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Manuel N. Melo at ITQB NOVA

@melolab.bsky.social

Using computers to solve biochemical challenges. All the fun, none of the dishwashing! https://www.itqb.unl.pt/labs/multiscale-modeling

31 Posts163 Follower121 Folgt
Holthuis Lab@holthuislab.bsky.social · 2mo ago

📯 Our paper “VPS13C/PARK23 initiates lipid transfer and membrane remodeling for efficient lysosomal repair” out now in Nature Communications rdcu.be/frKmN

VPS13C/PARK23 initiates lipid transfer and membrane remodeling for efficient lysosomal repair

Nature Communications - Not all components of the lysosome damage response pathway have been defined. Here, the authors discover that the bridge-like lipid transport protein VPS13C senses lysosomal...

rdcu.be

Manuel N. Melo at ITQB NOVA@melolab.bsky.social · last yr.

Cool new AMP pore structures and a membrane activity dependent on lipid shape, in our new paper by @marmakow.bsky.social! (Using the old-but-gold Martini 2 model from @cg-martini.bsky.social) #compchem #compbiophys #compbiol 🖥️🧪 pubs.acs.org/doi/full/10....

Lipid Shape as a Membrane Activity Modulator of a Fusogenic Antimicrobial Peptide

An intriguing feature of many bacterial membranes is their prevalence of non-bilayer-forming lipids, such as the cone-shaped phosphatidylethanolamines and cardiolipins. Many membrane-active antimicrob...

pubs.acs.org

Manuel N. Melo at ITQB NOVA@melolab.bsky.social · 2y ago

It was great to be part of this enormous effort spanning several years. Big cheers to the Martini 3 Lipid Taskforce crew, especially Kasper and @pauloctsouza.bsky.social! #compchem #moleculardynamics

Paulo C. T. Souza@pauloctsouza.bsky.social · 2y ago

Excited to announce the release of our preprint, "The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior", now available on @chemrxiv.bsky.social 👉 Read the full preprint here: chemrxiv.org/engage/chemr...

Manuel N. Melo at ITQB NOVA@melolab.bsky.social · 2y ago

In need of some Martini 3 CG parameters for stuff like ATP, NAD+/NADH or FAD? We just made parameters for those and several other molecules public while the preprint is in the works! Check out the lab's repository at github.com/MeloLab/Cofa... 🖥️🧑‍🔬

GitHub - MeloLab/CofactorParameterization: Nucleotide cofactor parameters developed for Martini 2.2 and 3.

Nucleotide cofactor parameters developed for Martini 2.2 and 3. - MeloLab/CofactorParameterization

github.com

Manuel N. Melo at ITQB NOVA@melolab.bsky.social · 3y ago

And after the GitHub soft opening, here's the preprint for our Martini 3 cholesterol parameterization! https://chemrxiv.org/engage/chemrxiv/article-details/64677ce5fb40f6b3eed8bb26 Big cheers, @SouzaPauloCT, @CG_Martini and the many others in this amazing collaborative endeavor!

Martini 3 Coarse-Grained Force Field for cholesterol

Cholesterol plays a crucial role in biomembranes by regulating various properties such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and the inclusion of new bead types and sizes. However, the release of the new model resulted in the need to re-parameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving overall behavior.

chemrxiv.org

Manuel N. Melo at ITQB NOVA@melolab.bsky.social · 4y ago

Congrats @MaryVallerio and Luís Borges-Araújo for the publication of our analysis of the SARS-CoV-2 RBD dynamics, and how it may explain some of the variants' success. Check it out 😃 https://www.frontiersin.org/articles/10.3389/fmedt.2022.1009451

Frontiers | SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is havi...

frontiersin.org

Manuel N. Melo at ITQB NOVA@melolab.bsky.social · 5y ago

Our shiny new CG parametrization of phosphoinositides, upgraded for @CG_Martini's Martini 3, is just out as a ChemRxiv preprint. Enjoy! https://t.co/uygbmTznih Be sure to check the goods at our development GitHub repo: https://t.co/hPWaxE7Cgp

Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse Grain Force Field

Phosphoinositides are a family of membrane phospholipids that play crucial roles in membrane regulatory events. As such, these lipids are often a key part of molecular dynamics simulation studies of biological membranes, in particular of those employing coarse-grain models because of the potential long times and sizes of the involved membrane processes. Version 3 of the widely used Martini coarse grain force field has been recently published, greatly refining many aspects of biomolecular interactions. In order to properly use it for lipid membrane simulations with phosphoinositides, we put forth the Martini 3-specific parameterization of inositol, phosphatidylinositol, the seven physiologically relevant phosphorylated derivatives of phosphatidylinositol. Compared to parameterizations for earlier Martini versions, focus was put on a more accurate reproduction of the behavior seen in both atomistic simulations and experimental studies, including the signaling relevant phosphoinositide interaction with divalent cations. The models we develop improve upon the conformational dynamics of phosphoinositides in the Martini force field and provide stable topologies at typical Martini timesteps. They are able to reproduce experimentally known protein-binding poses as well as phosphoinositide aggregation tendencies. The latter were tested both in the presence and absence of calcium, and include correct behavior of PI(4,5)P2 calcium-induced clusters, which can be of relevance for regulation.

chemrxiv.org