Building de novo cryo-electron microscopy structures collaboratively with citizen scientists

Firas Khatib,Scott Horowitz,Jeff Flatten,Zoran Popović,David Baker,Brian Koepnick,Ambroise Desfosses,Irina Gutsche,Seth Cooper

doi:10.1371/journal.pbio.3000472

Abstract

With the rapid improvement of cryo-electron microscopy (cryo-EM) resolution, new computational tools are needed to assist and improve upon atomic model building and refinement options. This communication demonstrates that microscopists can now collaborate with the players of the computer game Foldit to generate high-quality de novo structural models. This development could greatly speed the generation of excellent cryo-EM structures when used in addition to current methods.

Highlights

Less than a decade ago, before the “resolution revolution,” cryo-electron microscopy was indulgently called “blobology” [1,2,3,4]
Detailed accounts from all of the Foldit players who produced these 4 models are described in the “Foldit Player Testimonials” section in S2 Text. These results indicate that there are multiple routes toward cryo-electron microscopy (cryo-EM) model building and that Foldit players could greatly speed the arduous model-building process for many cryo-EM projects
To generate puzzles for Foldit players, the cryo-EM map (EMD-4782) sharpened with an overall b-factor of 105 Å2 [34] was segmented around each fitted monomer of Afp1, Afp5, Afp7, and Afp9 (PDB 6rao, [34]), with a radius of 3 Å around fitted atoms

Summary

Main text

Less than a decade ago, before the “resolution revolution,” cryo-electron microscopy (cryoEM) was indulgently called “blobology” [1,2,3,4]. Because of the absence of the phase problem, and unlike previous Foldit collaborations with crystallographic data [25,30], the structures from Foldit players that were the best in each puzzle as determined by Phenix validation [14] were the best according to the Foldit score function, which is based on the Rosetta score function [31], with terms that model properties such as electrostatics, hydrogen bonds, solvation, and torsion angles, with an additional parameter that accounts for electron potential map fit This observation suggests that by collaborating with Foldit, only minimal work will be required by microscopists to obtain an accurate, highquality model. Enlisting the help of citizen scientists, such as Foldit players, is one option to do so

Materials and methods

Ethics statement