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

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.

Editorial: Functions, working mechanisms, and regulation of rotary ATPases and Ductin proteins

“…Structural biology of membrane proteins is rapidly catching up thanks to improved experimental approaches (for example, cryo-EM) (e.g., Pinke et al, 2020 ; Gerle et al, 2022 ; Yamamori and Tomii, 2022 ) and structure predictions enhanced with artificial intelligence ( Versini et al, 2023 ; Wuyun et al, 2024 ). Structure models with atomic detail are already available, also for the F o , V o and A o domains.…”

Application of conformational space annealing to the protein structure modeling using cryo‐EM maps

“…[21][22][23][24][25][26][27] The most popular strategy for protein structure modeling from cryo-EM maps is fitting a known structure or a predicted structure into the map by rigid fitting methods and further refining the fitted model by flexible fitting and further refinement. [14][15][16][17][18]28,29 Rigid fitting of a structure into a cryo-EM map involves finding the optimal orientation and position of the structure in map based on a scoring function, such as cross-correlation [30][31][32][33] and mutual information. 12,30 These scoring functions evaluate the fitness between the structure and the cryo-EM map.…”