Mechanisms and regulation of protein synthesis in mitochondria

E Kummer, N Ban - Nature Reviews Molecular Cell Biology, 2021 - nature.com
Mitochondria are cellular organelles responsible for generation of chemical energy in the
process called oxidative phosphorylation. They originate from a bacterial ancestor and …

Challenges and opportunities in cryo-EM single-particle analysis

D Lyumkis - Journal of Biological Chemistry, 2019 - ASBMB
Cryogenic electron microscopy (cryo-EM) enables structure determination of
macromolecular objects and their assemblies. Although the techniques have been …

CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks

ED Zhong, T Bepler, B Berger, JH Davis - Nature methods, 2021 - nature.com
Cryo-electron microscopy (cryo-EM) single-particle analysis has proven powerful in
determining the structures of rigid macromolecules. However, many imaged protein …

3D variability analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM

A Punjani, DJ Fleet - Journal of structural biology, 2021 - Elsevier
Single particle cryo-EM excels in determining static structures of protein molecules, but
existing 3D reconstruction methods have been ineffective in modelling flexible proteins. We …

Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM

M Chen, SJ Ludtke - Nature methods, 2021 - nature.com
Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of
protein function. Cryogenic electron microscopy (cryo-EM) provides direct visualization of …

Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN

LF Kinman, BM Powell, ED Zhong, B Berger… - Nature protocols, 2023 - nature.com
Single-particle cryogenic electron microscopy (cryo-EM) has emerged as a powerful
technique to visualize the structural landscape sampled by a protein complex. However …

Addressing preferred specimen orientation in single-particle cryo-EM through tilting

YZ Tan, PR Baldwin, JH Davis, JR Williamson… - Nature …, 2017 - nature.com
We present a strategy for tackling preferred specimen orientation in single-particle cryogenic
electron microscopy by employing tilts during data collection. We also describe a tool to …

Assembly landscape for the bacterial large ribosomal subunit

K Sheng, N Li, JN Rabuck-Gibbons, X Dong… - Nature …, 2023 - nature.com
Assembly of ribosomes in bacteria is highly efficient, taking~ 2-3 min, but this makes the
abundance of assembly intermediates very low, which is a challenge for mechanistic …

Deregulation of ribosome biogenesis in nitrite-oxidizing bacteria leads to nitrite accumulation

W **ong, Y Ye, D He, S He, Y **ang… - Environmental …, 2023 - ACS Publications
Nitrite (NO2–) accumulation caused by nitrite-oxidizing bacteria (NOB) inhibition in
nitrification is a double-edged sword, ie, a disaster in aquatic environments but a hope for …

Cryo-EM captures early ribosome assembly in action

B Qin, SM Lauer, A Balke, CH Vieira-Vieira… - Nature …, 2023 - nature.com
Ribosome biogenesis is a fundamental multi-step cellular process in all domains of life that
involves the production, processing, folding, and modification of ribosomal RNAs (rRNAs) …