New advances in cross-linking mass spectrometry toward structural systems biology

C Yu, L Huang - Current opinion in chemical biology, 2023 - Elsevier
Elucidating protein–protein interaction (PPI) networks and their structural features within
cells is central to understanding fundamental biology and associations of cell phenotypes …

Chemical cross-linking and mass spectrometry enabled systems-level structural biology

L Botticelli, AA Bakhtina, NK Kaiser, A Keller… - Current Opinion in …, 2024 - Elsevier
Structural information on protein–protein interactions (PPIs) is essential for improved
understanding of regulatory interactome networks that confer various physiological and …

Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field

SS Chaturvedi, S Vargas, P Ajmera… - Journal of the …, 2024 - ACS Publications
To unravel why computational design fails in creating viable enzymes, while directed
evolution (DE) succeeds, our research delves into the laboratory evolution of protoglobin …

AlphaFold two years on: Validation and impact

O Kovalevskiy, J Mateos-Garcia… - Proceedings of the …, 2024 - pnas.org
Two years on from the initial release of AlphaFold, we have seen its widespread adoption as
a structure prediction tool. Here, we discuss some of the latest work based on AlphaFold …

Modeling flexible protein structure with AlphaFold2 and crosslinking mass spectrometry

K Manalastas-Cantos, KR Adoni, M Pfeifer… - Molecular & Cellular …, 2024 - mcponline.org
We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry
(XL-MS) to model the structure of proteins with multiple conformations. The pipeline consists …

Cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure

ARM Michael, BC Amaral, KL Ball, KH Eiriksson… - Nature …, 2024 - nature.com
Crosslinking mass spectrometry (XL-MS) has the potential to map the interactome of the cell
with high resolution and depth of coverage. However, current in vivo XL-MS methods are …

The potential of cross-linking mass spectrometry in the development of protein–protein interaction modulators

M Ruwolt, I Piazza, F Liu - Current Opinion in Structural Biology, 2023 - Elsevier
Cross-linking mass spectrometry (XL-MS) can provide a wealth of information on
endogenous protein–protein interaction (PPI) networks and protein binding interfaces …

[HTML][HTML] Structural biology in cellulo: Minding the gap between conceptualization and realization

FL Kyrilis, JKK Low, JP Mackay, PL Kastritis - Current Opinion in Structural …, 2024 - Elsevier
Recent technological advances have deepened our perception of cellular structure.
However, most structural data doesn't originate from intact cells, limiting our understanding …

DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples

F Jiao, C Yu, A Wheat, L Chen, TSM Lih… - Journal of proteome …, 2024 - ACS Publications
Protein–protein interactions (PPIs) are fundamental to understanding biological systems as
protein complexes are the active molecular modules critical for carrying out cellular …

Decoding Protein Dynamics in Cells Using Chemical Cross‐Linking and Hierarchical Analysis

B Zhang, Z Gong, L Zhao, Y An, H Gao… - Angewandte Chemie …, 2023 - Wiley Online Library
Protein dynamics play a crucial role in their diverse functions. The intracellular environment
significantly influences protein dynamics, particularly for intrinsically disordered proteins …