Advances and opportunities in RNA structure experimental determination and computational modeling

J Zhang, Y Fei, L Sun, QC Zhang - Nature methods, 2022 - nature.com
Beyond transferring genetic information, RNAs are molecules with diverse functions that
include catalyzing biochemical reactions and regulating gene expression. Most of these …

Macromolecular modeling and design in Rosetta: recent methods and frameworks

JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle… - Nature …, 2020 - nature.com
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …

Structure of human telomerase holoenzyme with bound telomeric DNA

GE Ghanim, AJ Fountain, AMM Van Roon, R Rangan… - Nature, 2021 - nature.com
Telomerase adds telomeric repeats at chromosome ends to compensate for the telomere
loss that is caused by incomplete genome end replication. In humans, telomerase is …

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

K Kappel, K Zhang, Z Su, AM Watkins, W Kladwang… - Nature …, 2020 - nature.com
The discovery and design of biologically important RNA molecules is outpacing three-
dimensional structural characterization. Here, we demonstrate that cryo-electron microscopy …

Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly

J He, P Lin, J Chen, H Cao, SY Huang - Nature Communications, 2022 - nature.com
Advances in microscopy instruments and image processing algorithms have led to an
increasing number of cryo-electron microscopy (cryo-EM) maps. However, building accurate …

Structure, folding and flexibility of co-transcriptional RNA origami

EKS McRae, HØ Rasmussen, J Liu, A Bøggild… - Nature …, 2023 - nature.com
RNA origami is a method for designing RNA nanostructures that can self-assemble through
co-transcriptional folding with applications in nanomedicine and synthetic biology. However …

Cryo-EM advances in RNA structure determination

H Ma, X Jia, K Zhang, Z Su - Signal Transduction and Targeted Therapy, 2022 - nature.com
Cryo-electron microscopy (cryo-EM) has emerged as an unprecedented tool to resolve
protein structures at atomic resolution. Structural insights of biological samples not …

FARFAR2: improved de novo rosetta prediction of complex global RNA folds

AM Watkins, R Rangan, R Das - Structure, 2020 - cell.com
Predicting RNA three-dimensional structures from sequence could accelerate
understanding of the growing number of RNA molecules being discovered across biology …

Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution

Z Su, K Zhang, K Kappel, S Li, MZ Palo, GD Pintilie… - Nature, 2021 - nature.com
Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique
for determining protein structures at atomic resolution,–. However, cryo-EM studies of protein …

A unified mechanism for intron and exon definition and back-splicing

X Li, S Liu, L Zhang, A Issaian, RC Hill, S Espinosa… - Nature, 2019 - nature.com
The molecular mechanisms of exon definition and back-splicing are fundamental
unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy …