A Fluorescent Probe for Stimulated Emission Depletion Super-Resolution Imaging of Vicinal-Dithiol-Proteins on Mitochondrial Membrane.

Realizing the significant roles of vicinal-dithiol proteins (VDPs) in maintaining the cellular redox homeostasis and their implication in many diseases, we synthesized a smart arsenate based fluorescent probe 1 which can preferentially target the mitochondrial membrane-bound vicinal dithiol proteins (VDPs), especially voltage-dependent anion channel (VDAC2). The probe targetability was demonstrated by in vitro studies such as colocalization, stimulated emission depletion (STED) super-resolution imaging, proteomic MS/MS analysis, and Western blot analysis. The probe represents a rare example of fluorescence labeling of mitochondrial membrane-bound VDPs and can provide a new way to construct VDPs-specific fluorescent probes to gain deeper understanding of their roles in mitochondrial-related disorders.

Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues.

The data-independent acquisition (DIA) approach has recently been introduced as a novel mass spectrometric method that promises to combine the high content aspect of shotgun proteomics with the reproducibility and precision of selected reaction monitoring. Here, we evaluate, whether SWATH-MS type DIA effectively translates into a better protein profiling as compared with the established shotgun proteomics. We implemented a novel DIA method on the widely used Orbitrap platform and used retention-time-normalized (iRT) spectral libraries for targeted data extraction using Spectronaut. We call this combination hyper reaction monitoring (HRM). Using a controlled sample set, we show that HRM outperformed shotgun proteomics both in the number of consistently identified peptides across multiple measurements and quantification of differentially abundant proteins. The reproducibility of HRM in peptide detection was above 98%, resulting in quasi complete data sets compared with 49% of shotgun proteomics. Utilizing HRM, we profiled acetaminophen (APAP)(1)-treated three-dimensional human liver microtissues. An early onset of relevant proteome changes was revealed at subtoxic doses of APAP. Further, we detected and quantified for the first time human NAPQI-protein adducts that might be relevant for the toxicity of APAP. The adducts were identified on four mitochondrial oxidative stress related proteins (GATM, PARK7, PRDX6, and VDAC2) and two other proteins (ANXA2 and FTCD). Our findings imply that DIA should be the preferred method for quantitative protein profiling.

Intramolecular Disulfide Bridges in Voltage-Dependent Anion Channel 2 (VDAC2) Protein from Rattus norvegicus Revealed by High-Resolution Mass Spectrometry.

Voltage-Dependent Anion Channel isoforms (VDAC1, VDAC2, and VDAC3) are relevant components of the outer mitochondrial membrane (OMM) and play a crucial role in regulation of metabolism and in survival pathways. As major players in the regulation of cellular metabolism and apoptosis, VDACs can be considered at the crossroads between two broad families of pathologies, namely, cancer and neurodegeneration, the former being associated with elevated glycolytic rate and suppression of apoptosis in cancer cells, the latter characterized by mitochondrial dysfunction and increased cell death. Recently, we reported the characterization of the oxidation pattern of methionine and cysteines in rat and human VDACs showing that each cysteine in these proteins is present with a preferred oxidation state, ranging from the reduced to the trioxidized form, and such an oxidation state is remarkably conserved between rat and human VDACs. However, the presence and localization of disulfide bonds in VDACs, a key point for their structural characterization, have so far remained undetermined. Herein we have investigated by nanoUHPLC/High-Resolution nanoESI-MS/MS the position of intramolecular disulfide bonds in rat VDAC2 (rVDAC2), a protein that contains 11 cysteines. To this purpose, extraction, purification, and enzymatic digestions were carried out at slightly acidic or neutral pH in order to minimize disulfide bond interchange. The presence of six disulfide bridges was unequivocally determined, including a disulfide bridge linking the two adjacent cysteines 4 and 5, a disulfide bridge linking cysteines 9 and 14, and the alternative disulfide bridges between cysteines 48, 77, and 104. A disulfide bond, which is very resistant to reduction, between cysteines 134 and 139 was also detected. In addition to the previous findings, these results significantly extend the characterization of the oxidation state of cysteines in rVDAC2 and show that it is highly complex and presents unusual features. Data are available via ProteomeXchange with the identifier PXD044041.

Expression and localization of voltage-dependent anion channels (VDAC) in human spermatozoa.

Voltage-dependent anion channels (VDAC), also known as mitochondrial porins, are a group of proteins first identified in the mitochondrial outer membrane that are able to form hydrophilic pore structures. VDAC allow the passage of the metabolites across the mitochondrial outer membrane, and are involved in metabolite transport and signal transduction. Several recent studies have indicated the important roles of VDAC in maintaining normal structure and motility of mammalian spermatozoa. To study the expression and localization of VDAC in human spermatozoa, different experimental approaches were applied: (1) specific primers were designed and VDAC gene sequences were cloned by PCR amplification from human testis cDNA library; (2) recombinant VDAC proteins were produced in the expression vector Escherichia coli BL21 (DE3); (3) human sperm VDAC proteins were extracted, separated and analyzed by Western blotting; (4) the localization of VDAC in human spermatozoa were detected using immunofluorescence. The three gene sequences and recombinant VDAC proteins were obtained, respectively. VDAC proteins were detected to be located in human spermatozoa, especially in sperm flagella. Our study elucidated for the first time that VDAC were synthesized and secreted at the testis level and eventually became an integral part of sperm proteins.