Chemical reduction of disulfides

Improved methods for total and chloroplast protein extraction from Cajanus species for two-dimensional gel electrophoresis and mass spectrometry

The recent advances in pigeon pea genomics, including high-quality whole genome and chloroplast genome sequence information helped develop improved varieties. However, a comprehensive Cajanus proteome, including the organelle proteome, is yet to be fully mapped. The spatial delineation of pigeon pea proteins at sub-cellular levels and inter-organelle communication could offer valuable insights into its defense mechanism against various stresses. However, the major bottleneck in the proteomic study is the lack of a suitable method of protein extraction and sample preparation compatible with two-dimensional gel electrophoresis (2D-PAGE), liquid chromatography-mass spectrometry (LCMS), or matrix-assisted laser desorption ionization-time of flight (MALDi-ToF). Our study introduces two efficient methods, one for isolating total proteins and another for organelle (chloroplast) proteins from various Cajanus spp. For total protein extraction, we have optimized a protocol using phenol in combination with a reducing agent (DTT) and protease inhibitor cocktail, also washing (6-7 times) with ice-cold acetone after overnight protein precipitation of total proteins. Our modified extraction method using phenol for total leaf protein yielded approximately 2-fold more proteins than the previously reported protocols from C. cajan (3.18 ± 0.11 mg/gm) and C. scarabaeoides (2.06 ± 0.08 mg/gm). We have also optimized a protocol for plastid protein extraction, which yielded 1.33 ± 0.25 mg/10 gm plastid proteins from C. cajan and 0.88 ± 0.19 mg/10 gm plastid proteins from C. scarabaeoides. The 2D-PAGE analysis revealed 678 ± 08 reproducible total protein spots from C. cajan and 597 ± 22 protein spots from C. scarabaeoides. Similarly, we found 566 ± 10 and 486 ± 14 reproducible chloroplast protein spots in C. cajan and C. scarabaeoides, respectively. We confirmed the plastid protein fractions through immunoblot analysis using antibodies against LHCb1/LHCⅡ type Ⅰ protein. We found both methods suitable for 2D-PAGE and mass spectrometry (MS). This is the first report on developing protocols for total and chloroplastic protein extraction of Cajanus spp. suitable for advanced proteomics research.

Light-triggered AND logic tetrapeptide dynamic covalent assembly

We demonstrate light-triggered dynamic covalent assembly of a linear short tetrapeptide containing two terminal cysteine residues in an AND logic manner. A photobase generator is introduced to accomplish light-mediated pH regulation to increase the reduction potential of thiols in the tetrapeptide, which activates its oxidative polymerization through disulfide bonds. Interestingly, it is elucidated that under light irradiation, mere co-existence of photobase generator and the oxidizing agent permits the polymerization performance of this tetrapeptide. Hence, a light-triggered AND logic dynamic covalent assembly of a tetrapeptide is achieved. Further, upon redox response, the reversible aggregation and disaggregation can be transformed for numerous times due to the dynamic covalent feature of disulfide bond. As a comparison, no assembly occurs for a short peptide containing one terminal cysteine residue under the same stimuli condition. This work offers a new approach to remotely control programmable molecular assembly of short linear peptides based on dynamic covalent bond, holding great potential in wide bioapplications.

Extraction of Soluble Proteins from Leaves

Protein biochemistry can provide valuable answers to better understand plant performance and responses to the surrounding environment. In this chapter, we describe the process of extracting proteins from plant leaf samples. We highlight the key aspects to take into consideration to preserve protein integrity, from sample collection to extraction and preparation or storage for subsequent analysis of protein abundance and/or enzymatic activities.

Molybdenum Cofactor Deficiency in Humans

Molybdenum cofactor (Moco) deficiency (MoCD) is characterized by neonatal-onset myoclonic epileptic encephalopathy and dystonia with cerebral MRI changes similar to hypoxic-ischemic lesions. The molecular cause of the disease is the loss of sulfite oxidase (SOX) activity, one of four Moco-dependent enzymes in men. Accumulating toxic sulfite causes a secondary increase of metabolites such as S-sulfocysteine and thiosulfate as well as a decrease in cysteine and its oxidized form, cystine. Moco is synthesized by a three-step biosynthetic pathway that involves the gene products of MOCS1, MOCS2, MOCS3, and GPHN. Depending on which synthetic step is impaired, MoCD is classified as type A, B, or C. This distinction is relevant for patient management because the metabolic block in MoCD type A can be circumvented by administering cyclic pyranopterin monophosphate (cPMP). Substitution therapy with cPMP is highly effective in reducing sulfite toxicity and restoring biochemical homeostasis, while the clinical outcome critically depends on the degree of brain injury prior to the start of treatment. In the absence of a specific treatment for MoCD type B/C and SOX deficiency, we summarize recent progress in our understanding of the underlying metabolic changes in cysteine homeostasis and propose novel therapeutic interventions to circumvent those pathological changes.

Glutathione, Cysteine, and D-Penicillamine Role in Exchange of Silver Metal from the Albumin Metal Complex

The purpose of this study is to investigate the exchange reaction taking place among the bovine serum albumin (BSA), 5,5'-dithiobis-(2-nitrobenzoic acid (ESSE), reduced glutathione, N-acetylcysteine, D-penicillamine (thiolates), and silver metal (AgI). For this purpose, stock solutions of BSA and Ellman's reagent were prepared by dissolving 264 mg of BSA in 5 ml of reaction buffer (0.1 M KH2PO4 at pH 7.8) and 23.8 mg of ESSE in 1.0 ml of reaction buffer which were mixed together. Mixture of BSA-AgI was prepared in a separate procedure by dissolving 0.17 mg of silver nitrate in 1 ml of reaction buffer and then dissolving BSA (200 mg) in the same solution of silver nitrate. Blocking of Cys-34 of BSA with AgI was confirmed by treating different dilutions of BSA-AgI (500 μM) solutions with the solutions of ESSE (85 μM) and ES- (85 μM) and recording the spectra (300-450) with a UV-visible spectrophotometer. The chromatographed AgI-modified BSA ((BSA-S)AgI)) samples (typically 500 μM) were subsequently mixed with thiolates (reduced glutathione, N-acetylcysteine, and D-penicillamine). AgI and modified BSA (typically 500 μM each) were treated with these low molecular weight thiolates and allowed to react overnight followed by chromatographic separation (Sephadex G25). The redox reactions of AgI-modified BSA with various low molecular weight thiols revealed a mechanically important phenomenon. In the case of reduced glutathione and N-acetylcysteine, we observed the rapid release of a commensurate amount of Ellman's anion, indicating that an exchange has taken place and low molecular weight thiols (RSH) substituted AgI species at the Cys-34 of BSA eventually forming disulfide (BSA-SSR) at Cys-34. It can be anticipated from the phase of study involving bovine serum albumin that low molecular weight thiolates (reduced glutathione and N-acetylcysteine) take off AgI which are attached to proteins elsewhere in the physiological system, making these toxic metals free for toxic action.

Mediation of metal chelation in cysteine-derived tetramate systems

A study of bicyclic tetramates modified with a bulky ester, which leads to steric hindrance of distal chelating atoms as a route for the alteration of metal binding ability is reported. This approach required the development of a direct method for the synthesis of different esters of cysteine from cystine, which then provided access to bicyclic tetramates by Dieckmann cyclisation. Further derivation to ketones and carboxamides by Grignard addition and transamination reactions respectively provided rapid access to a chemical library of tetramates with diverse substitution. Of interest is that bicyclic tetramate ketones and carboxamides showed different tautomeric and metal binding behaviour in solution. Significantly, in both systems, the incorporation of bulky C-5 esters at the bridging position not only reduced metal binding, but also enhanced antibacterial potencies against Gram-positive MRSA bacteria. Those tetramates with antibacterial activity which was not metal dependent showed physiochemical properties of MSA of 559-737 Ų, MW of 427-577 Da, clogP of 1.8-6.1, clogD_7.4 of -1.7 to 3.7, PSA of 83-109 Ų and relative PSA of 12-15% and were generally Lipinski rule compliant. A subset of tetramates exhibited good selectivity towards prokaryotic bacterial cells. Given that the work reported herein is synthesis-led, without the underpinning detailed mechanistic understanding of biological/biochemical mechanism, that the most active compounds occupy a small region of chemical space as defined by MW, clogP, PSA and %PSA is of interest. Overall, the bicyclic tetramate template is a promising structural motif for the development of novel antibacterial drugs, with good anti-MRSA potencies and appropriate drug-like physiochemical properties, coupled with a potential for multi-targeting mechanisms and low eukaryotic cytotoxicity.

Optimized reversed phase LC/MS methods for intact protein analysis and peptide mapping of adeno-associated virus (AAV) proteins

Recombinant adeno-associated viruses (AAVs) have emerged as the leading gene delivery platform owing to their nonpathogenic nature and long-term gene expression capability. The AAV capsid, in addition to protecting the viral genome, plays an important role in viral infectivity and gene transduction, indicating the value of the constituent viral proteins (VPs) being well-characterized as part of gene therapy development. However, the limited sample availability and sequence homology shared by the VPs pose challenges to adapt existing analytical methods developed for conventional biologics. In this study, we report the development of reversed-phase liquid chromatography/mass spectrometry-based methods for characterization of AAV capsid proteins at intact protein and peptide level with reduced sample consumptions. The developed methods allowed the measurement of VP expression with fluorescence detection and intact mass/post-translational modifications (PTMs) analysis through a benchtop time-of-flight mass spectrometer. The general applicability and validity of the methods for gene therapy product development were demonstrated by applying the optimized methods to multiple common AAV serotypes. A 1-h enzymatic digestion method was also developed using 1.25 μg of AAV VPs, providing >98% protein sequence coverage and reproducible relative quantification of various PTMs of the VPs. The efficient and sensitive analyses of AAV capsid proteins enabled by the reported methods provide further understanding and offer guidance in the development and manufacturing of AAV-related therapeutics.

Thiol- and Disulfide-Based Stimulus-Responsive Soft Materials and Self-Assembling Systems

Properties and applications of synthetic thiol- and disulfide-based materials, principally polymers, are reviewed. Emphasis is placed on soft and self-assembling materials in which interconversion of the thiol and disulfide groups initiates stimulus-responses and/or self-healing for biomedical and non-biomedical applications.

Identification of methionine -rich insoluble proteins in the shell of the pearl oyster, Pinctada fucata

The molluscan shell is a biomineral that comprises calcium carbonate and organic matrices controlling the crystal growth of calcium carbonate. The main components of organic matrices are insoluble chitin and proteins. Various kinds of proteins have been identified by solubilizing them with reagents, such as acid or detergent. However, insoluble proteins remained due to the formation of a solid complex with chitin. Herein, we identified these proteins from the nacreous layer, prismatic layer, and hinge ligament of Pinctada fucata using mercaptoethanol and trypsin. Most identified proteins contained a methionine-rich region in common. We focused on one of these proteins, NU-5, to examine the function in shell formation. Gene expression analysis of NU-5 showed that NU-5 was highly expressed in the mantle, and a knockdown of NU-5 prevented the formation of aragonite tablets in the nacre, which suggested that NU-5 was required for nacre formation. Dynamic light scattering and circular dichroism revealed that recombinant NU-5 had aggregation activity and changed its secondary structure in the presence of calcium ions. These findings suggest that insoluble proteins containing methionine-rich regions may be important for scaffold formation, which is an initial stage of biomineral formation.

Detection of specific IgE against linear epitopes from Gal d 1 has additional value in diagnosing hen's egg allergy in adults

Background

Although hen's egg allergy is more prevalent in children, up to 0.6% of adults from different European countries suffer from a persistent or newly onset hen's egg allergy, making accurate diagnosis in adults necessary. However, sensitization to hen's egg extracts, components and linear epitopes is solely studied in children.

Methods

Hen's egg allergic (n = 16) and tolerant (n = 19) adults were selected by sensitization towards recombinant components rGal d 1 and/or 3. Sensitization profiles towards egg white and yolk extract and the native components Gal d 1, 2, 3 and 4 were respectively evaluated with the ImmunoCAP or the EUROLINE system. Characterization of linear epitopes was performed with a peptide microarray containing 15mer peptides representing the entire sequence of mature Gal d 1 and 3.

Results

Overall, sIgE titres against hen's egg extracts and single components overlapped largely between allergic and tolerant adults. Although the median sIgE/sIgG4 ratio to Gal d 1 was increased in allergic adults, the range was comparable between both groups. Clinically relevant sensitization to Gal d 1 was confirmed by sIgE‐binding to the linear epitopes aa30‐41, aa39‐50 or aa84‐95 in 6/13 allergic adults, mainly suffering from objective symptoms. In comparison, these epitopes were recognized by 1/15 tolerant patient. Only a few linear epitopes were detected for Gal d 3, suggesting a greater importance of conformational epitopes for the recognition of Gal d 3.

Conclusion and Clinical Relevance

Specific IgE‐binding to linear epitopes of Gal d 1 is highly specific in identifying hen's egg allergic adults with objective symptoms.

Cysteine-specific protein multi-functionalization and disulfide bridging using 3-bromo-5-methylene pyrrolones

Many reagents have been developed for cysteine-specific protein modification. However, few of them allow for multi-functionalization of a single Cys residue and disulfide bridging bioconjugation. Herein, we report 3-bromo-5-methylene pyrrolones (3Br-5MPs) as a simple, robust, and versatile class of reagents for cysteine-specific protein modification. These compounds can be facilely synthesized via a one-pot mild reaction and they show comparable tagging efficiency but higher cysteine specificity than the maleimide counterparts. The addition of cysteine to 3Br-5MPs generates conjugates that are amenable to secondary addition by another thiol or cysteine, making 3Br-5MPs valuable for multi-functionalization of a single cysteine and disulfide bridging bioconjugation. The labeling reaction and subsequent treatments are mild enough to produce stable and active protein conjugates for biological applications.

Many reagents have been developed for cysteine-specific protein modification. However, few of them allow for multi-functionalization of a single Cys residue and disulfide bridging bioconjugation. Here the authors report 3-bromo-5-methylene pyrrolones as a simple, robust and versatile class of reagents for cysteine-specific protein modification.

pH and Redox Dual-Stimulated Wormlike Micelles Based on Cystamine and Conventional Anionic Surfactant

Redox-responsive soft materials have attracted considerable concerns throughout the last few decades. Herein, we report the preparation of dual-stimulated wormlike micelles (WLMs) based on N,N,N',N'-tetramethylcystamine dihydrochloride (TMCDD) and a conventional anionic surfactant, sodium dodecyl sulfate (SDS). The WLMs can be reversibly switched on and off by adjusting pH, resulting from the reversible protonation of TMCDD. Moreover, the WLMs can be destroyed by a redox reaction after addition of dithiothreitol (DTT), originating from the cleavage of the disulfide bonds in TMCDD. The dual responsiveness of the WLMs allowed for the smart control of the "sol-gel" transition or thickening of viscoelastic solutions, and the micelles will have a wider range of applications in the development of functional materials for pharmaceutical or biomedical materials.

Multiplexed in-gel microfluidic immunoassays: characterizing protein target loss during reprobing of benzophenone-modified hydrogels

From whole tissues to single-cell lysate, heterogeneous immunoassays are widely utilized for analysis of protein targets in complex biospecimens. Recently, benzophenone-functionalized hydrogel scaffolds have been used to immobilize target protein for immunoassay detection with fluorescent antibody probes. In benzophenone-functionalized hydrogels, multiplex target detection occurs via serial rounds of chemical stripping (incubation with sodium-dodecyl-sulfate (SDS) and β-mercaptoethanol at 50-60 °C for ≥1 h), followed by reprobing (interrogation with additional antibody probes). Although benzophenone facilitates covalent immobilization of proteins to the hydrogel, we observe 50% immunoassay signal loss of immobilized protein targets during stripping rounds. Here, we identify and characterize signal loss mechanisms during stripping and reprobing. We posit that loss of immobilized target is responsible for ≥50% of immunoassay signal loss, and that target loss is attributable to disruption of protein immobilization by denaturing detergents (SDS) and incubation at elevated temperatures. Furthermore, our study suggests that protein losses under non-denaturing conditions are more sensitive to protein structure (i.e., hydrodynamic radius), than to molecular mass (size). We formulate design guidance for multiplexed in-gel immunoassays, including that low-abundance proteins be immunoprobed first, even when targets are covalently immobilized to the gel. We also recommend careful scrutiny of the order of proteins targets detected via multiple immunoprobing cycles, based on the protein immobilization buffer composition.

Identification of an Exceptionally Long Intron in the HAC1 Gene of Candida parapsilosis

The unfolded protein response (UPR) responds to the build-up of misfolded proteins in the endoplasmic reticulum. The UPR has wide-ranging functions from fungal pathogenesis to applications in biotechnology. The UPR is regulated through the splicing of an unconventional intron in the HAC1 gene. This intron has been described in many fungal species and is of variable length. Until now it was believed that some members of the CTG-Ser1 clade such as C. parapsilosis did not contain an intron in HAC1, suggesting that the UPR was regulated in a different manner. Here we demonstrate that HAC1 plays an important role in regulating the UPR in C. parapsilosis. We also identified an unusually long intron (626 bp) in C. parapsilosisHAC1. Further analysis showed that HAC1 orthologs in several species in the CTG-Ser1 clade contain long introns.

The unfolded protein response (UPR) in the endoplasmic reticulum (ER) is well conserved in eukaryotes from metazoa to yeast. The transcription factor HAC1 is a major regulator of the UPR in many eukaryotes. Deleting HAC1 in the yeast Candida parapsilosis rendered cells more sensitive to DTT, a known inducer of the UPR. The deletion strain was also sensitive to Congo red, calcofluor white, and the antifungal drug ketoconazole, indicating that HAC1 has a role in cell wall maintenance. Transcriptomic analysis revealed that treatment of the wild type with DTT resulted in the increased expression of 368 genes. Comparison with mutant cells treated with DTT reveals that expression of 137 of these genes requires HAC1. Enriched GO term analysis includes response to ER stress, cell wall biogenesis and glycosylation. Orthologs of many of these are associated with UPR in Saccharomyces cerevisiae and Candida albicans. Unconventional splicing of an intron from HAC1 mRNA is required to produce a functional transcription factor. The spliced intron varies in length from 19 bases in C. albicans to 379 bases in Candida glabrata, but has not been previously identified in Candida parapsilosis and related species. We used RNA-seq data and in silico analysis to identify the HAC1 intron in 12 species in the CTG-Ser1 clade. We show that the intron has undergone major contractions and expansions in this clade, reaching up to 848 bases. Exposure to DTT induced splicing of the long intron in C. parapsilosisHAC1, inducing the UPR.

IMPORTANCE The unfolded protein response (UPR) responds to the build-up of misfolded proteins in the endoplasmic reticulum. The UPR has wide-ranging functions from fungal pathogenesis to applications in biotechnology. The UPR is regulated through the splicing of an unconventional intron in the HAC1 gene. This intron has been described in many fungal species and is of variable length. Until now it was believed that some members of the CTG-Ser1 clade such as C. parapsilosis did not contain an intron in HAC1, suggesting that the UPR was regulated in a different manner. Here we demonstrate that HAC1 plays an important role in regulating the UPR in C. parapsilosis. We also identified an unusually long intron (626 bp) in C. parapsilosisHAC1. Further analysis showed that HAC1 orthologs in several species in the CTG-Ser1 clade contain long introns.

Reductive Cleavage of Organic Peroxides by Iron Salts and Thiols

Despite the low bond strength of the oxygen-oxygen bond, organic peroxides are often surprisingly resistant to cleavage by nucleophiles and reductants. As a result, achieving decomposition under mild conditions can be challenging. Herein, we explore the reactivity of a selection of peroxides toward thiolates, phenyl selenide, Fe(II) salts, and iron thiolates. Peroxides activated by conjugation, strain, or stereoelectronics are rapidly cleaved at room temperature by thiolate anions, phenylselenide, or Fe(II) salts. Under the same conditions, unhindered dialkyl peroxides are only marginally reactive; hindered peroxides, including triacetone triperoxide and diacetone diperoxide (DADP), are inert. In contrast, all but the most hindered of peroxides are rapidly (<1 min at concentrations down to ∼40 mM) cleaved by mixtures of thiols and iron salts. Our observations suggest the possible intermediacy of strongly reducing complexes that are readily regenerated in the presence of stoichiometric thiolate or hydride. In the case of DADP, an easily prepared explosive of significant societal concern, catalytic amounts of iron and thiol are capable of promoting rapid and complete disproportionation. The availability of inexpensive and readily available catalysts for the mild reductive degradation of all but the most hindered of peroxides could have significant applications for controlled remediation of explosives or unwanted radical initiators.

Development of an LC-MS/MS peptide mapping protocol for the NISTmAb

Peptide mapping is a component of the analytical toolbox used within the biopharmaceutical industry to aid in the identity confirmation of a protein therapeutic and to monitor degradative events such as oxidation or deamidation. These methods offer the advantage of providing site-specific information regarding post-translational and chemical modifications that may arise during production, processing or storage. A number of such variations may also be induced by the sample preparation methods themselves which may confound the ability to accurately evaluate the true modification levels. One important focus when developing a peptide mapping method should therefore be the use of sample preparation conditions that will minimize the degree of artificial modifications induced. Unfortunately, the conditions that are amenable to effective reduction, alkylation and digestion are often the same conditions that promote unwanted modifications. Here we describe the optimization of a tryptic digestion protocol used for peptide mapping of the NISTmAb IgG1κ which addresses the challenge of balancing maximum digestion efficiency with minimum artificial modifications. The parameters on which we focused include buffer concentration, digestion time and temperature, as well as the source and type of trypsin (recombinant vs. pancreatic; bovine vs porcine) used. Using the optimized protocol we generated a peptide map of the NISTmAb which allowed us to confirm its identity at the level of primary structure. Graphical abstract Peptide map of the NISTmAb RM 8671 monoclonal antibody. Tryptic digestion was performed using an optimized protocol and followed by LC-UV-MS analysis. The trace represents the total ion chromatogram. Each peak was mapped to peptides identified using mass spectrometry data.

Au–Mesoporous silica nanoparticles gated with disulfide-linked oligo(ethylene glycol) chains for tunable cargo delivery mediated by an integrated enzymatic control unit

Acetylcholinesterase-functionalized Au–mesoporous silica capped with a thiol-responsive gate is reported.

Use of Protein Folding Reagents

The reagents and methods for purification and use of the most commonly used denaturants, guanidine hydrochloride (guanidine-HCl) and urea, are described. Other protein denaturants and reagents used to fold proteins are briefly mentioned. Sulfhydryl reagents (reducing agents) and "oxido-shuffling" (or oxidative regeneration) systems are also described.

Structural aspects of a protein-surfactant assembly: native and reduced States of human serum albumin

The inherently present seventeen disulfide bonds of the circulatory protein, human serum albumin (HSA) provide the necessary structural stability. Various spectroscopic approaches were used to investigate the effect of reduction of these disulfide bonds and its binding with the anionic surfactant, sodium dodecyl sulfate (SDS). Based on several spectroscopic analyses, our investigations highlight the following interesting aspects: (1) HSA on reduction loses not only its tertiary structure but also a significant amount of secondary structure as well. However, the reduced state of the protein is not like the molten-globule, (2) this structural loss of the protein due to reduction is more prominent than that caused by higher SDS concentrations alone and can certainly be attributed to the role of disulfide bonds, (3) lower surfactant concentrations provide marginal structural rigidity to the native state of the protein, whereas, higher concentrations of SDS induces secondary structure to the reduced state of HSA, (4) the binding of SDS with both the native and reduced states of HSA, occurred in three distinct stages which was followed by a saturation stage. However, the nature of such binding is different for both the states as investigated by using the Stern-Volmer equations and estimating the thermodynamic parameters. Besides, in contrast to the native state, the reduced state of HSA shows that the lone tryptophan residue gets more buried. However, there occurs a sudden decrement in the lifetime of the tryptophan and the hydrodynamic diameter increases by twofold.

Lipoates as building blocks of sulfur-containing branched macromolecules

Under radical polymerization conditions, 2-acryloyloxyethyl lipoate (AOELp) yielded, prior to gelation, soluble, highly branched, reductively degradable disulfide-containing polymers. The reduction of AOELp afforded a dithiol acrylate, which participated in radical or ionic step-growth thiol-ene reactions, yielding highly branched reductively non-degradable polymers with thioether-type sulfur atoms in the backbones.

A Review on the Synthesis and Controlled Release Properties of Novel Responsive Carrier

Interest in the stimuli-responsive polymers has been going on for decades, and a lot of work has been dedicated to the development of environmentally sensitive macromolecules that can be crafted into novel responsive carrier materials. This article reviews the state-of-the art in smart responsive carriers for controlled drug delivery applications. And the preparation methods of different responsive materials, sustained and controlled release performance are summarized. The significance and future of smart responsive materials are also commented.

Reversible native chemical ligation: a facile access to dynamic covalent peptides

The broad interest of using reversible covalent bonds in chemistry, in particular at its interfaces with biology and materials science, has been recently established through numerous examples in the literature. However, the challenging exchange of peptide fragments using a dynamic covalent peptide bond has not yet been achieved without enzymatic catalysis because of its high thermodynamic stability. Here we show that peptide fragments can be exchanged by a chemoselective and reversible native chemical ligation (NCL) which can take place at N-(methyl)-cysteine residues. This very mild reaction is efficient in aqueous solution, is buffered at physiological pH in the presence of dithiothreitol (DTT), and shows typical half-times of equilibration in the 10 h range.

Nitric oxide releasing Tygon materials: studies in donor leaching and localized nitric oxide release at a polymer-buffer interface

Tygon is a proprietary plasticized poly(vinyl chloride) polymer that is used widely in bioapplications, specifically as extracorporeal circuits. To overcome issues with blood clot formation and infection associated with the failure of these medical devices upon blood contact, we consider a Tygon coating with the ability to release the natural anticlotting and antibiotic agent, nitric oxide (NO), under simulated physiological conditions. These coatings are prepared by incorporating 20 w/w% S-nitrosoglutathione (GSNO) donor into a Tygon matrix. These films release NO on the order of 0.64 ± 0.5 × 10(-10) mol NO cm(-2) min(-1), which mimics the lower end of natural endothelium NO flux. We use a combination of assays to quantify the amount of GSNO that is found intact at different time points throughout the film soak, as well as monitor the total thiol content in the soaking solution due to any analyte that has leached from the polymer film. We find that a burst of GSNO is released from the material surface within 5 min to 1 h of soaking, which only represents 0.25% of the total GSNO contained in the film. After 1 h of film soak, no additional GSNO is detected in the soaking solution. By further considering the total thiol content in solution relative to the intact GSNO, we demonstrate that the amount of GSNO leached from the material into the buffer soaking solution does not contribute significantly to the total NO released from the GSNO-incorporated Tygon film (<10% total NO). Further surface analysis using SEM-EDS traces the elemental S on the material surface, demonstrating that within 5 min -1 h soaking time, 90% of the surface S is removed from the material. Surface wettability and roughness measurements indicate no changes between the GSNO-incorporated films pre- to postsoak that will be significant toward the adsorption of biological components, such as proteins, relative to the presoaked donor-incorporated film. Overall, we demonstrate that, for a 20 w/w% GSNO-incorporated Tygon film, relatively minimal GSNO leaching is experienced, and the lost GSNO is from the material surface. Varying the donor concentration from 5 to 30 w/w% GSNO within the film does not result in significantly different NO release profiles. Additionally, the steady NO flux associated with the system is predominantly due to localized release from the material, and not donor lost to soaking solution. The surface properties of these materials generally imply that they are useful for blood-contacting applications.

The structural model of Salmonella typhimurium ethanolamine ammonia-lyase directs a rational approach to the assembly of the functional [(EutB-EutC)₂]₃ oligomer from isolated subunits

Ethanolamine ammonia-lyase (EAL) is a 5'-deoxyadenosylcobalamin-dependent bacterial enzyme that catalyzes the deamination of the short-chain vicinal amino alcohols, aminoethanol and (S)- and (R)-2-aminopropanol. The coding sequence for EAL is located within the 17-gene eut operon, which encodes the broad spectrum of proteins that comprise the ethanolamine utilization (eut) metabolosome suborganelle structure. A high-resolution structure of the ∼500 kDa EAL [(EutB-EutC)₂]₃ oligomer from Escherichia coli has been determined by X-ray crystallography, but high-resolution spectroscopic determinations of reactant intermediate-state structures and detailed kinetic and thermodynamic studies of EAL have been conducted for the Salmonella typhimurium enzyme. Therefore, a statistically robust homology model for the S. typhimurium EAL is constructed from the E. coli structure. The model structure is used to describe the hierarchy of EutB and EutC subunit interactions that construct the native EAL oligomer and, specifically, to address the long-standing challenge of reconstitution of the functional oligomer from isolated, purified subunits. Model prediction that the (EutB₂)₃ oligomer assembly will occur from isolated EutB, and that this hexameric structure will template the formation of the complete, native [(EutB-EutC)₂]₃ oligomer, is verified by biochemical methods. Prediction that cysteine residues on the exposed subunit-subunit contact surfaces of isolated EutB and EutC will interfere with assembly by cystine formation is verified by activating effects of disulfide reducing agents. Angstrom-scale congruence of the reconstituted and native EAL in the active site region is shown by electron paramagnetic resonance spectroscopy. Overall, the hierarchy of subunit interactions and microscopic features of the contact surfaces, which are revealed by the homology model, guide and provide a rationale for a refined genetic and biochemical approach to reconstitution of the functional [(EutB-EutC)₂]₃ EAL oligomer. The results establish a platform for further advances in understanding the molecular mechanism of EAL catalysis and for insights into therapy-targeted manipulation of the bacterial eut metabolosome.

Advances in polymeric systems for tissue engineering and biomedical applications

The characteristics of tissue engineered scaffolds are major concerns in the quest to fabricate ideal scaffolds for tissue engineering applications. The polymer scaffolds employed for tissue engineering applications should possess multifunctional properties such as biocompatibility, biodegradability and favorable mechanical properties as it comes in direct contact with the body fluids in vivo. Additionally, the polymer system should also possess biomimetic architecture and should support stem cell adhesion, proliferation and differentiation. As the progress in polymer technology continues, polymeric biomaterials have taken characteristics more closely related to that desired for tissue engineering and clinical needs. Stimuli responsive polymers also termed as smart biomaterials respond to stimuli such as pH, temperature, enzyme, antigen, glucose and electrical stimuli that are inherently present in living systems. This review highlights the exciting advancements in these polymeric systems that relate to biological and tissue engineering applications. Additionally, several aspects of technology namely scaffold fabrication methods and surface modifications to confer biological functionality to the polymers have also been discussed. The ultimate objective is to emphasize on these underutilized adaptive behaviors of the polymers so that novel applications and new generations of smart polymeric materials can be realized for biomedical and tissue engineering applications.

Synthesis, Functionalization and Reductive Degradation of Multibrominated Disulfide-containing Hyperbranched Polymers

Reductively degradable hyperbranched polymethacrylates with multiple peripheral alkyl bromide groups were synthesized by the azobis(2-isobutyronitrile)-initiated copolymerization of diethylene glycol methyl ether methacrylate or oligo(ethylene oxide) methyl ether methacrylate with the disulfide-containing crosslinker bis(2-methacryloyloxyethyl)disulfide (2.5–10.0 mol-% relative to the monomer) in the presence of carbon tetrabromide (10–40-fold excess relative to the radical initiator) as efficient chain transfer agent. The alkyl bromide groups initiated the atom-transfer radical polymerization of methyl methacrylate, and star copolymers with hyperbranched disulfide-containing cores were formed. Both the macroinitiators and the star copolymers derived from them were degraded in reducing environment.

Synthesis of amphiphilic triblock copolymers as multidentate ligands for biocompatible coating of quantum dots

One barrier to apply current tri-octylphosphine oxide (TOPO) based quantum dots (QDs) to biomedical imaging is that the TOPO on TOPO-QDs can be replaced by the proteins in living system, which may cause the degradation of QDs and/or deactivation of protein. In order to develop biocompatible optical imaging agents, a novel triblock copolymer, designed as a multidentate ligand, was synthesized to coat quantum dot nanocrystals (QDs). The copolymer consists of a polycarboxylic acid block at one end and a polythiol block at the other end with an intervening cross-linked poly(styrene-co-divinylbenzene) block bridging the ends. The multiple mercapto groups from the polythiol block act as multidentate ligands to stabilize QDs, while the polycarboxylic acid block improves the water solubility of QDs and offers reaction sites for surface modification or conjugation with bimolecules. The cross-linked poly(styrene-co-divinylbenzene) block provides a densely compacted hydrophobic shell. This shell will act as a barrier to inhibit the degradation of QDs by preventing the diffusion of ions and small molecules into the core of QDs. This new multidentate polymer coating facilitates the transfer of QDs from organic solvent into aqueous phase. The QDs directly bound to multidentate mercapto groups instead of TOPO are less likely to be affected by the mercapto or disulfide groups within proteins or other biomolecules. Therefore, this research will provide an alternative coating material instead of TOPO to produce QDs which could be more suitable for in vivo use under complex physiological conditions.

Stabilization of proteins for storage

Following isolation and purification, it is often necessary to store proteins and peptides for extended periods of time before performing detailed biophysical, enzymatic, and structural proteomics. Therefore, it is essential that the pure target protein maintain its original biological (or functional) behavior over an extended period of storage which may range from weeks to years. Protein pharmaceuticals must remain viable following extensive shipping and storage, and they must remain devoid of all possible inactivation processes. The shelf life of a protein depends on both the intrinsic nature of the protein and the storage conditions. Proteins (especially enzymes) must be stored at an appropriate temperature and pH range and frequently in the presence of concentrated (approximately 1 M) glycerol, sucrose, or a similar substance, for the proteins to retain activity and prevent aggregation. This article discusses the major causes of protein inactivation and describes a range of measures that can be adopted to maintain the stability and solubility of proteins.

Oxidative folding pathway of onconase, a ribonuclease homologue: insight into oxidative folding mechanisms from a study of two homologues

The oxidative folding pathways of two four-disulfide proteins of the ribonuclease family, ONC and RNase A, which have similar three-dimensional folds but only 30% sequence homology, are compared. In this study, a mechanism for the oxidative folding pathway of ONC is proposed. In particular, the kinetic roles and thermodynamic characteristics of key intermediates along the oxidative folding pathway, specifically, the structured intermediates, I(1), I(2), and I(3), previously identified as des-[19-68,30-75], des-[30-75], and des-[19-68], respectively, are discussed. In addition, the effects of temperature on the oxidative folding pathway have been examined. Differences in the folding mechanism between ONC and RNase A are attributed to the differences in their amino acid sequences and related inter-residue interactions, including differences in hydrophobic interactions. Compared to RNase A, ONC utilizes more efficient interactions along the oxidative folding pathway to adopt its native fold more rapidly.

Temporal evolution of the composition of mixed monolayers on TiO2 surfaces: evidence for a dimerization-induced chelate effect

Mixed monolayers of octanoic acid (OA) and 16-mercaptohexadecanoic acid (MHDA) were adsorbed to nanocrystalline TiO(2) films from mixed solutions in tetrahydrofuran. For a range of solution compositions, the mole fraction of MHDA within the mixed monolayers (chi (MHDA,surf)) exceeded that of the coadsorption solution. In addition, chi (MHDA,surf) increased with time, while the sum of the surface coverages of MHDA and OA remained constant. To account for these effects, we propose a mechanism involving disulfide formation between the terminal thiol groups of surface-adsorbed MHDA molecules. Disulfide formation leads to an increase in the surface adduct formation constant ( K(ad)) of dimeric MHDA, causing the gradual displacement of OA from the surface. The mechanism is supported by spectroscopic evidence and desorption kinetics. These are the first examples of mixed monolayers that undergo time-dependent compositional changes as a result of covalent bond formation between surfactants. Our findings illustrate that dimerization and other intermolecular interactions between surfactants may dramatically influence the composition and terminal functionalization of a wide range of mixed monolayer systems.

Use of protein folding reagents

The reagents and methods for purification of the denaturants guanidine hydrochloride (guanidine-HCl) and urea are described. Sulfhydryl reagents (reducing agents) and "oxido-shuffling" (or oxidative regeneration) systems are also discussed.

Is dihydrolipoic acid among the reductive activators of parasite CysHis proteases?

Activities of mature CysHis proteases depend upon relative rates of oxidations vs. reductions of catalytic sulfur by multiple enzymatic and non-enzymatic reactions. CysHis peptidolysis is inhibited by Fe3+ but not Fe2+. Others report the paradox that malarial parasites require exogenous free lipoic acid (LA) from human host, although the apicoplast organelle produces it. Extra-cellular LA disulfide can be taken up and reduced to dihydrolipoic acid (DHLA) by reductases of any cell type. Here, the opposing effects of DHLA vs. Fe3+ on the falcipain-2 hemoglobinase were investigated employing Z-Phe-Arg-AMC substrate. Despite limited solubility, non-regenerated DHLA (10 microM, threshold 2 microM) was found to be the most potent activator of the air-inactivated (sulfoxygenated) protease discovered thus far. Activation was preemptively opposed by Fe3+, but not Fe2+. However, cruzain from T. cruzi, and cathepsin B from mammal were indistinguishable in their responsiveness to DHLA and Fe redox. Thus, DHLA activation vs. Fe3+ inhibition is not unique to falcipain-2 or apicomplexans but is rather a primordial feature of CysHis peptidolysis. Free LA and/or unassociated lipoylated enzyme subunits could be among multiple pathways shuttling reducing equivalents to reduction of proteins, including CysHis proteases. It is discussed that opposing DHLA-Fe3+ modification of plasmodial proteolysis might be a specialized adaptation to intra-erythrocytic growth.

An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments

The application of single-molecule fluorescence techniques to complex biological systems places demands on the performance of single fluorophores. We present an enzymatic oxygen scavenging system for improved dye stability in single-molecule experiments. We compared the previously described protocatechuic acid/protocatechuate-3,4-dioxygenase system to the currently employed glucose oxidase/catalase system. Under standardized conditions, we observed lower dissolved oxygen concentrations with the protocatechuic acid/protocatechuate-3,4-dioxygenase system. Furthermore, we observed increased initial lifetimes of single Cy3, Cy5, and Alexa488 fluorophores. We further tested the effects of chemical additives in this system. We found that biological reducing agents increase both the frequency and duration of blinking events of Cy5, an effect that scales with reducing potential. We observed increased stability of Cy3 and Alexa488 in the presence of the antioxidants ascorbic acid and n-propyl gallate. This new O(2)-scavenging system should have wide application for single-molecule fluorescence experiments.

Aqueous dispersion, surface thiolation, and direct self-assembly of carbon nanotubes on gold

We report the efficient aqueous dispersion of pristine HiPco single-walled carbon nanotubes (SWNTs) with ionic liquid (IL)-based surfactants 1-dodecyl-3-methylimidazolium bromide (1) and 1-(12-mercaptododecyl)-3-methylimidazolium bromide (2), the thiolation of nanotube sidewalls with 2, and the controlled self-assembly of positively charged SWNT-1,2 composites on gold. Optical absorption spectra and resonance Raman (RR) data of obtained aqueous SWNT-1,2 dispersions are consistent with debundled and noncovalently functionalized nanotubes whose electronic properties have not been disturbed. Additionally, the dispersion of pristine nanotube material with surfactants 1 and 2 leads to a high degree of purification from carbonaceous particles. The chiralities of the 14 smallest semiconducting HiPco SWNTs in resonance with Raman excitation at 1064 nm (1.165 eV) were determined in SWNT-2 aqueous dispersion using UV-vis-NIR and RR spectra. X-ray photoelectron spectroscopy (XPS) and surface-enhanced resonance Raman scattering (SERRS) spectroscopy of SWNT-2 submonolayers on gold verified the encapsulation of individualized SWNTs with IL surfactants, the cleavage of S-S disulfide bonds formed in aqueous SWNT-2 suspensions, and the direct chemisorption of the SWNT-2 composite on bare gold via the Au-S bond. Aqueous dispersions of SWNTs with IL-based surfactants add biofunctionality to carbon nanotubes by imparting the positive surface charge necessary for interactions with cell membranes. Our technique, which purifies pristine nanotube material and produces water-soluble, positively charged nanotubes with pendent surface-active thiol groups, may also be translated to other carbon nanotubes and carbon nanostructures. Self-assembled, positively charged submonolayers of SWNTs can be further used for applications in cell biology and sensor technology.

Quantification of protein thiols and dithiols in the picomolar range using sodium borohydride and 4,4'-dithiodipyridine

Experimental determination of the number of thiols in a protein requires methodology that combines high sensitivity and reproducibility with low intrinsic thiol oxidation disposition. In detection of disulfide bonds, it is also necessary to efficiently reduce disulfides and to quantify the liberated thiols. Ellman's reagent (5,5'-dithiobis-[2-nitrobenzoic acid], DTNB) is the most widely used reagent for quantification of protein thiols, whereas dithiothreitol (DTT) is commonly used for disulfide reduction. DTNB suffers from a relatively low sensitivity, whereas DTT reduction is inconvenient because the reagent must be removed before thiol quantification. Furthermore, both reagents require a reaction pH > 7.0 where oxidation by ambient molecular oxygen is significant. Here we describe a quick and highly sensitive assay for protein thiol and dithiol quantification using the reducing agent sodium borohydride and the thiol reagent 4,4'-dithiodipyridine (4-DPS). Because borohydride is efficiently destroyed by the addition of acid, the complete reduction and quantification can be performed conveniently in one tube without desalting steps. Furthermore, the use of reverse-phase high-performance liquid chromatography for the thiol quantification by 4-DPS reduces the detection limit to the picomolar range (equivalent to 1 microg of a 50-kDa protein containing 1 thiol) while at the same time maintaining low pH throughout the procedure.