GōMartini 3: From large conformational changes in proteins to environmental bias corrections

Abstract

Coarse-grained modeling has become an important tool to supplement experimental measurements, allowing access to spatio-temporal scales beyond all-atom based approaches. The GōMartini model combines structure- and physics-based coarse-grained approaches, balancing computational efficiency and accurate representation of protein dynamics with the capabilities of studying proteins in different biological environments. This paper introduces an enhanced GōMartini model, which combines a virtual-site implementation of Gō models with Martini 3. The implementation has been extensively tested by the community since the release of the new version of Martini. This work demonstrates the capabilities of the model in diverse case studies, ranging from protein-membrane binding to protein-ligand interactions and AFM force profile calculations. The model is also versatile, as it can address recent inaccuracies reported in the Martini protein model. Lastly, the paper discusses the advantages, limitations, and future perspectives of the Martini 3 protein model and its combination with Gō models.

Martini without the twist: Unveiling a mechanically correct microtubule through bottom-up coarse-graining in Martini 3

“…[55][56][57][58] A recently developed proxy for elastic network are GO-like models that encode conformational dynamics more effectively, similar to GO-Martini. 59,60 This will possibly help in capturing more disordered states at microtubule tips, and binding-unbinding dynamics of tubulins. Furthermore, this will build a stronger bridge with thermodynamics through carefully parametrizing the GO model to reproduce experimental binding affinities.…”

Exploring the Ligand Binding and Conformational Dynamics of the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ

“…Together, the differences in size and polarity allow us to discriminate between these amino acids at the Martini level of resolution. More details about the amino acid force field are given in ref . For all systems in the presence of the ligand, the movements of the ligand were limited to reside within the selected distance from the protein (20 Å), using a flat-bottom potential.…”