HypDB: A functionally annotated web-based database of the proline hydroxylation proteome

Crosslinking-mediated Interactome Analysis Identified PHD2-HIF1α Interaction Hotspots and the Role of PHD2 in Regulating Protein Neddylation

Prolyl Hydroxylase Domain protein 2 (PHD2) targets Hypoxia Inducible Factor alpha subunits (HIFα) for oxygen-dependent proline hydroxylation that leads to subsequent ubiquitination and degradation of HIFα. In addition to HIF proteins, growing evidence suggested that PHD2 may exert its multifaceted function through hydroxylase-dependent or independent activities. Given the critical role of PHD2 in diverse biological processes, it is important to comprehensively identify potential PHD2 interacting proteins. In this study, we engineered HeLa cells that stably express HTBH-tagged PHD2 to facilitate the identification of PHD2 interactome. Using DSSO-based cross-linking mass spectrometry (XL-MS) technology and LC-MSn analysis, we mapped PHD2-HIF1α interaction hotspots and identified over 300 PHD2 interacting proteins. Furthermore, we validated the COP9 Signalosome (CSN) complex, a major deneddylase complex, as a novel PHD2 interactor. DMOG treatment promoted interaction between PHD2 and CSN complex and enhanced the deneddylase activity of the CSN complex, resulting in increased level of free Cullin and reduced target protein ubiquitination. This mechanism may serve as a negative feedback regulation of the HIF transcription pathway.

Proteomic insights into the extracellular matrix: a focus on proteoforms and their implications in health and disease

INTRODUCTION

The extracellular matrix (ECM) is a highly organized and dynamic network of proteins and glycosaminoglycans that provides critical structural, mechanical, and biochemical support to cells. The functions of the ECM are directly influenced by the conformation of the proteins that compose it. ECM proteoforms, which can result from genetic, transcriptional, and/or post-translational modifications, adopt different conformations and, consequently, confer different structural properties and functionalities to the ECM in both physiological and pathological contexts.

AREAS COVERED

In this review, we discuss how bottom-up proteomics has been applied to identify, map, and quantify post-translational modifications (e.g. additions of chemical groups, proteolytic cleavage, or cross-links) and ECM proteoforms arising from alternative splicing or genetic variants. We further illustrate how proteoform-level information can be leveraged to gain novel insights into ECM protein structure and ECM functions in health and disease.

EXPERT OPINION

In the Expert opinion section, we discuss remaining challenges and opportunities with an emphasis on the importance of devising experimental and computational methods tailored to account for the unique biochemical properties of ECM proteins with the goal of increasing sequence coverage and, hence, accurate ECM proteoform identification.

High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF

The extracellular matrix (ECM) is a complex assembly of proteins that provide interstitial scaffolding and elastic recoil for human lungs. The pulmonary extracellular matrix is increasingly recognized as an independent bioactive entity, by creating biochemical and mechanical signals that influence disease pathogenesis, making it an attractive therapeutic target. However, the pulmonary ECM proteome ("matrisome") remains challenging to analyze by mass spectrometry due to its inherent biophysical properties and relatively low abundance. Here, we introduce a strategy designed for rapid and efficient characterization of the human pulmonary ECM using the photocleavable surfactant Azo. We coupled this approach with trapped ion mobility MS with diaPASEF to maximize the depth of matrisome coverage. Using this strategy, we identify nearly 400 unique matrisome proteins with excellent reproducibility that are known to be important in lung biology, including key core matrisome proteins.