Nonenzymatic acetylation of ubiquitin Lys side chains is modulated by their neighboring residues

A map of glycation and glycoxidation sites in collagen I of human cortical bone: Effects of sex and type 2 diabetes

Complications of diabetes is a major health problem affecting multiple organs including bone, where the chronic disease increases the risk of fragility fractures. One hypothesis suggests a pathogenic role for hyperglycemia-induced modification of proteins, a.k.a. advanced glycation end products (AGEs), resulting in structural and functional damage to bone extracellular matrix (ECM). Evidence supporting this hypothesis has been limited by the lack of comprehensive information about the location of AGEs that accumulate in vivo at specific sites within the proteins of bone ECM. Analyzing extracts from cortical bone of cadaveric femurs by liquid chromatography tandem mass spectrometry, we generated a quantitative AGE map of human collagen I for male and female adult donors with and without diabetes. The map describes the chemical nature, sequence position, and levels of four major physiological AGEs, e.g. carboxymethyllysine, and an AGE precursor fructosyllysine within the collagen I triple-helical region. The important features of the map are: 1) high map reproducibility in the individual bone extracts, i.e. 20 male and 20 female donors; 2) localization of modifications to distinct clusters: 10 clusters containing 34 AGE sites in male donors and 9 clusters containing 28 sites in female donors; 3) significant increases in modification levels in diabetes at multiple sites: 26 out of 34 sites in males and in 17 out of 28 sites in females; and 4) generally higher modification levels in male vs. female donors. Moreover, the AGE levels at multiple individual sites correlated with total bone pentosidine levels in male but not in female donors. Molecular dynamics simulations and molecular modeling predicted significant impact of modifications on solvent exposure, charge distribution, and hydrophobicity of the triple helix as well as disruptions to the structure of collagen I fibril. In summary, the AGE map of collagen I revealed diabetes-induced, sex-specific non-enzymatic modifications at distinct triple helical sites that can disrupt collagen structure, thus proposing a specific mechanism of AGE contribution to diabetic complications in human bone.

Mapping glycation and glycoxidation sites in collagen I of human cortical bone

Accumulation of advanced glycation end products (AGEs), particularly in long-lived extracellular matrix proteins, has been implicated in pathogenesis of diabetic complications and in aging. Knowledge about specific locations of AGEs and their precursors within protein primary structure is critical for understanding their physiological and pathophysiological impact. However, the information on specific AGE sites is lacking. Here, we identified sequence positions of four major AGEs, carboxymethyllysine, carboxyethyllysine, 5-hydro-5-methyl imidazolone, and 5-hydro-imidazolone, and an AGE precursor fructosyllysine within the triple helical region of collagen I from cortical bone of human femurs. The presented map provides a basis for site-specific quantitation of AGEs and other non-enzymatic post-translational modifications and identification of those sites affected by aging, diabetes, and other diseases such as osteoporosis; it can also help in guiding future studies of AGE impact on structure and function of collagen I in bone.

MUL1‐RING recruits the substrate, p53‐TAD as a complex with UBE2D2–UB conjugate

The RING domain of MUL1 (RING_MUL1) alone mediates ubiquitylation of the p53‐transactivation domain (TAD_p53). To elucidate the mechanism underlying the simultaneous recruitment of UBE2D2 and the substrate TAD_p53 by RING_MUL1, we determined the complex structure of RING_MUL1:UBE2D2 and studied the interaction between RING_MUL1 and TAD_p53 in the presence of UBE2D2–UB thioester (UBE2D2~UB) mimetics. The RING_MUL1‐binding induced the closed conformation of UBE2D2^S22R/C85S–UB^K48R oxyester (UBE2D2^RS–UB^R_OE), and strongly accelerated its hydrolysis, which was suppressed by the additional N77A‐mutation of UBE2D2. Interestingly, UBE2D2^{S22R/N77A/C85S}–UB^K48R oxyester (UBE2D2^RAS–UB^R_OE) already formed a closed conformation in the absence of RING_MUL1. Although TAD_p53 exhibited weak binding for RING_MUL1 or UBE2D2 alone, its binding affinity was enhanced and even further for RING_MUL1:UBE2D2 and RING_MUL1:UBE2D2^RAS–UB^R_OE, respectively. The recognition of TAD_p53 by RING_MUL1 as a complex with UBE2D2~UB is related to the multivalency of the binding events and underlies the ability of RING_MUL1 to ubiquitylate the intrinsically disordered protein, TAD_p53.

Site-Specific Detection and Characterization of Ubiquitin Carbamylation

The physiological consequences of varying in vivo CO₂ levels point to a general mechanism for CO₂ to influence cellular homeostasis beyond regulating pH. Aside from a few instances where CO₂ has been observed to cause post-translational protein modification, by forming long-lived carbamates, little is known about how transitory and ubiquitous carbamylation events could induce a physiological response. Ubiquitin is a versatile protein involved in a multitude of cellular signaling pathways as polymeric chains of various lengths formed through one of the seven lysines or N-terminal amine. Unique polyubiquitin (polyUb) compositions present recognition signals for specific ubiquitin-receptors which enables this one protein to be involved in many different cellular processes. Advances in proteomic methods have allowed the capture and identification of protein carbamates in vivo, and Ub was found carbamylated at lysines K48 and K33. This was shown to negatively regulate ubiquitin-mediated signaling by inhibiting polyUb chain formation. Here, we expand upon these observations by characterizing the carbamylation susceptibility for all Ub amines simultaneously. Using NMR methods which directly probe ¹⁵N resonances, we determined carbamylation rates under various environmental conditions and related them to the intrinsic pK_as. Our results show that the relatively low pK_as for half of the Ub amines are correlated with enhanced susceptibility to carbamylation under physiological conditions. Two of these carbamylated amines, not observed by chemical capture, appear to be physiologically relevant post-translational modifications. These findings point to a mechanism for varying the levels of CO₂ due to intracellular localization, cellular stresses, and metabolism to affect certain polyUb-mediated signaling pathways.

Ubiquitin is a carbon dioxide-binding protein

The identification of CO₂-binding proteins is crucial to understanding CO₂-regulated molecular processes. CO₂ can form a reversible posttranslational modification through carbamylation of neutral N-terminal α-amino or lysine ε-amino groups. We have previously developed triethyloxonium (TEO) ion as a chemical proteomics tool for covalent trapping of carbamates, and here, we deploy TEO to identify ubiquitin as a mammalian CO₂-binding protein. We use ¹³C-NMR spectroscopy to demonstrate that CO₂ forms carbamates on the ubiquitin N terminus and ε-amino groups of lysines 6, 33, 48, and 63. We demonstrate that biologically relevant pCO₂ levels reduce ubiquitin conjugation at lysine-48 and down-regulate ubiquitin-dependent NF-κB pathway activation. Our results show that ubiquitin is a CO₂-binding protein and demonstrates carbamylation as a viable mechanism by which mammalian cells can respond to fluctuating pCO₂.

Protein Acetylation/Deacetylation: A Potential Strategy for Fungal Infection Control

Protein acetylation is a universal post-translational modification that fine-tunes the major cellular processes of many life forms. Although the mechanisms regulating protein acetylation have not been fully elucidated, this modification is finely tuned by both enzymatic and non-enzymatic mechanisms. Protein deacetylation is the reverse process of acetylation and is mediated by deacetylases. Together, protein acetylation and deacetylation constitute a reversible regulatory protein acetylation network. The recent application of mass spectrometry-based proteomics has led to accumulating evidence indicating that reversible protein acetylation may be related to fungal virulence because a substantial amount of virulence factors are acetylated. Additionally, the relationship between protein acetylation/deacetylation and fungal drug resistance has also been proven and the potential of deacetylase inhibitors as an anti-infective treatment has attracted attention. This review aimed to summarize the research progress in understanding fungal protein acetylation/deacetylation and discuss the mechanism of its mediation in fungal virulence, providing novel targets for the treatment of fungal infection.

Small molecules that target the ubiquitin system

Eukaryotic life depends upon the interplay between vast networks of signaling pathways composed of upwards of 109-1010 proteins per cell. The integrity and normal operation of the cell requires that these proteins act in a precise spatial and temporal manner. The ubiquitin system is absolutely central to this process and perturbation of its function contributes directly to the onset and progression of a wide variety of diseases, including cancer, metabolic syndromes, neurodegenerative diseases, autoimmunity, inflammatory disorders, infectious diseases, and muscle dystrophies. Whilst the individual components and the overall architecture of the ubiquitin system have been delineated in some detail, how ubiquitination might be successfully targeted, or harnessed, to develop novel therapeutic approaches to the treatment of disease, currently remains relatively poorly understood. In this review, we will provide an overview of the current status of selected small molecule ubiquitin system inhibitors. We will further discuss the unique challenges of targeting this ubiquitous and highly complex machinery, and explore and highlight potential ways in which these challenges might be met.