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 …

Hydroxyl radical protein footprinting: a mass spectrometry-based structural method for studying the higher order structure of proteins

A McKenzie-Coe, NS Montes, LM Jones - Chemical reviews, 2021 - ACS Publications
Hydroxyl radical protein footprinting (HRPF) coupled to mass spectrometry has been
successfully used to investigate a plethora of protein-related questions. The method, which …

Targeting intrinsically disordered proteins at the edge of chaos

H Ruan, Q Sun, W Zhang, Y Liu, L Lai - Drug discovery today, 2019 - Elsevier
Highlights•Intrinscially disordered proteins (IDPs) are abundant and involved in many
diseases.•Advances and challenges in drug design targeting IDPs are discussed.•Known …

Protein complex prediction using Rosetta, AlphaFold, and mass spectrometry covalent labeling

ZC Drake, JT Seffernick, S Lindert - Nature communications, 2022 - nature.com
Covalent labeling (CL) in combination with mass spectrometry can be used as an analytical
tool to study and determine structural properties of protein-protein complexes. However …

[HTML][HTML] Hybrid methods for combined experimental and computational determination of protein structure

JT Seffernick, S Lindert - The Journal of chemical physics, 2020 - pubs.aip.org
Knowledge of protein structure is paramount to the understanding of biological function,
developing new therapeutics, and making detailed mechanistic hypotheses. Therefore …

Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions

P Limpikirati, T Liu, RW Vachet - Methods, 2018 - Elsevier
Using mass spectrometry (MS) to obtain information about a higher order structure of protein
requires that a protein's structural properties are encoded into the mass of that protein …

Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution

DN Kim, BC Thiel, T Mrozowich, SP Hennelly… - Nature …, 2020 - nature.com
Long non-coding RNAs (lncRNAs) constitute a significant fraction of the transcriptome,
playing important roles in development and disease. However, our understanding of …

[PDF][PDF] New system for archiving integrative structures

B Vallat, B Webb, M Fayazi, S Voinea… - … Section D: Structural …, 2021 - journals.iucr.org
Structures of many complex biological assemblies are increasingly determined using
integrative approaches, in which data from multiple experimental methods are combined. A …

Federating structural models and data: outcomes from a workshop on archiving integrative structures

HM Berman, PD Adams, AA Bonvin, SK Burley… - Structure, 2019 - cell.com
Structures of biomolecular systems are increasingly computed by integrative modeling. In
this approach, a structural model is constructed by combining information from multiple …

Structural proteomics methods to interrogate the conformations and dynamics of intrinsically disordered proteins

R Beveridge, AN Calabrese - Frontiers in chemistry, 2021 - frontiersin.org
Intrinsically disordered proteins (IDPs) and regions of intrinsic disorder (IDRs) are abundant
in proteomes and are essential for many biological processes. Thus, they are often …