Macromolecular complexes: from ab initio and integrative modelling to functional dynamics
CECAM-HQ-EPFL, Lausanne, Switzerland
The intersection of recent breakthroughs in protein structure prediction (1), steadily advances in multiscale molecular simulations of biological systems (2) and continuous progresses in data-intensive experimental characterization of protein complexes (e.g., cryo-electron microscopy (3) and mass spectrometry (4)) has allowed for the investigation of large macromolecular assemblies with unprecedented accuracy down to the atomistic scale (5-7). This conjuncture has opened incredible possibilities to study the mechanistic details of important cellular machineries with extreme molecular resolution, shifting the established paradigm in structural biology from “one structure - one function” to the realization that a vast conformational landscape determines instead biological function (8,9) . At the same time, however, these recent progresses also raise key questions on the limitations of the different approaches, and on the extent to which it is possible to utilize these techniques without falling into overinterpretation pitfalls (10). Amongst those, just to name a few, are the ability of predicted protein structures to provide information on protein conformational flexibility; the possibility to correctly predict protein-protein interactions (11), specifically in the case of flexible or unstructured protein regions; the accuracy of molecular mechanics force fields at different resolutions (12); or the relevance of in vitro high-resolution structures in comparison with low-resolution in situ structures obtained using cryo-electron tomography (13).
In this context, community-wide assessments are gaining even more importance (11), and methodological developments will be key to address and overcome the key limitations of current computational methods. To address this problem, blending expertises from the experimental and theoretical backgrounds, this workshop aims at bringing together experts from three distinct but interconnected fields: (i) ab initio modelling of protein complexes, (ii) integrative modelling and (iii) dynamical studies of protein complexes' function at different scales. We hope to provide the community with a clear understanding of the possibility and limitations of current methodologies. In particular, we will extensively focus on how to investigate dynamical and functional aspects of large macromolecular complexes by integrating ab initio or integrative modeling approaches with molecular dynamics simulations at different scales. We will discuss the current state-of-the-art in the field, contributing to forecast and possibly foster possible developments and breakthroughs over the next 3-5 years.
Maya Topf (Centre of Structural Systems Biology, LIV/UKE Hamburg) - Organiser
Matteo Dal Peraro (Swiss Federal Institute of Technology Lausanne (EPFL) ) - Organiser
Stefano Vanni (University of Fribourg) - Organiser
Pilar Cossio (Flatiron Institute) - Organiser