Local computational methods to improve the interpretability and analysis of cryo-EM maps

Satinder Kaur,Javier Vargas,Ruben Sanchez-Garcia,Khanh Huy Bui,Josue Gomez-Blanco,Ahmad A Z Khalifa,Daniel Wrapp,Jason S Mclellan,Swathi Adinarayanan

doi:10.1038/s41467-021-21509-5

Satinder Kaur, Javier Vargas + Show 7 more

Open Access

https://doi.org/10.1038/s41467-021-21509-5

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Abstract

Cryo-electron microscopy (cryo-EM) maps usually show heterogeneous distributions of B-factors and electron density occupancies and are typically B-factor sharpened to improve their contrast and interpretability at high-resolutions. However, ‘over-sharpening’ due to the application of a single global B-factor can distort processed maps causing connected densities to appear broken and disconnected. This issue limits the interpretability of cryo-EM maps, i.e. ab initio modelling. In this work, we propose 1) approaches to enhance high-resolution features of cryo-EM maps, while preventing map distortions and 2) methods to obtain local B-factors and electron density occupancy maps. These algorithms have as common link the use of the spiral phase transformation and are called LocSpiral, LocBSharpen, LocBFactor and LocOccupancy. Our results, which include improved maps of recent SARS-CoV-2 structures, show that our methods can improve the interpretability and analysis of obtained reconstructions.

Highlights

Cryo-electron microscopy maps usually show heterogeneous distributions of Bfactors and electron density occupancies and are typically B-factor sharpened to improve their contrast and interpretability at high-resolutions
Current reconstructions from Cryo-electron microscopy (cryo-EM) do not provide essential information to build accurate ab initio atomic models as atomic Debye–Waller factors (B-factors) or atomic occupancies, while their counterparts from X-ray crystallography do by analysing the attenuation of scattered intensity represented at Bragg peaks
In the global sharpening approach[6,7,8], the B-factor is automatically computed by determining the line that best fits the decay of the spherically averaged noise-weighted amplitude structure factors, within a resolution range given by [15–10 Å, Rmax], with Rmax the maximum resolution in the map given by the Fourier Shell Correlation (FSC)

Summary

Introduction

Cryo-electron microscopy (cryo-EM) maps usually show heterogeneous distributions of Bfactors and electron density occupancies and are typically B-factor sharpened to improve their contrast and interpretability at high-resolutions. We propose 1) approaches to enhance high-resolution features of cryo-EM maps, while preventing map distortions and 2) methods to obtain local Bfactors and electron density occupancy maps. The presence of heterogeneity in cryo-EM maps leads to high variability in resolution within different regions of the same map This directs to challenges and errors in the process of building an atomic model from a cryo-EM reconstruction. Methods to determine local B-factors are much needed to accurately analyse cryo-EM maps and improve the quality of fitted atomic models Another local parameter usually provided by X-ray crystallography in contrast with cryoEM are atomic occupancies (or Q-values). The occupancy estimates the presence of an atom at its mean position and it ranges between 0.0 to 1.0 Note that these parameters can be refined by model building packages if the electron density map is of sufficient resolution. They reported that 40% of models analysed show cross-correlations between cryo-EM maps and respective models below 0.5, and they indicated as a possible hypothesis an incomplete optimisation of the model parameters (coordinates, occupancies and Bfactors)

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