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.

Identification of 113 new histone marks by CHiMA, a tailored database search strategy.

Shotgun proteomics has been widely used to identify histone marks. Conventional database search methods rely on the "target-decoy" strategy to calculate the false discovery rate (FDR) and distinguish true peptide-spectrum matches (PSMs) from false ones. This strategy has a caveat of inaccurate FDR caused by the small data size of histone marks.

HDAC6 Regulates Radiosensitivity of Non-Small Cell Lung Cancer by Promoting Degradation of Chk1.

We have previously discovered that HDAC6 regulates the DNA damage response (DDR) via modulating the homeostasis of a DNA mismatch repair protein, MSH2, through HDAC6's ubiquitin E3 ligase activity. Here, we have reported HDAC6's second potential E3 ligase substrate, a critical cell cycle checkpoint protein, Chk1. We have found that HDAC6 and Chk1 directly interact, and that HDAC6 ubiquitinates Chk1 in vivo and in vitro.

Label-Free Interactome Analysis Revealed an Essential Role of CUL3-KEAP1 Complex in Mediating the Ubiquitination and Degradation of PHD2.

Prolyl hydroxylase domain-containing protein 2 (PHD2/EGLN1) is a key regulatory enzyme that plays a fundamental role in the cellular hypoxic response pathway, mediating proline hydroxylation-dependent protein degradation of selected target proteins. However, the regulation of PHD2 homeostasis at the protein level is not well understood. Here, we perform label-free quantitative interactome analysis through immunoprecipitation coupled with mass spectrometry analysis.

Site-specific determination of lysine acetylation stoichiometries on the proteome-scale.

Posttranslational modification of proteins (PTMs) offers a versatile mechanism to fine-tune the structure, activity, and interactions of the target proteins. Understanding the dynamics and prevalence of the PTM at the site-specific level will provide mechanistic insight into the physiological significance of the modification pathway in cells and diseases. In this chapter, we describe a highly efficient chemical proteomic workflow for the absolute quantification of lysine acetylation stoichiometry.

Performance of rapid influenza H1N1 diagnostic tests: a meta-analysis.

Background: Following the outbreaks of 2009 pandemic H1N1 infection, rapid influenza diagnostic tests have been used to detect H1N1 infection. However, no meta-analysis has been undertaken to assess the diagnostic accuracy when this manuscript was drafted.

Methods: The literature was systematically searched to identify studies that reported the performance of rapid tests.