Electrostatic stabilization and general base catalysis in the active site of the human protein disulfide isomerase a domain monitored by hydrogen exchange

The nucleophilic Cys36 thiol of the human protein disulfide isomerase a domain is positioned over the N terminus of the alpha(2) helix. Amides in the active site exhibit diffusion-limited, hydroxide-catalyzed exchange, indicating that the local positive electrostatic potential decreases the pK value for peptide anion formation by at least 2 units so as to equal or exceed the acidity of water. In stark contrast to the pH dependence of exchange for simple peptides, the His38 amide in the reduced enzyme exhibits a maximum rate of exchange at pH 5 due to efficient general base catalysis by the neutral imidazole of its own side chain and suppression of its exchange by the ionization of the Cys36 thiol. Ionization of this thiol and deprotonation of the His38 side chain suppress the Cys39 amide hydroxide-catalyzed exchange by a million-fold. The electrostatic potential within the active site monitored by these exchange experiments provides a means of stabilizing the two distinct transition states that lead to substrate reduction and oxidation. Molecular modeling offers a role for the conserved Arg103 in coordinating the oxidative transition-state complex, thus providing further support for mechanisms of disulfide isomerization that utilize enzymatic catalysis at each step of the overall reaction.     

Electrochemical and spectroscopic study of C12H25X molecules adsorption on copper sheets, X (-SH, -S-S-, -SeH and -Se-Se-)

In this contribution, we explored the possibility of using selenol and selenide molecules to form self-assembled monolayers (SAMs) on copper, in order to check the influence of anchoring groups on SAMs quality and compared it to well-known thiolate assemblies (formed with thiol and disulfide molecules). Precisely, monolayers of pure alkane chains have been self-assembled on electroreduced bulk copper. The different selected molecules present the following reactive anchoring groups: thiol (R-SH), disulfide (R-S-S-R), selenol (R-SeH) and diselenide (R-Se-Se-R), where R = C₁₂H₂₅-. Electrochemical (cyclic voltammetry and scanning electrochemical microscopy) techniques and spectroscopic (X-ray photoelectron and polarization modulation infrared reflection absorption spectroscopy) have been used to characterize the surface composition and monolayer organization. Atomic force microscopy (AFM) measurements complete this study. All molecules analyzed have been shown to form monolayers of variable quality. The R-SH and R-SeH monolayers seem to lead to better organized and insulating layers than the R-S-S-R and R-Se-Se-R monolayers. However, the case of the diselenide is more complex and could lead to some interesting properties.     

Interchain cysteine bridges control entry of progesterone to the central cavity of the uteroglobin dimer

The progesterone–binding protein uteroglobin has beenexpressed in Escherichia coli in an unfused, soluble form. likemature uteroglobin from rabbit endometrium (UG), the E.coliproduceduteroglobin (UG1) dimerizes in vitro, forms an antiparalleldimer with Cys3–Cys69' and Cys69–Cys3' disulfidebonds and binds progesterone under reducing conditions. In orderto analyze the dimerization and the reduction dependence ofprogesterone binding in more detail, we separately replacedcysteine 3 and cysteine 69 by serines. Under reducing conditions,both uteroglobin variants (UGl–3Ser and UGl–69Ser)bind progesterone with the same affinity as the wild–typesuggesting that both cysteine residues are not directly involvedin progesterone binding. In contrast to the wild–typeprotein, both cysteine variants also bind progesterone withhigh affinity in the absence of reducing agents. In addition,UGl-3Ser and UGl-69Ser both form covalently linked homodimers.Thus, unnatural Cys69–69' and Cys3–3' disulfidebonds exist in UG1–3Ser and UG1–69Ser, respectively.These data together with computer models based on X-ray diffractiondata strongly support the idea that progesterone reaches itsbinding site located in an internal hydrophobic cavity via ahydrophobic tunnel along helices 1 and 4. Under non–reducingconditions the tunnel is closed by two disulfide bridges (Cys3–Cys69'(and Cys69–Cys3') that lie in the most flexible regionof the dimer. Reduction or replacement of a cysteine residueenables conformational changes that open the channel allowingprogesterone to enter.     

The role of the Cys191-Cys220 disulfide bond in trypsin: new targets for engineering substrate specificity

The S1 binding site of trypsin is cross-linked by the conserved Cys191- Cys220 disulfide bond. The substitution of Cys191 and Cys220 with Ala decreases the activity of trypsin by 20-200-fold as measured by kcat/K(m) for the hydrolysis of amide substrates; in contrast, ester hydrolysis is decreased by < 10-fold. Similar decreases are observed in the hydrolysis of oligopeptide and single amino acid substrates. This decrease in activity results from a decrease in the acylation rate. The substrate binding and deacylation rate are not affected by the loss of the disulfide bond. C191A/C220A binds BPTI with the same affinity as trypsin, although the affinity of benzamidine is decreased 10-fold and the affinity of leupeptin is decreased 1000-fold. The CD spectrum of C191A/C220A displays significant differences from that of trypsin; these differences most likely result from the loss of the disulfide chromophore, although perturbation of enzyme structure cannot be discounted. The loss of the Cys191-Cys220 disulfide has no effect on the stability of trypsin as measured by urea denaturation. Single and double substitutions of Ser at positions 191 and 220 have a similar activity to C191A/C220A. These results indicate that the Cys191-Cys220 disulfide bond is not essential for the function, structure or stability of trypsin.      

Role of free Cys121 in stabilization of bovine beta-lactoglobulin B

Mixed disulfide derivatives of bovine beta-lactoglobulin (BLG) were studied by circular dichroism (CD), gel-permeation HPLC and high- sensitivity differential scanning calorimetry (HS-DSC). It was shown that modification of Cys121 with mercaptopropionic acid and mercaptoethanol does not affect the secondary structure of BLG, but results instead in tertiary and quaternary structure changes. At neutral pH, the equilibrium dimer<==>monomer of modified beta- lactoglobulin is shifted towards monomeric form. In contrast to native BLG, thermal denaturation of modified beta-lactoglobulin is fully reversible in neutral and acidic pH as demonstrated by CD and HS-DSC measurements. Modification of Cys121 results in a significant decrease of transition temperature (-6 degrees C) and enthalpy (-106 kJ/mol) at pH 2.05 while unfolding heat capacity increment remains unchanged. Thermal unfolding transitions of native and modified beta-lactoglobulin at pH 2.05 are well approximated by a two-state model suggesting that no intermediate states appear after modification. The difference in Gibbs energy of denaturation between native and modified beta- lactoglobulin, 8.5 kJ/mol at 37 degrees C and pH 2.05, does not depend on the nature of the introduced group (charged or neutral). Computer analysis of possible interactions involving Cys121 in a three- dimensional structure of beta-lactoglobulin revealed that the thiol group is too far away from neighboring residues to form side-chain hydrogen bonds. This suggests that the sulfhydryl group of Cys121 may contribute to the maintenance of BLG tertiary structure via water mediated H-bonding.      

Buried water molecules contribute to the conformational stability of a protein

This study sought to attain a better understanding of the contributionof buried water molecules to protein stability. The 3SS humanlysozyme lacks one disulfide bond between Cys77 and Cys95 andis significantly destabilized compared with the wild-type humanlysozyme (4SS). We examined the structure and stability of theI59A-3SS mutant human lysozyme, in which a cavity is createdat the mutation site. The crystal structure of I59A-3SS indicatedthat there were ordered new water molecules in the cavity created.The stability of I59A-3SS is 5.5 kJ/mol less than that of 3SS.The decreased stability of I59A-3SS (5.5 kJ/mol) is similarto that of Ile to Ala mutants with newly introduced water moleculesin other globular proteins (6.3 ± 2.1 kJ/mol), but isless than that of Ile/Leu to Ala mutants with empty cavities(13.7 ± 3.1 kJ/mol). This indicates that water moleculespartially compensate for the destabilization by decreasing hydrophobicand van der Waals interactions. These results provide furtherevidence that buried water molecules contribute to protein stability.     

Patterns of functional proteins formed by local electrochemical desorption of self-assembled monolayers

Patterned self-assembled monolayers (SAMs) were formed using the scanning electrochemical microscope (SECM). The procedures is based on the local electrochemical desorption of an alkanethiolate monolayer by applying a 5 kHz square-wave voltage of 2 V (peak-to-peak) to a two-electrode configuration consisting of an ultramicroelectrode (UME) of 10 μm diameter placed about 5 μm above a macroscopic SAM-covered gold electrode. Desorption occurs on well-defined regions with a diameter of (12.8±2.8) μm. These regions of bare gold are able to chemisorb a ω-functionalized thiol or disulfide such as cystamine to form patterns of amino-terminated surfaces. Functional proteins can be coupled to the amino groups present at the modified regions of the monolayer. This approach was demonstrated by imaging the activity of horseradish peroxidase bound to the patterned SAMs in the generation–collection mode of the SECM. A considerable improvement of the procedure could be achieved by performing the desorption in a solution containing a millimolar concentration of the ω-functionalized thiol/disulfide ensuring effective refilling of the monolayer by the desired molecules and hence high concentration of the immobilized proteins. The method is discussed with respect to prospective application in the field of chip-based bioanalytical assays.     

The activation of electrophile, nucleophile and leaving group during the reaction catalysed by pI258 arsenate reductase

The reduction of arsenate to arsenite by pI258 arsenate reductase (ArsC) combines a nucleophilic displacement reaction with a unique intramolecular disulfide cascade. Within this reaction mechanism, the oxidative equivalents are translocated from the active site to the surface of ArsC. The first reaction step in the reduction of arsenate by pI258 ArsC consists of a nucleophilic displacement reaction carried out by Cys10 on dianionic arsenate. The second step involves the nucleophilic attack of Cys82 on the Cys10-arseno intermediate formed during the first reaction step. The onset of the second step is studied here by using quantum chemical calculations in a density functional theory context. The optimised geometry of the Cys10-arseno adduct in the ArsC catalytic site (sequence motif: Cys10-Thr11-Gly12-Asn13-Ser14-Cys15-Arg16-Ser17) forms the starting point for all subsequent calculations. Thermodynamic data and a hard and soft acids and bases (HSAB) reactivity analysis show a preferential nucleophilic attack on a monoanionic Cys10-arseno adduct, which is stabilised by Ser17. The P-loop active site of pI258 ArsC activates first a hydroxy group and subsequently arsenite as the leaving group, as is clear from an increase in the calculated nucleofugality of these groups upon going from the gas phase to the solvent phase to the enzymatic environment. Furthermore, the enzymatic environment stabilises the thiolate form of the nucleophile Cys82 by 3.3 pH units through the presence of the eight-residue alpha helix flanked by Cys82 and Cys89 (redox helix) and through a hydrogen bond with Thr11. The importance of Thr11 in the pKa regulation of Cys82 was confirmed by the observed decrease in the kcat value of the Thr11Ala mutant as compared to that of wild-type ArsC. During the final reaction step, Cys89 is activated as a nucleophile by structural alterations of the redox helix that functions as a pKa control switch for Cys89; this final step is necessary to expose a Cys82-Cys89 disulfide.     

Evidence for an initiation site for hen lysozyme folding from the reduced form using its dissected peptide fragments

We prepared two dissected fragments of hen lysozyme and examinedwhether or not these two fragments associated to form a native-likestructure. One (Fragment I) is the peptide fragment Asn59–homoserine-105containing Cys64–Cys80 and Cys76–Cys94. The other(Fragment II) is the peptide fragment Lys1–homoserine-58connected by two disulfide bridges, Cys6–Cys127 and Cys30–Cys115,to the peptide fragment Asn106–Leu129. It was found thatthe Fragment I immobilized in the cuvette formed an equimolarcomplex with Fragment II (K_d = 3.3x10^–4 M at pH 8 and25°C) by means of surface plasmon resonance. Moreover, fromanalyses by circular dichroism spectroscopy and ion-exchangechromatography of the mixture of Fragments I and II at pH 8under non-reducing conditions, it was suggested that these fragmentsassociated to give the native-like structure. However, the mutantFragment I in which Cys64–Cys80 and Cys76–Cys94are lacking owing to the mutation of Cys to Ala, or the mutantfragment in which Trp62 is mutated to Gly, did not form thenative-like species with Fragment II, because the mutant FragmentI derived from mutant lysozymes had no local conformation dueto mutations. Considering our previous results where the preferentialoxidation of two inside disulfide bonds, Cys64–Cys80 andCys76–Cys94, occurred in the refolding of the fully reducedFragment I, we suggest that the peptide region correspondingto Fragment I is an initiation site for hen lysozyme folding.     

The consequences of engineering an extra disulfide bond in the Penicillium camembertii mono-and diglyceride specific lipase

The extracellular lipase from Penicillium camembertii has uniquesubstrate specificity restricted to mono- and diglycerides.The enzyme is a member of a homologous family of lipases fromfilamentous fungi. Four of these proteins, from the fungi Rhizomucormiehei, Humicola lanuginosa, Rhizopus delemar and P.camembertii,have had their structures elucidated by X-ray crystallography.In spite of pronounced sequence similarities the enzymes exhibitsignificant differences. For example, the thermo-stability ofthe P.camembertii lipase is considerably lower than that ofthe H.lanuginosa enzyme. Since only the P.camembertii enzymelacks the characteristic long disulfide bridge, correspondingto Cys22–Cys268 in the H.lanuginosa lipase, we have engineeredthis disulfide into the former enzyme in the hope of obtaininga significantly more stable fold. The properties of the doublemutant (Y22C and G269C) were assessed by a variety of biophysicaltechniques. The extra disulfide link was found to increase themelting temperature of the protein from 51 to 63°C. However,no difference is observed under reducing conditions, indicatingan intrinsic instability of the new disulfide. The optimal temperaturefor catalytic activity decreased by 10°C and the optimumpH was shifted by 0.7 units to more acidic.     

Comparison of the structural and functional effects of monomeric and dimeric human apolipoprotein A-II in high density lipoprotein particles

High density lipoprotein (HDL) is throught to play a significant role in the process of reverse cholesterol transport. It has become clear that the apolipoprotein (apo) composition of HDL is important in determining the metabolic fate of this particle. The major proteins of human HDL are apoAI and APOAII; the latter protein is a disulfide-linked dimer in humans and higher primates but monomeric in the other species. The consequences of the apo Cys6-Cys6 disulfide bridge in apoAII for human HDL structure and function are not known. To address this issue, the influence of the Cys6-Cys6 disulfide bridge on the interaction of human apoAII with palmitoyl-oleoyl phosphatidylcholine has been studied. The size and valence of a series of homogeneous discoidal complexes containing either monomeric (reduced and carboxymethylated) or dimeric apoAII have been determined, and their ability to remove cholesterol from rat Fu5AH hepatoma cells grown in culture has been compared. The apoAII dimer and monomer form discoidal complexes of similar size, with twice as many of the latter molecule required per disc. Removal of the disulfide bond influences the stability of the helical segments around the edge of the disc as seen by a decrease in α-helix content of the monomeric protein. The discoidal particles containing the monomeric form of apoAII are somewhat more effective than particles containing either dimeric apoAII or apoAI in removing cellular cholesterol. Overall, reduction of the disulfide bridge of apoAII probably does not have a major effect in the determination of HDL particle sizein vivo. It follows that the evolution of the Cys6-Cys6 disulfide bond in higher primates probably has not had a major effect on the function of the apoAII molecule.     

Detailed Structure and Pathophysiological Roles of the IgA-Albumin Complex in Multiple Myeloma

Immunoglobulin A (IgA)-albumin complexes may be associated with pathophysiology of multiple myeloma, although the etiology is not clear. Detailed structural analyses of these protein–protein complexes may contribute to our understanding of the pathophysiology of this disease. We analyzed the structure of the IgA-albumin complex using various electrophoresis, mass spectrometry, and in silico techniques. The data based on the electrophoresis and mass spectrometry showed that IgA in the sera of patients was dimeric, linked via the J chain. Only dimeric IgA can bind to albumin molecules leading to IgA-albumin complexes, although both monomeric and dimeric forms of IgA were present in the sera. Molecular interaction analyses in silico implied that dimeric IgA and albumin interacted not only via disulfide bond formation, but also via noncovalent bonds. Disulfide bonds were predicted between Cys34 of albumin and Cys311 of IgA, resulting in an oxidized form of albumin. Furthermore, complex formation prolongs the half-life of IgA molecules in the IgA-albumin complex, leading to excessive glycation of IgA molecules and affects the accumulation of IgA in serum. These findings may demonstrate why complications such as hyperviscosity syndrome occur more often in patients with IgA dimer producing multiple myeloma.     

Improvement of Fc-erythropoietin structure and pharmacokinetics by modification at a disulfide bond

Erythropoietin (Epo) is a cytokine that controls the production of red blood cells (RBCs). Epo acts continuously on RBC precursors to prevent apoptosis, so it is important to maintain high levels of Epo activity when treating anemic patients. We describe here modified human Epo [Epo(NDS)] with mutations His32Gly, Cys33Pro, Trp88Cys and Pro90Ala that result in the rearrangement of the disulfide bonding pattern from Cys29-Cys33 to Cys29-Cys88 and that, in the context of an Fc-Epo(NDS) fusion protein, lead to significantly improved properties. Fc-Epo was secreted from NS/0 myeloma cells as about 35% high molecular weight aggregates, was unstable upon removal of N-linked oligosaccharides and showed poor pharmacokinetics and little efficacy in mice. In contrast, a corresponding Fc-Epo(NDS) was secreted almost exclusively as a unit dimer, was relatively stable to removal of N-linked oligosaccharides, had much improved pharmacokinetic properties and had a significantly improved effect on RBC production. These results indicate that rearrangement of the disulfide bonding pattern in a therapeutic protein can have a significant effect on pharmacokinetics and, potentially, the dosing schedule of a protein drug.     

Oxidative folding of proteins

The oxidative folding of proteins is reviewed and illustrated with bovine pancreatic ribonuclease A (RNase A). The mutual effects of conformational folding and disulfide bond regeneration are emphasized, particularly the "locking in" of native disulfide bonds by stable tertiary structure in disulfide intermediates. Two types of structured metastable disulfide species are discerned, depending on the relative protection of their disulfide bonds and thiol groups. Four generic pathways for oxidative folding are identified and characterized.     

Aqueous solution properties of disulfide linked gemini and cleaved monomeric thiol surfactants

Monomeric thiol surfactants, [C(n)H(2n+1)N(CH(3))(2)CH(2)CH(2)SH]Br, were produced by the cleavage of gemini surfactant containing a disulfide bond in the spacer chain, [C(n)H(2n+1)N(CH(3))(2)CH(2)CH(2)SSCH(2)CH(2)N(CH(3))(2)C(n)H(2n+1)]2Br. The disulfide bond was completely reduced by the addition of four times moles of dithiothreitol in water at room temperature. The critical micelle concentrations of monomeric surfactants were significantly increased in comparison with original gemini surfactants. The monomeric thiol surfactants were stable in the presence of dithiothreitol, whereas they returned gradually to their original gemini surfactants within several days due to air oxidation in water without dithiothreitol. The micelle formation induced by the disulfide linkage formation was suggested by the fluorescence intensity ratio of pyrene. The time course of decrease in thiol concentration associated with the recovery of gemini surfactants was confirmed by the absorption spectra utilizing the reactions with 4,4'-dithiopyridine.     

Biophysical Features of Bacillithiol,the Glutathione Surrogate of Bacillus subtilis and other Firmicutes

Bacillithiol (BSH) is the major low‐molecular‐weight (LMW) thiol in many low‐G+C Gram‐positive bacteria (Firmicutes). Evidence now emerging suggests that BSH functions as an important LMW thiol in redox regulation and xenobiotic detoxification, analogous to what is already known for glutathione and mycothiol in other microorganisms. The biophysical properties and cellular concentrations of such LMW thiols are important determinants of their biochemical efficiency both as biochemical nucleophiles and as redox buffers. Here, BSH has been characterised and compared with other LMW thiols in terms of its thiol pK_a, redox potential and thiol–disulfide exchange reactivity. Both the thiol pK_a and the standard thiol redox potential of BSH are shown to be significantly lower than those of glutathione whereas the reactivities of the two compounds in thiol–disulfide reactions are comparable. The cellular concentration of BSH in Bacillus subtilis varied over different growth phases and reached up to 5 mM , which is significantly greater than previously observed from single measurements taken during mid‐exponential growth. These results demonstrate that the biophysical characteristics of BSH are distinctively different from those of GSH and that its cellular concentrations can reach levels much higher than previously reported.     

Elucidation of the Bridging Pattern of the Lantibiotic Pseudomycoicidin

Lantibiotics are post-translationally modified antibiotic peptides with lanthionine thioether bridges that represent potential alternatives to conventional antibiotics. The lantibiotic pseudomycoicidin is produced by Bacillus pseudomycoides DSM 12442 and is effective against many Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus. While prior work demonstrated that pseudomycoicidin possesses one disulfide bridge and four thioether bridges, the ring topology has so far remained unclear. Here, we analyzed several pseudomycoicidin analogues that are affected in ring formation via MALDI-TOF-MS and tandem mass spectrometry with regard to their dehydration and fragmentation patterns, respectively. As a result, we propose a bridging pattern involving Thr8 and Cys13, Thr10 and Cys16, Ser18 and Cys21, and Ser20 and Cys26, thus, forming two double ring systems. Additionally, we localized the disulfide bridge to connect Cys3 and Cys7 and, therefore, fully elucidated the bridging pattern of pseudomycoicidin.     

Synthesis of DNA-Encoded Disulfide- and Thioether-Cyclized Peptides

DNA-encoded chemical library technologies enable the screening of large combinatorial libraries of chemically and structurally diverse molecules, including short cyclic peptides. A challenge in the combinatorial synthesis of cyclic peptides is the final step, the cyclization of linear peptides that typically suffers from incomplete reactions and large variability between substrates. Several efficient peptide cyclization strategies rely on the modification of thiol groups, such as the formation of disulfide or thioether bonds between cysteines. In this work, we established a strategy and reaction conditions for the efficient chemical synthesis of cyclic peptide–DNA conjugates based on linking the side chains of cysteines. We tested two different thiol-protecting groups and found that tert-butylthio (S-tBu) works best for incorporating a pair of cysteines, and we show that the DNA-linked peptides can be efficiently cyclized through disulfide and thioether bond formation. In combination with established procedures for DNA encoding, the strategy for incorporation of cysteines may be readily applied for the generation and screening of disulfide- and thioether-cyclized peptide libraries.     

Identification of anchor points for chemical modification of a small cysteine-rich protein by using a cysteine scan

Chemical modifications of proteins are increasingly important in the development of protein drugs with fine-tuned properties. Regioselective modification, such as the chemoselective alkylation of an unpaired cysteine residue, is a prerequisite for obtaining homogenous protein products. The introduction of an unpaired Cys into the Cys-rich protein, insulin, was investigated by using a Cys scan. This was challenging as the introduced Cys could interfere with insulin's three existing disulfide bonds. However, eight insulin precursors were expressed in Saccharomyces cerevisiae with good yields. Although extensive post-translational modifications of the unpaired Cys were observed, the majority could be removed by selective reduction. An example Cys(7) insulin analogue was modified with a PEGylated maleimide moiety. The new variant was active in in vitro and in vivo models. Our results show that even small Cys-rich proteins can be expressed with additional unpaired Cys in meaningful yields and further chemically modified, while maintaining their biological activity.     

Effect of the intermolecular disulfide bond on the conformation and stability of glial cell line-derived neurotrophic factor

Glial cell line-derived neurotrophic factor (GDNF) is a memberof the TGF-ß superfamily of proteins. It exists asa covalent dimer in solution, with the 15 kDa monomers linkedby an interchain disulfide bond through the Cys101 residues.Sedimentation equilibrium and velocity experiments demonstratedthat, after removal of the interchain disulfide bond, GDNF remainsas a non-covalent dimer and is stable at pH 7.0. To investigatethe effect of the intermolecular disulfide on the structureand stability of GDNF, we compared the solution structures ofthe wild-type protein and a cysteine-101 to alanine (C101A)mutant using Fourier transform infrared (FTIR), FT-Raman andcircular dichroism (CD) spectroscopy and sedimentation analysis.The elimination of the intermolecular disulfide bond causesonly minor changes (