The GōMartini Approach: Revisiting the Concept of Contact Maps and the Modelling of Protein Complexes

L.F. Cofas-Vargasa, R.A. Moreirab, S. Pobletec, d, M. Chwastyke, A.B. Pomaa aBiosystems and Soft Matter Division, Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland bBCAM, Basque Center for Applied Mathematics, Mazarredo 14, 48009 Bilbao, Bizkaia, Spain cCentro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Avenida del Valle Norte 725, 8580702 Santiago, Chile dFacultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista 7, 8420524 Santiago, Chile eInstitute of Physics, Polish Academy of Sciences, al. Lotników 32/46, PL-02668 Warsaw, Poland

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We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance threshold. Such contact maps are mostly based on physical and chemical construction, and yet they are sensitive to some parameters (e.g., distances or atomic radii) and can neglect some key interactions. Furthermore, we also comment on a new class of contact maps that only requires geometric arguments. The contact map is a necessary ingredient to build a robust GōMartini model for proteins and their complexes in the Martini 3 force field. We present the extension of a popular structure-based Gō-like approach to the study of protein–sugar complexes, and the limitations of this approach are also discussed. The GōMartini approach was first introduced by Poma et al. (J. Chem. Theory Comput. 13, 1366 (2017)) in Martini 2 force field, and recently, it has gained the status of gold standard for protein simulation undergoing conformational changes in Martini 3 force field. We discuss several studies that have provided support for this approach in the context of the biophysical community.

DOI:10.12693/APhysPolA.145.S9 topics: Martini 3, structure-based coarse-graining, single-molecule force microscopy, biomolecules