Fitting Atomic Structures into Cryo-EM Maps by Coupling Deep Learning-Enhanced Map Processing with Global-Local Optimization DOI

Yaxian Cai,

Ziying Zhang, Xiangyu Xu

et al.

Journal of Chemical Information and Modeling, Journal Year: 2025, Volume and Issue: unknown

Published: March 28, 2025

With the breakthroughs in protein structure prediction technology, constructing atomic structures from cryo-electron microscopy (cryo-EM) density maps through structural fitting has become increasingly critical. However, accuracy of constructed models heavily relies on precision structure-to-map fitting. In this study, we introduce DEMO-EMfit, a progressive method that integrates deep learning-based backbone map extraction with global-local pose search to fit into maps. DEMO-EMfit was extensively evaluated benchmark data set comprising both tomography (cryo-ET) and cryo-EM nucleic acid complexes. The results demonstrate outperforms state-of-the-art approaches, offering an efficient accurate tool for

Language: Английский

Mettl15-Mettl17 modulates the transition from early to late pre-mitoribosome DOI Creative Commons
Yu.O. Zgadzay, Claudio Mirabello,

George Wanes

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 4, 2025

The assembly of the mitoribosomal small subunit involves folding and modification rRNA, its association with proteins. This process is assisted by a dynamic network factors. Conserved methyltransferases Mettl15 Mettl17 act on solvent-exposed surface rRNA. Binding associated early stage, whereas involved in late but mechanism transition between two was unclear. Here, we integrate structural data from Trypanosoma brucei mammalian homologs molecular dynamics simulations. We reveal how interplay intermediate steps links distinct stages assembly. analysis suggests model wherein acts as platform for recruitment. Subsequent release allows conformational change substrate recognition. Upon methylation, adopts loosely bound state which ultimately leads to replacement initiation factors, concluding Together, our results indicate that factors cooperate regulate biogenesis process, present resource understanding adaptations mitoribosome.

Language: Английский

Citations

0
Fitting Atomic Structures into Cryo-EM Maps by Coupling Deep Learning-Enhanced Map Processing with Global-Local Optimization DOI

Yaxian Cai,

Ziying Zhang, Xiangyu Xu

et al.

Journal of Chemical Information and Modeling, Journal Year: 2025, Volume and Issue: unknown

Published: March 28, 2025

With the breakthroughs in protein structure prediction technology, constructing atomic structures from cryo-electron microscopy (cryo-EM) density maps through structural fitting has become increasingly critical. However, accuracy of constructed models heavily relies on precision structure-to-map fitting. In this study, we introduce DEMO-EMfit, a progressive method that integrates deep learning-based backbone map extraction with global-local pose search to fit into maps. DEMO-EMfit was extensively evaluated benchmark data set comprising both tomography (cryo-ET) and cryo-EM nucleic acid complexes. The results demonstrate outperforms state-of-the-art approaches, offering an efficient accurate tool for

Language: Английский

Citations

0