Towards design of drugs and delivery systems with the Martini coarse-grained model

Abstract

Coarse-grained (CG) modeling with the Martini force field (FF) has come of age. By combining a variety of bead types and sizes with a new mapping approach, the newest version of the model is able to accurately simulate large biomolecular complexes at millisecond timescales. In this

Probing the dynamical interaction of the para-sulfonato-calix[4]arene with an antifungal protein

“…S2, ESI †): inspection of our MD followed by cluster analysis reveal two main protein binding sites (Site 1 and Site 2, shown in Fig. 2) serving as anchor points for sclx 4 . In Site 1, sclx 4 encapsulates in its hydrophobic cage lysine K30, whose side chain adopts an inchworm conformation, identified in the co-crystallized X-ray structure of PAF 25 and for other proteins.…”

“…Functionalizable ligands have attracted growing interest, mostly for their potential applications, spanning from chemistry, 1,2 pharmaceutical fields 3,4 to material science. 5 Interaction of proteins with smaller ligands is a hallmark in Biochemistry, and has recently been implied in the conception of high-resolution tunable protein assemblies, with an increasing number of X-ray structures reported in the PDB databank.…”

Effective Molecular Dynamics from Neural Network-Based Structure Prediction Models

“…In this study, we have tested the combination of the AF-ENM method with the MARTINI3 coarse-grained force field. The MARTINI model is widely used to study large-scale dynamics of complex systems due to its compatibility with a wide range of (bio-)­molecules. ,, However, the structure-based character and design of the MARTINI protein model may limit its application for the exploration of large-scale conformational changes in proteins, particularly if transitions in the secondary structure elements are involved. cgMD models and MARTINI3 are commonly employed together with an elastic network, which introduces a strong bias toward the starting conformation.…”

A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptorα1

“…The use of coarse-grained (CG) models preserving chemical specificity such as the Martini force field 20 has emerged as a powerful and cost-effective strategy to probe the spatial and temporal evolution of biomolecules, 21,22 particularly for pharmacological applications. 23,24 This modeling strategy provides a smoother potential energy surface that allows for integration time steps up to 30 fs in molecular dynamics (MD) simulations 25 . The latter yields a speed-up of 2-3 orders of magnitude relative to all-atom MD, which opens to the exploration of time and size scales that were previously out of reach.…”