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 …

[HTML][HTML] Histone ubiquitination: an integrative signaling platform in genome stability

F Mattiroli, L Penengo - Trends in Genetics, 2021 - cell.com
Complex mechanisms are in place to maintain genome stability. Ubiquitination of chromatin
plays a central role in these mechanisms. The ever-growing complexity of the ubiquitin (Ub) …

BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1

SR Witus, AL Burrell, DP Farrell, J Kang… - Nature structural & …, 2021 - nature.com
Mutations in the E3 ubiquitin ligase RING domains of BRCA1/BARD1 predispose carriers to
breast and ovarian cancers. We present the structure of the BRCA1/BARD1 RING …

The ubiquitin codes in cellular stress responses

X Sheng, Z Xia, H Yang, R Hu - Protein & cell, 2024 - academic.oup.com
Ubiquitination/ubiquitylation, one of the most fundamental post-translational modifications,
regulates almost every critical cellular process in eukaryotes. Emerging evidence has shown …

Small-molecule inhibitors targeting Polycomb repressive complex 1 RING domain

S Shukla, W Ying, F Gray, Y Yao, ML Simes… - Nature chemical …, 2021 - nature.com
Abstract Polycomb repressive complex 1 (PRC1) is an essential chromatin-modifying
complex that monoubiquitinates histone H2A and is involved in maintaining the repressed …

Preserving genome integrity and function: the DNA damage response and histone modifications

JJ Kim, SY Lee, KM Miller - Critical reviews in biochemistry and …, 2019 - Taylor & Francis
Modulation of chromatin templates in response to cellular cues, including DNA damage,
relies heavily on the post-translation modification of histones. Numerous types of histone …

A methyl-TROSY approach for NMR studies of high-molecular-weight DNA with application to the nucleosome core particle

G Abramov, A Velyvis, E Rennella… - Proceedings of the …, 2020 - National Acad Sciences
The development of methyl-transverse relaxation-optimized spectroscopy (methyl-TROSY)–
based NMR methods, in concert with robust strategies for incorporation of methyl-group …

Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides

T Altenburg, SH Giese, S Wang, T Muth… - Nature Machine …, 2022 - nature.com
Mass spectrometry-based proteomics provides a holistic snapshot of the entire protein set of
living cells on a molecular level. Currently, only a few deep learning approaches exist that …

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 …

Epstein-Barr virus protein BKRF4 restricts nucleosome assembly to suppress host antiviral responses

J Chen, Z Lu, W Gong, X Xiao, X Feng… - Proceedings of the …, 2022 - National Acad Sciences
Inhibition of host DNA damage response (DDR) is a common mechanism used by viruses to
manipulate host cellular machinery and orchestrate viral life cycles. Epstein-Barr virus …