Biology subjects

Frank DiMaio

Publications and source records attributed to Frank DiMaio.

2 recordsLinked to original sources

bioRxiv2016

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

Cryo-EM has revealed many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5[A]), providing biological phenomena with molecular descriptions. However, at these resolutions accurately positioning individual atoms remains challenging and may be error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining or improving the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.

Biochemistry↗

bioRxiv2015

Side-chain-directed model and map validation for 3D Electron Cryomicroscopy

Advances in electron cryomicroscopy allow for the building of de novo atomic models into high resolution Coulomb potential maps. While established validation metrics independently assess map quality and model geometry, methods to assess the precise fitting of an atomic model into the map and to validate the interpretation of high resolution features are less well developed. Here, we present EMRinger, which tests model-to-map agreement using side-chain dihedral-directed map density measurements. These measurements reveal local map density peaks and show that peaks located at rotameric angles are a sensitive marker of whether the backbone is correctly positioned. The EMRinger Score can be improved by model refinement, suggesting its utility as an effective model-to-map validation metric. Additionally, EMRinger sampling identifies how radiation damage alters scattering from negatively charged amino acids during data collection. EMRinger will be useful in assessing how advances in cryo-EM increase the ability to resolve and model high-resolution features.

Biophysics↗