Biophysical Society Thematic Meeting | Trieste 2024

Emerging Theoretical Approaches to Complement Single-Particle Cryo-EM

Tuesday Speaker Abstracts

INFERRING THE CONFORMATIONAL LANDSCAPE OF MULTISTATE PROTEIN ASSEMBLIES USING COARSE-GRAINED SAMPLING OF TRANSITION PATHWAYS Milosz Wieczor 1,2 ; Pilar Cossio 4 ; James Krieger 3 ; Modesto Orozco 1 ; 1 IRB Barcelona, MMB, Barcelona, Spain 2 Gdansk University of Technology, Dept of Physical Chemistry, Gdansk, Poland 3 Centro Nacional de Biotecnologia, Dept of Macromolecular Structures, Madrid, Spain 4 Flatiron Institute, Center for Computational Mathematics, New York, NY, USA An increasing number of molecular systems solved with cryo-electron microscopy is characterized by the presence of multiple conformational states, either discrete or with a continuum of flexible geometries. While advanced clustering algorithms allow for discerning and refining individual conformations, the information about the pathways connecting these discrete states is usually unavailable due to the low statistical weights of the conformational intermediates, and the well-established effects of finite-rate cooling. To address this, we repurpose a physics-based coarse-grained discrete molecular dynamics (dMD) engine, augmented with a Maxwell-demon acceptance criterion and a metadynamics-like enhanced sampling algorithm, to rapidly explore viable conformational transitions between experimentally resolved endpoints. The pool of candidate intermediates can then be scored and subsampled based on multiple criteria, from Bayesian estimation of consistency with the raw cryo-EM images to knowledge-based potentials, and input into fully atomistic string-based pathway optimization methods.

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