Mass spectrometry-based protein footprinting for higher-order structure analysis: fundamentals and applications

XR Liu, MM Zhang, ML Gross - Chemical reviews, 2020 - ACS Publications
Proteins adopt different higher-order structures (HOS) to enable their unique biological
functions. Understanding the complexities of protein higher-order structures and dynamics …

Understanding the transcriptome through RNA structure

Y Wan, M Kertesz, RC Spitale, E Segal… - Nature Reviews …, 2011 - nature.com
RNA structure is crucial for gene regulation and function. In the past, transcriptomes have
largely been parsed by primary sequences and expression levels, but it is now becoming …

RNA design rules from a massive open laboratory

J Lee, W Kladwang, M Lee, D Cantu… - Proceedings of the …, 2014 - National Acad Sciences
Self-assembling RNA molecules present compelling substrates for the rational interrogation
and control of living systems. However, imperfect in silico models—even at the secondary …

Disease-associated mutations that alter the RNA structural ensemble

M Halvorsen, JS Martin, S Broadaway… - PLoS genetics, 2010 - journals.plos.org
Genome-wide association studies (GWAS) often identify disease-associated mutations in
intergenic and non-coding regions of the genome. Given the high percentage of the human …

[图书][B] Chemical reagents for protein modification

RL Lundblad - 2004 - taylorfrancis.com
Revised and updated, Chemical Reagents for Protein Modification, Third Edition is an
encyclopedic work describing the many approaches to the site-specific modification of …

Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates

MY Angela, PM Gasper, L Cheng, LB Lai, S Kaur… - Molecular cell, 2021 - cell.com
The series of RNA folding events that occur during transcription can critically influence
cellular RNA function. Here, we present reconstructing RNA dynamics from data (R2D2), a …

The RNA structurome: transcriptome-wide structure probing with next-generation sequencing

CK Kwok, Y Tang, SM Assmann… - Trends in biochemical …, 2015 - cell.com
RNA folds into intricate structures that enable its pivotal roles in biology, ranging from
regulation of gene expression to ligand sensing and enzymatic functions. Therefore …

Modeling RNA secondary structure folding ensembles using SHAPE mapping data

A Spasic, SM Assmann, PC Bevilacqua… - Nucleic acids …, 2018 - academic.oup.com
RNA secondary structure prediction is widely used for developing hypotheses about the
structures of RNA sequences, and structure can provide insight about RNA function. The …

Computational analysis of conserved RNA secondary structure in transcriptomes and genomes

SR Eddy - Annual review of biophysics, 2014 - annualreviews.org
Transcriptomics experiments and computational predictions both enable systematic
discovery of new functional RNAs. However, many putative noncoding transcripts arise …

Finding the target sites of RNA‐binding proteins

X Li, H Kazan, HD Lipshitz… - Wiley Interdisciplinary …, 2014 - Wiley Online Library
RNA–protein interactions differ from DNA–protein interactions because of the central role of
RNA secondary structure. Some RNA‐binding domains (RBDs) recognize their target sites …