Accurate flexible refinement of atomic models against medium-resolution cryo-EM maps using damped dynamics

Abstract

BackgroundDramatic progress has recently been made in cryo-electron microscopy technologies, which now make possible the reconstruction of a growing number of biomolecular structures to near-atomic resolution. However, the need persists for fitting and refinement approaches that address those cases that require modeling assistance.MethodsIn this paper, we describe algorithms to optimize the performance of such medium-resolution refinement methods. These algorithms aim to automatically optimize the parameters that define the density shape of the flexibly fitted model, as well as the time-dependent damper cutoff distance. Atomic distance constraints can be prescribed for cases where extra containment of parts of the structure is helpful, such as in regions where the density map is poorly defined. Also, we propose a simple stopping criterion that estimates the probable onset of overfitting during the simulation.ResultsThe new set of algorithms produce more accurate fitting and refinement results, and yield a faster rate of convergence of the trajectory toward the fitted conformation. The latter is also more reliable due to the overfitting warning provided to the user.ConclusionsThe algorithms described here were implemented in the new Damped-Dynamics Flexible Fitting simulation tool “DDforge” in the Situs package.Electronic supplementary materialThe online version of this article (10.1186/s12900-018-0089-0) contains supplementary material, which is available to authorized users.

Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules

“…The initial approaches combining MD and cryo-EM methods used MD as a fitting scheme to predict the structure of a biomolecule, using the low-resolution EM map to constrain the protein conformation. For this purposes, two commonly used packages are the MD Flexible Fitting (MDFF) ( Trabuco et al, 2008 ) and the Situs ( Kovacs et al, 2018 ) codes, where the first one guides MD simulation toward the cryo-EM density biasing the MD potential energy form to reduce the gradient of the experimental electronic density, while the second one minimizes the discrepancy between the map derived from the MD model and the original cryo-EM map. Hybrid approaches harnessing docking algorithms have also been developed, such as including a rigid fitting stage followed by a refinement based on MD ( Topf et al, 2008 ), or introducing a coarse-grained force field to allow flexibility during the docking search ( de Vries and Zacharias ATTRACT-, 2012 ).…”

Microtubule plus-end regulation by centriolar cap proteins

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