Cross-linking mass spectrometry for investigating protein conformations and protein–protein interactions─ a method for all seasons

L Piersimoni, PL Kastritis, C Arlt, A Sinz - Chemical Reviews, 2021 - ACS Publications
Mass spectrometry (MS) has become one of the key technologies of structural biology. In this
review, the contributions of chemical cross-linking combined with mass spectrometry (XL …

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 …

Labeling preferences of diazirines with protein biomolecules

AV West, G Muncipinto, HY Wu, AC Huang… - Journal of the …, 2021 - ACS Publications
Diazirines are widely used in photoaffinity labeling (PAL) to trap noncovalent interactions
with biomolecules. However, design and interpretation of PAL experiments is challenging …

Enhanced mapping of small-molecule binding sites in cells

JM Wozniak, W Li, P Governa, LY Chen… - Nature Chemical …, 2024 - nature.com
Photoaffinity probes are routinely utilized to identify proteins that interact with small
molecules. However, despite this common usage, resolving the specific sites of these …

Protein chemistry combined with mass spectrometry for protein structure determination

EV Petrotchenko, CH Borchers - Chemical Reviews, 2021 - ACS Publications
The advent of soft-ionization mass spectrometry for biomolecules has opened up new
possibilities for the structural analysis of proteins. Combining protein chemistry methods with …

Design and evaluation of a cyclobutane Diazirine Alkyne tag for photoaffinity labeling in cells

AV West, Y Amako, CM Woo - Journal of the American Chemical …, 2022 - ACS Publications
Alkyl diazirines are frequently used in photoaffinity labeling to map small molecule–protein
interactions in target identification studies. However, the alkyl diazirines can preferentially …

Evaluation of fully-functionalized diazirine tags for chemical proteomic applications

LP Conway, AM Jadhav, RA Homan, W Li… - Chemical …, 2021 - pubs.rsc.org
The use of photo-affinity reagents for the mapping of noncovalent small molecule–protein
interactions has become widespread. Recently, several 'fully-functionalized'(FF) chemical …

Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping

Y Jiang, X Zhang, H Nie, J Fan, S Di, H Fu… - Nature …, 2024 - nature.com
While photo-cross-linking (PXL) with alkyl diazirines can provide stringent distance restraints
and offer insights into protein structures, unambiguous identification of cross-linked residues …

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 …

Photoaffinity labeling chemistries used to map biomolecular interactions

AV West, CM Woo - Israel Journal of Chemistry, 2023 - Wiley Online Library
Photoaffinity labeling (PAL) is one of the few biochemical techniques that can give direct
evidence of biomolecular interactions in cells. Several photoactivatable functional groups …