini contributed to unravel the details of the structure and functioning of this megacomplex.

For details, see:  Zhang et al., Nature Chem. 2021.