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

  • 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.

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Author:Paulo Cesar Telles de SouzaORCiD, Luis P. Borges AraujoORCiD, Chris BrasnettORCiD, Rodrigo Azevedo Moreira da SilvaORCiD, Fabian GrünewaldORCiD, Peter ParkORCiD, Liguo WangORCiD, Hafez RazmazmaORCiD, Ana Carolina Borges AraújoORCiD, Luis Fernando Cofas-VargasORCiD, Luca MonticelliORCiD, Raul Mera-AdasmeORCiD, Manuel Nuno MeloORCiD, Sangwook WuORCiD, Siewert J. MarrinkORCiDGND, Adolfo B. PomaORCiD, Sebastian ThallmairORCiD
URN:urn:nbn:de:hebis:30:3-838121
URL:https://www.biorxiv.org/content/10.1101/2024.04.15.589479v1
DOI:https://doi.org/10.1101/2024.04.15.589479
Parent Title (English):bioRxiv
Publisher:bioRxiv
Document Type:Preprint
Language:English
Date of Publication (online):2024/04/16
Date of first Publication:2024/04/16
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2024/04/22
Issue:2024.04.15.589479 Version 1
Edition:Version 1
Page Number:50
HeBIS-PPN:518169073
Institutes:Wissenschaftliche Zentren und koordinierte Programme / Frankfurt Institute for Advanced Studies (FIAS)
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Sammlungen:Universitätspublikationen
Licence (German):License LogoCreative Commons - CC BY-NC-ND - Namensnennung - Nicht kommerziell - Keine Bearbeitungen 4.0 International