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Ubiquitin is a common posttranslational modification canonically associated with targeting proteins to the 26S proteasome for degradation and also plays a role in numerous other nondegradative cellular processes. Ubiquitination at certain sites destabilizes the substrate protein, with consequences for proteasomal processing, while ubiquitination at other sites has little energetic effect. How this site specificity-and, by extension, the myriad effects of ubiquitination on substrate proteins-arises remains unknown. Here, we systematically characterize the atomic-level effects of ubiquitination at various sites on a model protein, barstar, using a combination of NMR, hydrogen-deuterium exchange mass spectrometry, and molecular dynamics simulation. We find that, regardless of the site of modification, ubiquitination does not induce large structural rearrangements in the substrate. Destabilizing modifications, however, increase fluctuations from the native state resulting in exposure of the substrate's C terminus. Both of the sites occur in regions of barstar with relatively high conformational flexibility. Nevertheless, destabilization appears to occur through different thermodynamic mechanisms, involving a reduction in entropy in one case and a loss in enthalpy in another. By contrast, ubiquitination at a nondestabilizing site protects the substrate C terminus through intermittent formation of a structural motif with the last three residues of ubiquitin. Thus, the biophysical effects of ubiquitination at a given site depend greatly on local context. Taken together, our results reveal how a single posttranslational modification can generate a broad array of distinct effects, providing a framework to guide the design of proteins and therapeutics with desired degradation and quality control properties.

Current liquid chromatography-tandem mass spectrometry (LC-MS/MS) applications for circulating androgen measurements are technically diverse. Previously, variable results have been reported for testosterone. Data are scarce for androstenedione and absent for dehydroepiandrosterone sulfate (DHEAS). We assessed the agreement of androstenedione, DHEAS and testosterone LC-MS/MS measurements among nine European centers and explored benefits of calibration system unification. Androgens were measured twice by laboratory-specific procedures in 78 patient samples and in EQA materials. Results were obtained by in-house and external calibration. Intra- and inter-laboratory performances were valued. Intra-laboratory CVs ranged between 4.2–13.2 % for androstenedione, 1.6–10.8 % for DHEAS, and 4.3–8.7 % and 2.6–7.1 % for female and male testosterone, respectively. Bias and trueness in EQA materials were within ±20 %. Median inter-laboratory CV with in-house vs. external calibration were 12.0 vs. 9.6 % for androstenedione (p<0.001), 7.2 vs. 4.9 % for DHEAS (p<0.001), 6.4 vs. 7.6 % for female testosterone (p<0.001) and 6.8 and 7.4 % for male testosterone (p=0.111). Median bias vs. all laboratory median with in-house and external calibration were −13.3 to 20.5 % and −4.9 to 18.7 % for androstenedione, −10.9 to 4.8 % and −3.4 to 3.5 % for DHEAS, −2.7 to 6.5 % and −11.3 to 6.6 % for testosterone in females, and −7.0 to 8.5 % and −7.5 to 11.8 % for testosterone in males, respectively. Methods showed high intra-laboratory precision but variable bias and trueness. Inter-laboratory agreement was remarkably good. Calibration system unification improved agreement in androstenedione and DHEAS, but not in testosterone measurements. Multiple components, such as commutability of calibrators and EQA materials and internal standard choices, likely contribute to inter-laboratory variability. [ABSTRACT FROM AUTHOR]

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) panels that include glucocorticoid-related steroids are increasingly used to characterize and diagnose adrenal cortical diseases. Limited information is currently available about reproducibility of these measurements among laboratories. The aim of the study was to compare LC-MS/MS measurements of corticosterone, 11-deoxycortisol and cortisone at eight European centers and assess the performance after unification of calibration. Seventy-eight patient samples and commercial calibrators were measured twice by laboratory-specific procedures. Results were obtained according to in-house and external calibration. We evaluated intra-laboratory and inter-laboratory imprecision, regression and agreement against performance specifications derived from 11-deoxycortisol biological variation. Intra-laboratory CVs ranged between 3.3 and 7.7%, 3.3 and 11.8% and 2.7 and 12.8% for corticosterone, 11-deoxycortisol and cortisone, with 1, 4 and 3 laboratories often exceeding the maximum allowable imprecision (MAI), respectively. Median inter-laboratory CVs were 10.0, 10.7 and 6.2%, with 38.5, 50.7 and 2.6% cases exceeding the MAI for corticosterone, 11-deoxycortisol and cortisone, respectively. Median laboratory bias vs. all laboratory-medians ranged from −5.6 to 12.3% for corticosterone, −14.6 to 12.4% for 11-deoxycortisol and −4.0 to 6.5% for cortisone, with few cases exceeding the total allowable error. Modest deviations were found in regression equations among most laboratories. External calibration did not improve 11-deoxycortisol and worsened corticosterone and cortisone inter-laboratory comparability. Method imprecision was variable. Inter-laboratory performance was reasonably good. However, cases with imprecision and total error above the acceptable limits were apparent for corticosterone and 11-deoxycortisol. Variability did not depend on calibration but apparently on imprecision, accuracy and specificity of individual methods. Tools for improving selectivity and accuracy are required to improve harmonization. [ABSTRACT FROM AUTHOR]

Background: The adrenocorticotropic hormone (ACTH) stimulation test is a widely used diagnostic tool to assess the adrenal gland function. Beyond that the ACTH test can be used in stress research to induce a biochemical stress response under standardized conditions. To study the impact of the stress response on protein metabolism, time-course plasma amino acid profiling in healthy individuals was performed with high performance liquid chromatography tandem-mass spectrometry (HPLC-MS/MS). Methods: A set of 39 samples (pre/post 30´ and 60´ IV-ACTH) from 13 healthy individuals (age range 26 - 58, 3 female and 10 male) was investigated. Plasma amino acids were quantified by LC-MS/MS using the AbsoluteIDQ ® p180 Kit (Biocrates Life Science, Innsbruck, Austria) including 19 biogenic amino acids, ornithine, and citrulline. Results: Statistically significant decreases were observed for 11 proteinogenic amino acids (alanine, asparagine, isoleucine, leucine, tyrosine, phenylalanine, tryptophan, valine, methionine, aspartate, and threonine). The amino acids alanine, asparagine, and isoleucine showed markedly pronounced relative changes with short-term reduction of median inter-individual plasma concentrations of up to 25%. Conclusions: Amino acid profiling with LC-MS/MS revealed highly dynamic plasma alterations upon application of exogenous corticotropin as a stress model. Our findings provide novel insights into the biochemical stress response and improve our understanding of short-term metabolic consequences. Further studies should elucidate the impact of corticotropin mediated stress responses on amino acid catabolism. [ABSTRACT FROM AUTHOR]