Application of Homology Modeling by Enhanced Profile-Profile Alignment and Flexible-Fitting Simulation to Cryo-EM Based Structure Determination.

Yu Yamamori,Kentaro Tomii

doi:10.3390/ijms23041977

Abstract

Application of cryo-electron microscopy (cryo-EM) is crucially important for ascertaining the atomic structure of large biomolecules such as ribosomes and protein complexes in membranes. Advances in cryo-EM technology and software have made it possible to obtain data with near-atomic resolution, but the method is still often capable of producing only a density map with up to medium resolution, either partially or entirely. Therefore, bridging the gap separating the density map and the atomic model is necessary. Herein, we propose a methodology for constructing atomic structure models based on cryo-EM maps with low-to-medium resolution. The method is a combination of sensitive and accurate homology modeling using our profile–profile alignment method with a flexible-fitting method using molecular dynamics simulation. As described herein, this study used benchmark applications to evaluate the model constructions of human two-pore channel 2 (one target protein in CASP13 with its structure determined using cryo-EM data) and the overall structure of Enterococcus hirae V-ATPase complex.

Highlights

Advances in cryo-electron microscopy (cryo-EM) technology and software have made it possible to obtain data with near-atomic resolution, but the method is still often capable of producing only a density map with up to medium resolution, either partially or entirely
Its achievements are underscored by the recent increase in the number of Protein Data Bank (PDB) archive entries related to cryo-EM [9]
As an application of our developed homology modeling method [38], we propose a new scheme of atomic structure modeling based on a cryo-EM density map with subnanometer or higher resolution

Summary

Introduction

Advances in cryo-EM technology and software have made it possible to obtain data with near-atomic resolution, but the method is still often capable of producing only a density map with up to medium resolution, either partially or entirely. Its achievements are underscored by the recent increase in the number of Protein Data Bank (PDB) archive entries related to cryo-EM [9] Improvements in both cryo-EM technology and software enable us to obtain near-atomic-resolution EM data [4], it is likely that only a medium-to-low resolution density map is obtained, either partially or completely. The Rosetta software suite includes an automatic de novo modeling protocol, which assembles fragment structures from a protein-structure library with subsequent optimization, to be fitted to an EM map [12,13] Another recently developed fully automatic method, MAINMAST, is a method connecting local dense points identified as main-chain or side-chain positions by presuming a minimum spanning tree. Initial structures are provided from known X-ray structures [17] or are based on the results of homology modeling [18]

Methods

Results

Conclusion