Identification of sulfenylated cysteines in Arabidopsis thaliana proteins using a disulfide-linked peptide reporter

In proteins, hydrogen peroxide (H2O2) reacts with redox-sensitive cysteines to form cysteine sulfenic acid, also known asS-sulfenylation. These cysteine oxidation events can steer diverse cellular processes by altering protein interactions, trafficking, conformation, and function. Previously, we had identifiedS-sulfenylated proteins by using a tagged proteinaceous probe based on the yeast AP-1-like (Yap1) transcription factor that specifically reacts with sulfenic acids and traps them through a mixed disulfide bond. However, the identity of theS-sulfenylated amino acid residues within a protein remained enigmatic. By using the same transgenic YAP1C probe, we present here a technological advancement to identifyin situsulfenylated cysteine sites inArabidopsis thalianacells under control condition and oxidative stress. Briefly, the total extract of transgenic YAP1CA. thalianacells was initially purified on IgG-Sepharose beads, followed by a tryptic digest. Then, the mixed disulfide-linked peptides were further enriched at the peptide level on an anti-YAP1C-derived peptide (C598SEIWDR) antibody. Subsequent mass spectrometry analysis with pLink 2 identified 1,745 YAP1C cross-linked peptides, indicating sulfenylated cysteines in over 1,000 proteins. Approximately 55% of these YAP1C-linked cysteines had previously been reported as redox-sensitive cysteines (S-sulfenylation,S-nitrosylation, and reversibly oxidized cysteines). The presented methodology provides a noninvasive approach to identify sulfenylated cysteines in any species that can be genetically modified

Small sized EGFR1 and HER2 specific bifunctional antibody for targeted cancer therapy

licenses/by-nc-nd/3.0/). Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. Received: 2014.07.10; Accepted: 2015.01.05; Published: 2015.01.21 Targeting tumors using miniature antibodies is a novel and attractive therapeutic approach, as these biomolecules exhibit low immunogenicity, rapid clearance, and high targeting specificity. However, most of the small-sized antibodies in existence do not exhibit marked anti-tumor ef-fects, which limit their use in targeted cancer immunotherapy. To overcome this difficulty in targeting multiple biomarkers by combination therapies, we designed a new bifunctional antibody, named MaAbNA (multivalent antibody comprised of nanobody and affibody moieties), capable of targeting EGFR1 and HER2, which are widely overexpressed in a variety of tumor types. The small-sized (29 kDa) MaAbNA, which was expressed in E.coli, consists of one anti-EGFR1 nano-body and two anti-HER2 affibodies, and possesses high affinity (KD) for EGFR1 (~4.1 nM) and HER2 (~4.7 nM). In order to enhance its anti-tumor activity, MaAbNA was conjugated with adriamycin (ADM) using a PEG2000 linker, forming a new complex anticancer drug, MaAbNA-PEG2000-ADM. MaAbNA exhibited high inhibitory effects on tumor cell

Nucleophilic covalent ligand discovery for the cysteine redoxome

The convergence of reactive cysteine-targeted electrophilic fragments and chemoproteomics have dramatically accelerated the discovery of ligandable sites in the proteome. Our genome encodes 214,000 cysteine residues, at least 20% of which are estimated to be redox-active. Oxidation blunts sulfur reactivity toward electrophiles but opens the door to a new class of nucleophilic covalent ligands that target cysteinyl sulfenic acids, which are widespread post-translational modifications. Here we report a quantitative analysis of nucleophilic fragments screened against the human sulfenome. Ligands were discovered for >500 sulfenated cysteines in >400 proteins, including sites not targeted by electrophiles with the same scaffold. Among these were compounds that preferentially react with hepatoma-derived growth factor (HDGF)-related proteins (HRPs) one of which was able to block nuclear transport of this oncoprotein. Nucleophilic fragments provide a rich resource for chemical biology and drug discovery, where ligandability in the human proteome extends beyond protein thiols

A Filter-Based and Parallel Unknown Tag Identification Protocol in Open RFID Systems

Unknown tag identification plays a pivotal role in radio frequency identification (RFID) systems, but it has not been fully investigated. This paper proposes a filter-based and parallel unknown tag identification protocol (FPUI) for open RFID systems. The FPUI adopts an RSQF-based fingerprint filter to reconcile the collision slots and discriminate the known tags from unknown tags. Meanwhile, it collects the IDs of unknown tags in parallel. FPUI achieves high performance through the following three steps: (1) adopting the RSQF-based filter to build an indicator vector, thus improving the space efficiency; (2) building a fingerprint filter to discriminate known tags from unknown tags, thus reducing the false positive rate; (3) employing a parallel identification scheme to collect the IDs of unknown tags, thus improving identification efficiency. The identification time of our protocol was minimized by conducting a theoretical analysis of the relevant parameters. Furthermore, the performance of our protocol was evaluated by conducting a wide range of simulation experiments. The theoretical analysis and simulation results indicated that our protocol significantly outperformed the current advanced protocols

A Filter-Based and Parallel Unknown Tag Identification Protocol in Open RFID Systems

Unknown tag identification plays a pivotal role in radio frequency identification (RFID) systems, but it has not been fully investigated. This paper proposes a filter-based and parallel unknown tag identification protocol (FPUI) for open RFID systems. The FPUI adopts an RSQF-based fingerprint filter to reconcile the collision slots and discriminate the known tags from unknown tags. Meanwhile, it collects the IDs of unknown tags in parallel. FPUI achieves high performance through the following three steps: (1) adopting the RSQF-based filter to build an indicator vector, thus improving the space efficiency; (2) building a fingerprint filter to discriminate known tags from unknown tags, thus reducing the false positive rate; (3) employing a parallel identification scheme to collect the IDs of unknown tags, thus improving identification efficiency. The identification time of our protocol was minimized by conducting a theoretical analysis of the relevant parameters. Furthermore, the performance of our protocol was evaluated by conducting a wide range of simulation experiments. The theoretical analysis and simulation results indicated that our protocol significantly outperformed the current advanced protocols

Dynamic redox balance directs the oocyte-to-embryo transition via developmentally controlled reactive cysteine changes

The metabolic and redox state changes during the transition from an arrested oocyte to a totipotent embryo remain uncharacterized. Here, we applied state-of-the-art, integrated methodologies to dissect these changes in Drosophila. We demonstrate that early embryos have a more oxidized state than mature oocytes. We identified specific alterations in reactive cysteines at a proteome-wide scale as a result of this metabolic and developmental transition. Consistent with a requirement for redox change, we demonstrate a role for the ovary-specific thioredoxin Deadhead (DHD). dhd-mutant oocytes are prematurely oxidized and exhibit meiotic defects. Epistatic analyses with redox regulators link dhd function to the distinctive redox-state balance set at the oocyte-to-embryo transition. Crucially, global thiol-redox profiling identified proteins whose cysteines became differentially modified in the absence of DHD. We validated these potential DHD substrates by recovering DHD-interaction partners using multiple approaches. One such target, NO66, is a conserved protein that genetically interacts with DHD, revealing parallel functions. As redox changes also have been observed in mammalian oocytes, we hypothesize a link between developmental control of this cell-cycle transition and regulation by metabolic cues. This link likely operates both by general redox state and by changes in the redox state of specific proteins. The redox proteome defined here is a valuable resource for future investigation of the mechanisms of redox-modulated control at the oocyte-to-embryo transition

Chemoproteomics Reveals Unexpected Lysine/Arginine-Specific Cleavage of Peptide Chains as a Potential Protein Degradation Machinery

Proteins can undergo oxidative cleavage by in vitro metal-catalyzed oxidation (MCO) in either the α-amidation or the diamide pathway. However, whether oxidative cleavage of polypeptide-chain occurs in biological systems remains unexplored. We describe a chemoproteomic approach to globally and site-specifically profile electrophilic protein degradants formed from peptide backbone cleavages in human proteomes, including the known N-terminal α-ketoacyl products and >1000 unexpected N-terminal formyl products. Strikingly, such cleavages predominantly occur at the carboxyl side of lysine (K) and arginine (R) residues across native proteomes in situ, while MCO-induced oxidative cleavages randomly distribute on peptide/protein sequences in vitro. Furthermore, ionizing radiation-induced reactive oxygen species (ROS) also generate random oxidative cleavages in situ. These findings suggest that the endogenous formation of <i>N</i>-formyl and <i>N</i>-α-ketoacyl degradants in biological systems is more likely regulated by a previously unknown mechanism with a trypsin-like specificity, rather than the random oxidative damage as previously thought. More generally, our study highlights the utility of quantitative chemoproteomics in combination with unrestricted search tools as a viable strategy to discover unexpected chemical modifications of proteins labeled with active-based probes