Cross-linking mass spectrometry (XL-MS): An emerging technology for interactomics and structural biology

C Yu, L Huang - Analytical chemistry, 2017 - pmc.ncbi.nlm.nih.gov
Protein-protein interactions are fundamental to the formation of intricate interaction networks
and the assembly of multisubunit protein complexes that represent the functional …

Crosslinking and mass spectrometry: an integrated technology to understand the structure and function of molecular machines

A Leitner, M Faini, F Stengel, R Aebersold - Trends in biochemical …, 2016 - cell.com
In recent years, chemical crosslinking of protein complexes and the identification of
crosslinked residues by mass spectrometry (XL-MS; sometimes abbreviated as CX-MS) has …

Inert and seed-competent tau monomers suggest structural origins of aggregation

H Mirbaha, D Chen, OA Morazova, KM Ruff… - Elife, 2018 - elifesciences.org
Tauopathies feature progressive accumulation of tau amyloids. Pathology may begin when
these amplify from a protein template, or seed, whose structure is unknown. We have …

Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

E Yuriev, J Holien, PA Ramsland - Journal of Molecular …, 2015 - Wiley Online Library
Molecular docking is a computational method for predicting the placement of ligands in the
binding sites of their receptor (s). In this review, we discuss the methodological …

Efficient and robust proteome-wide approaches for cross-linking mass spectrometry

O Klykov, B Steigenberger, S Pektaş, D Fasci… - Nature protocols, 2018 - nature.com
Cross-linking mass spectrometry (XL-MS) has received considerable interest, owing to its
potential to investigate protein–protein interactions (PPIs) in an unbiased fashion in complex …

Cross‐linking/mass spectrometry for studying protein structures and protein–protein interactions: where are we now and where should we go from here?

A Sinz - Angewandte Chemie International Edition, 2018 - Wiley Online Library
Structural mass spectrometry (MS) is gaining increasing importance for deriving valuable
three‐dimensional structural information on proteins and protein complexes, and it …

Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine–lysine distances

ED Merkley, S Rysavy, A Kahraman, RP Hafen… - Protein …, 2014 - Wiley Online Library
Integrative structural biology attempts to model the structures of protein complexes that are
challenging or intractable by classical structural methods (due to size, dynamics, or …

Leveraging crosslinking mass spectrometry in structural and cell biology

A Graziadei, J Rappsilber - Structure, 2022 - cell.com
Crosslinking mass spectrometry (crosslinking-MS) is a versatile tool providing structural
insights into protein conformation and protein-protein interactions. Its medium-resolution …

Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes

A Leitner, LA Joachimiak… - Proceedings of the …, 2014 - National Acad Sciences
The study of proteins and protein complexes using chemical cross-linking followed by the
MS identification of the cross-linked peptides has found increasingly widespread use in …

Protocols for molecular modeling with Rosetta3 and RosettaScripts

BJ Bender, A Cisneros III, AM Duran, JA Finn, D Fu… - Biochemistry, 2016 - ACS Publications
Previously, we published an article providing an overview of the Rosetta suite of
biomacromolecular modeling software and a series of step-by-step tutorials [Kaufmann, KW …