Seminar: Advancing the GōMartini 3 Approach for Conformational Dynamics of Protein Assemblies

Описание: Dr hab. Adolfo Poma, IPPT PAN - Instytut Podstawowych Problemów Techniki Polskiej Akademii Nauk

Recent developments in machine learning, together with the increasing availability of high-resolution structural data from cryo-electron microscopy, are positioning molecular simulations at the forefront of studying large biomolecular systems. Together, these methods underscore the need for computational strategies capable of capturing biologically relevant conformational changes over extended timescales. While all-atom molecular dynamics (AA-MD) simulations provide detailed, high-resolution insights, their application to large and complex systems is limited by substantial computational costs.

The recently introduced GōMartini 3 approach (Nat Commun 16, 4051, 2025) extends the Martini 3 coarse-grained force field to study conformational changes in proteins, offering significant potential for biomedical and therapeutic applications. Here, we discuss alternative strategies that integrate dynamic protein contacts derived from AA-MD to more efficiently explore conformational space. We showcase several molecular studies and validated the new approach by investigating the nanomechanics of nanobodies binding to the SARS-CoV-2 spike (S) protein as well as the long-time scale dynamics of S variants. The optimized framework is openly available at https://github.com/GoMartini3-tools/C....

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