Lipid dependent protein-protein binding

cd44-FERM.PNG

 

Martini based simulations reveal the molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2, and how this affects binding to FERM. Check for details:

Sun, Schroer, Palacios, et al., PLoS Comp. Biol., online.

Membrane assisted toppling

ECF-memdeform.jpg

Remarkable lipid gymnastics: collective bending of the membrane around an energy coupling factor (ECF) transporter facilitates toppling of the mobile (S-) component mediating substrate transport. Predictions of the simulations concerning the importance of certain lipid types are nicely confirmed experimentally. For details, see:

Faustino, Abdizadeh et al., Nature Commun. 11, 1763 (2020). doi:10.1038/s41467-020-15554-9

Protein-lipid interplay

The diversity of protein-lipid interactions remains a fascinating topic. This paper from the Sansom group is a nice illustration of how multiple lipids fight with each other to sit next to the big guys. Duncan, Corey & Sansom, PNAS, 2020.

2020 Martini Workshop

!!!!! Cancelled !!!!

Announcing the 2020 Martini Coarse-Graining Workshop

Where: University of Groningen, Groningen, The Netherlands.

Links to the venue and city:

  1. Address and info of the venue
  2. Location of the venue
  3. Directions from Martini hotel to the venue

When: August 23-28, 2020. The workshop starts on Sunday, August 23 at 8 pm (welcome reception), first lecture on Monday, August 24 at 9 am, and finishes on Friday, August 28 at 1 pm.

What:

  • Lectures about background, philosophy and theory of coarse-grained models in general but mostly specifically about the Martini coarse-grained model.
  • Hands-on sessions where one can experience the aspects of the model, get practical experience with setting-up, running and developing new or refined Martini models. Experienced users are available for guidance and discussion.

Who: Anyone interested! However, we assume that you have a working knowledge of the Linux operating system and some experience on running MD simulations. The idea is that everyone, from beginner to experienced modeller will be able to work and progress on their own. Keep in mind that you will gain more from the workshop if you invest time in some modelling tools before the workshop starts. All hands-on exercises use a recent GROMACS version. We advise you to get some practice with GROMACS before the workshop, in this way you will spend more time on learning coarse-graining than on learning GROMACS.

Read more: 2020 Martini Workshop

Actin membrane binding

Actin fibres are important for the shape, strength and movement of cells. They can bind to the cell membrane, providing it with support. However, exactly how they bind is unknown. Martini-based simulations (what else ?), supported by experiments, reveal how divalent ions can either enhance or suppress the binding strength dependent on lipid composition. For details, see: Schroer et al., PNAS, online.

actin-membrane.jpg

Martini 2.3 featuring cation-π interactions

Check out this improved version of Martini, now able to represent cation-π interactions and allowing a much more realistic binding of peripheral membrane proteins. The version is coined 2.3, but should not be confused with the forthcoming release of Martini 3 which concerns a thorough recalibration of the full interaction matrix. For details, see:

H.M. Khan et al., Capturing choline-aromatics cation-π interactions in the MARTINI force field, JCTC, 2020. doi.org/10.1021/acs.jctc.9b01194

The new parameter definitions can be downloaded here.