The superreactive disulfide bonds in α-lactalbumin and lysozyme

The disulfide reduction kinetics in equine lysozyme (ELZ), which is a Ca²⁺-binding lysozyme, and human (HLA) and equineα-lactalbumin (ELA) at pH 8.5 and 25°C by excess dithiothreitol were studied, and it was found that in ELZ there is no superreactive disulfide bond, while one of the disulfides is reduced very quickly by the reducing agent in HLA and ELA, as in bovineα-lactalbumin. The local conformation around the surface disulfide in ELZ seems to be more similar to that in hen egg-white lysozyme than inα-lactalbumin. The four disulfides in ELZ were reduced slowly in an apparently single-exponential form, and the bound Ca²⁺ lowered the reduction rate. The torsion energy on each of the disulfides in threeα-lactalbumin and eight c-type lysozymes whose native conformations have been experimentally or theoretically analyzed was calculated, and it was found that torsion imposed on the surface disulfide between Cys 6 and Cys 120 inα-lactalbumin is a main cause of the superreactivity and all of lysozymes, including the Ca²⁺-binding ones, have no such strained surface bond.     

Evidence for essential disulfide bonds in the β-subunit of (Na+ + K+)-ATPase

$\text{(Na}{}^{\mathrm{+}}\text{+ K}{}^{\mathrm{+}}\text{)-ATPase}$ from dog kidney lost its activity when heated at 55°C in the presence of 0.3 M 2-mercaptoethanol. Either heat treatment alone or addition of reducing agent at around 25°C caused little inactivation. One disulfide bond per protomer (mol. wt. 146000) was reduced in the inactivated sample but in active samples no reduction occurred. Neither K⁺-dependent phosphatase activity nor phosphoenzyme formation in the presence of Na⁺ was detected in the inactivated sample, suggesting that the disulfide bond was essential for the catalytic cycle of $\text{(Na}{}^{\mathrm{+}}\text{+ K}{}^{\mathrm{+}}\text{)-ATPase}$. This essential disulfide bond belonged to the β-subunit, the glycoprotein component of the enzyme, indicating that the β-subunit may be an integral component of the $\text{(Na}{}^{\mathrm{+}}\text{+ K}{}^{\mathrm{+}}\text{)-ATPase}$ system.     

Conformational analysis by quantitative NOE measurements of the β-proton pairs across individual disulfide bonds in proteins

NOEs between the β-protons of cysteine residues across disulfide bonds in proteins provide direct information on the connectivities and conformations of these important cross-links, which are otherwise difficult to investigate. With conventional [U-¹³C, ¹⁵N]-proteins, however, fast spin diffusion processes mediated by strong dipolar interactions between geminal β-protons prohibit the quantitative measurements and thus the analyses of long-range NOEs across disulfide bonds. We describe a robust approach for alleviating such difficulties, by using proteins selectively labeled with an equimolar mixture of (2R, 3S)-[β-¹³C; α,β-²H₂] Cys and (2R, 3R)-[β-¹³C; α,β-²H₂] Cys, but otherwise fully deuterated. Since either one of the prochiral methylene protons, namely β2 (proS) or β3 (proR), is always replaced with a deuteron and no other protons remain in proteins prepared by this labeling scheme, all four of the expected NOEs for the β-protons across disulfide bonds could be measured without any spin diffusion interference, even with long mixing times. Therefore, the NOEs for the β2 and β3 pairs across each of the disulfide bonds could be observed at high sensitivity, even though they are 25% of the theoretical maximum for each pair. With the NOE information, the disulfide bond connectivities can be unambiguously established for proteins with multiple disulfide bonds. In addition, the conformations around disulfide bonds, namely χ² and χ³, can be determined based on the precise proton distances of the four β-proton pairs, by quantitative measurements of the NOEs across the disulfide bonds. The feasibility of this method is demonstrated for bovine pancreatic trypsin inhibitor, which has three disulfide bonds.     

Accumulation of β-conglycinin in soybean cotyledon through the formation of disulfide bonds between α'- and α-subunits

β-Conglycinin, one of the major soybean (Glycine max) seed storage proteins, is folded and assembled into trimers in the endoplasmic reticulum and accumulated into protein storage vacuoles. Prior experiments have used soybean β-conglycinin extracted using a reducing buffer containing a sulfhydryl reductant such as 2-mercaptoethanol, which reduces both intermolecular and intramolecular disulfide bonds within the proteins. In this study, soybean proteins were extracted from the cotyledons of immature seeds or dry beans under nonreducing conditions to prevent the oxidation of thiol groups and the reduction or exchange of disulfide bonds. We found that approximately half of the α'- and α-subunits of β-conglycinin were disulfide linked, together or with P34, prior to amino-terminal propeptide processing. Sedimentation velocity experiments, size-exclusion chromatography, and two-dimensional polyacrylamide gel electrophoresis (PAGE) analysis, with blue native PAGE followed by sodium dodecyl sulfate-PAGE, indicated that the β-conglycinin complexes containing the disulfide-linked α'/α-subunits were complexes of more than 720 kD. The α'- and α-subunits, when disulfide linked with P34, were mostly present in approximately 480-kD complexes (hexamers) at low ionic strength. Our results suggest that disulfide bonds are formed between α'/α-subunits residing in different β-conglycinin hexamers, but the binding of P34 to α'- and α-subunits reduces the linkage between β-conglycinin hexamers. Finally, a subset of glycinin was shown to exist as noncovalently associated complexes larger than hexamers when β-conglycinin was expressed under nonreducing conditions.     

Localization of disulfide bonds in α1-acid glycoprotein and their effect on the ability of the protein to interact with ethidium bromide

α1-Acid glycoprotein (orosomucoid) was purified from the human and murine blood sera using phenol deproteinization. As opposed to the murine protein, the human orosomucoid bound the fluorescent dye ethidium bromide but lost this ability after treatment with β-mercaptoethanol, which breaks disulfide bonds. Disulfide bonds between the Cys²³ and Cys¹⁶⁵ residues of the human orosomucoid and between the Cys⁹¹ and Cys¹⁸⁴ residues of the murine orosomucoid were identified.     

The unusual conformation of cross-strand disulfide bonds is critical to the stability of β-hairpin peptides

The cross-strand disulfides (CSDs) found in β-hairpin antimicrobial peptides (β-AMPs) show a unique disulfide geometry that is characterized by unusual torsion angles and a short Cα-Cα distance. While the sequence and disulfide bond connectivity of disulfide-rich peptides is well studied, much less is known about the disulfide geometry found in CSDs and their role in the stability of β-AMPs. To address this, we solved the nuclear magnetic resonance (NMR) structure of the β-AMP gomesin (Gm) at 278, 298, and 310 K, examined the disulfide bond geometry of over 800 disulfide-rich peptides, and carried out extensive molecular dynamics (MD) simulation of the peptides Gm and protegrin. The NMR data suggests Cα-Cα distances characteristic for CSDs are independent of temperature. Analysis of disulfide-rich peptides from the Protein Data Bank revealed that right-handed and left-handed rotamers are equally likely in CSDs. The previously reported preference for right-handed rotamers was likely biased by restricting the analysis to peptides and proteins solved using X-ray crystallography. Furthermore, data from MD simulations showed that the short Cα-Cα distance is critical for the stability of these peptides. The unique disulfide geometry of CSDs poses a challenge to biomolecular force fields and to retain the stability of β-hairpin fold over long simulation times, restraints on the torsion angles might be required.     

Mutations in the RAM network confer resistance to the thiol oxidant 4,4′-dipyridyl disulfide

Thiol oxidants are expected to have multiple effects in living cells. Hence, mutations giving resistance to such agents are likely to reveal important targets and/or mechanisms influencing the cellular capacity to withstand thiol oxidation. A screen for mutants resistant to the thiol-specific oxidant dipyridyl disulfide (DPS) yielded tao3-516, which is impaired in the function of the RAM signaling network protein Tao3/Pag1p. We suggest that the DPS-resistance of the tao3-516 mutant might be due to deficient cell-cycle-regulated production of the chitinase Cts1p, which functions in post-mitotic cell separation and depends on Tao3p and the RAM network for regulated expression. Consistent with this, deletion of other RAM genes or CTS1 also resulted in increased resistance to DPS. Exposure to DPS caused extensive depolarization of the actin cytoskeleton. We found that tao3-516 is resistant to latrunculin, a specific inhibitor of actin polymerization, and that ram, Deltaace2, and Deltacts1 mutants are resistant to benomyl, a microtubule-destabilizing drug. Since septum build-up depends on the organization of cytoskeletal proteins, the resistance to cytoskeletal stress of Cts1p-deficient mutants might relate to bypass for abnormal septum-associated protein sorting. The broad resistance toward oxidants (DPS, diamide and H(2)O(2)) of the Deltacts1 strain links cell wall function to the resistance to oxidative stress and suggests the existence of targets that are common for these oxidants.     

Reconsideration of an early dogma,saying “there is no evidence for disulfide bonds in proteins from archaea”

Stability and function of a large number of proteins are crucially dependent on the presence of disulfide bonds. Recent genome analysis has pointed out an important role of disulfide bonds for the structural stabilization of intracellular proteins from hyperthermophilic archaea and bacteria. These findings contradict the conventional view that disulfide bonds are rare in those proteins. A specific protein, known as protein disulfide oxidoreductase (PDO) is recognized as a potential key enzyme in intracellular disulfide-shuffling in hyperthermophiles. The structure of this protein consists of two combined thioredoxin-related units which together, in tandem-like manner, form a closed protein domain. Each of these units contains a distinct CXXC active site motif. Both sites seem to have different redox properties. A relation to eukaryotic protein disulfide isomerase is suggested by the observed structural and functional characteristics of the protein. Enzymological studies have revealed that both, the archaeal and bacterial forms of this protein show oxidative and reductive activity and are able to isomerize protein disulfides. The variety of active site disulfides found in PDO’s from hyperthermophiles is puzzling. It is assumed, that PDO enzymes in hyperthermophilic archaea and bacteria may be part of a complex system involved in the maintenance of protein disulfide bonds.     

Identification of an intra-molecular disulfide bond in the sodium channel β1-subunit

The sodium channel β1 subunit is non-covalently associated with the pore-forming α-subunits, and has been proposed to act as a modulator of channel activity, regulator of channel cell surface expression and cell adhesion molecule. Its importance is evident since mutations of the β1 subunit cause neurologic and cardiovascular disorders. The first described β1 subunit mutation is the C121W, that is related to generalized epilepsy with febrile seizures plus (GEFS+), a childhood genetic epilepsy syndrome. This mutation changed a conserved cysteine residue in position 121 into a tryptophan, putatively disrupting a disulfide bridge that should normally maintain the β1 extracellular immunoglobulin-like fold. Using the 2-D-diagonal-SDS-PAGE technique, we demonstrated the existence of this putative disulfide bridge in the Ig-like extracellular domain of the β1 subunit and its disruption in the epileptogenic C121W mutant.     

Evidence for the presence of a critical disulfide bond in the mouse EP3γ receptor

To determine the contribution of cysteines to the function of the mouse E-prostanoid subtype 3 gamma (mEP3γ), we tested a series of cysteine-to-alanine mutants. Two of these mutants, C107A and C184A, showed no agonist-dependent activation in a cell-based reporter assay for mEP3γ, whereas none of the other cysteine-to-alanine mutations disrupted mEP3γ signal transduction. Total cell membranes prepared from HEK293 cells transfected with mEP3γ C107A or C184A had no detectable radioligand binding. Other mutant mEP3γ receptors had radioligand affinities and receptor densities similar to wild-type. Cell-surface ELISA against the N-terminal HA-tag of C107A and C184A demonstrated 40% and 47% reductions respectively in receptor protein expression at the cell surface, and no radioligand binding was detected as assessed by intact cell radioligand binding experiments. These data suggest a key role for C107 and C184 in both receptor structure/stability and function and is consistent with the presence of a conserved disulfide bond between C107 and C184 in mouse EP3 that is required for normal receptor expression and function. Our results also indicate that if a second disulfide bond is present in the native receptor it is non-essential for receptor assembly or function.     

Rectification ratio based determination of disulfide bonds of β2 extracellular loop of BK channel

Large-conductance Ca²⁺-activated K⁺ (BK) channels are composed of a pore-forming α and a variable number of auxiliary β subunits and play important roles in regulating excitability, action potential waveforms and firing patterns, particularly in neurons and endocrine and cardiovascular cells. The β2 subunits increase the diversity of gating and pharmacological properties. Its extracellular loop contains eight cysteine residues, which can pair to form a high-order structure, underlying the stability of the extracellular loop of β2 subunits and the functional effects on BK channels. However, how these cysteines form disulfide bonds still remains unclear. To address this, based on the fact that the rectification and association of BK α to β2 subunits are highly sensitive to disruption of the disulfide bonds in the extracellular loop of β2, we developed a rectification ratio based assay by combining the site-directed mutagenesis, electrophysiology and enzymatic cleavage. Three disulfide bonds: C1(C84)-C5(C113), C3(C101)-C7(C148) and C6(C142)-C8C(174) are successfully deduced in β2 subunit in complex with a BK α subunit, which are helpful to predict structural model of β2 subunits through computational simulation and to understand the interface between the extracellular domain of the β subunits and the pore-forming α subunit.     

Amino acid sequence of proteinase K from the mold Tritirachium album Limber: Proteinase K — a subtilisin-related enzyme with disulfide bonds

The amino acid sequence of proteinase K (EC 3.4.21.14) from Tritirachium album Limber has been determined by analysis of fragments generated by cleavage with CNBr or BNPS-skatole. The enzyme consists of a single peptide chain containing 277 amino acid residues, corresponding to M_r 28 930. Comparison of the sequence with those of the serine proteinases reveals a high degree of homology (about 35%) to the subtilisin-related enzyme. But in contrast to the subtilisins, proteinase K contains 2 disulfide bonds and a free cysteine residue. This finding may indicate that proteinase K is a member of a new subfamily of the subtilisins.     

Male–male relationships in chimpanzees and the evolution of human pair bonds

The evolution of monogamy has been a central question in biological anthropology. An important avenue of research has been comparisons across “socially monogamous” mammals, but such comparisons are inappropriate for understanding human behavior because humans are not “pair living” and are only sometimes “monogamous.” It is the “pair bond” between reproductive partners that is characteristic of humans and has been considered unique to our lineage. I argue that pair bonds have been overlooked in one of our closest living relatives, chimpanzees. These pair bonds are not between mates but between male “friends” who exhibit enduring and emotional social bonds. The presence of such bonds in male–male chimpanzees raises the possibility that pair bonds emerged earlier in our evolutionary history. I suggest pair bonds first arose as “friendships” and only later, in the human lineage, were present between mates. The mechanisms for these bonds were co-opted for male-female bonds in humans.     

Alteration of N-linked oligosaccharide structures of human chorionic gonadotropin β-subunit by disruption of disulfide bonds

The human chorionic gonadotropin β-subunit (hCGβ) is a glycoprotein in which 12 cysteine residues pair to form six intramolecular disulfide bonds. In order to elucidate the effect of each disulfide bond on glycosylation of the molecule, we analysed structures of asparagine-linked oligosaccharides of various recombinant hCGβ produced in Chinese hamster ovary (CHO) cells: wild-type hCGβ (βWT) and mutants in which any one of the six intramolecular disulfide bonds had been disrupted by site-directed mutagenesis. SDS-PAGE analysis of βWT and these mutants before and after digestion with endoglycosidase F and H revealed structural changes in the oligosaccharide moieties of some mutants. In addition, structural analysis of oligosaccharides obtained from metabolically labeled βWT and a mutant showed that the mutant contained additional high mannose type oligosaccharides. These results suggest that elimination of a specific disulfide bond, resulting in a change in the protein conformation, disturbs the normal assembly of the mature complex type oligosaccharides in the hCGβ molecule. Abbreviations: hCGβ, human chorionic gonadotropin β-subunit; βWT, wild type hCGβ; CHO, Chinese hamster ovary; Endo-H, endoglycosidase H; Endo-F, endoglycosidase F This revised version was published online in November 2006 with corrections to the Cover Date.     

Conformational changes of α-lactalbumin induced by the stepwise reduction of its disulfide bridges: The effect of the disulfide bridges on the structural stability of the protein in sodium dodecyl sulfate solution

Four disulfide bridges of bovineα-lactalbumin (α-lact) were selectively reduced to obtain its derivatives with three, two, and zero disulfide bridges (designated as 3SS, 2SS, and OSSα-lact, respectively). The original helicity was almost maintained in 3SSα-lact missing only the Cys6-Cysl20 bridge. Upon the reduction of both Cys28-Cys111 and Cys6-Cys120 bridges, various changes occurred in the protein. In particular, the maximum fluorescence of 1-anilinonaphthalene-8-sulfonic acid was observed in this stage. Upon the reduction of all disulfide bridges, the hydrophobic box of the protein, formed by Trp60, Ile95, Tyr103, and Trp104, was disrupted and an internal helical structure was destroyed. The conformation of each derivative was examined mainly in a solution of sodium dodecyl sulfate. In the surfactant solution, the helicity increased from 33% to 37% in 3SSα-lact, from 26% to 31% in 2SSα-lact, and from 18% to 37% in OSSα-lact, as against from 34% to 44% in intactα-lact. On the other hand, the tryptophan fluorescence of each derivative was affected in very low surfactant concentrations, suggesting that the tertiary structure considerably changed prior to the secondary structural change in the surfactant solution.     

Complete amino acid sequence and location of the five disulfide bridges in porcine pancreatic α-amylase

Porcine pancreatic α-amylase (1,4-α-d-glucan glucanohydrolase EC 3.2.1.1), a single polypeptide chain, contains nine residues of methionine. Eight different fragments resulting from cleavage of this molecule by cyanogen bromide were characterized. The sequences of six of them have previously been reported. Two missing fragments, CN2 (82 residues) and CN3b1 (76 residues) were purified after breaking of the interpeptidic disulfide bridge and their complete sequence as well as that of the previously purified CN1 peptide (102 residues) are reported here. The location of the three disulfide bridges present in these peptides was determined. Ordering of the carboxymethylated cyanogen bromide fragments was carried out by pulse labeling the amylase chain in vivo. The complete sequence of the porcine pancreatic amylase chain (496 residues) and the location of its five disulfide bridges is presented. Comparison with human and mouse pancreatic and salivary α-amylases and with rat pancreatic amylase obtained from the corresponding cDNA nucleotidic sequences shows a high degree of homology between mammalian α-amylases.     

Glutathione disulfide liposomes – A research tool for the study of glutathione disulfide associated functions and dysfunctions

Glutathione disulfide (GSSG) is the oxidized form of glutathione (GSH). GSH is a tripeptide present in the biological system in mM concentration and is the major antioxidant in the body. An increase in GSSG reflects an increase in intracellular oxidative stress and is associated with disease sates. The increase has also been demonstrated to lead to an increase in protein S-glutathionylation that can affect the structure and function of proteins. Protein S-glutathionylation serves as a regulatory mechanism during cellular oxidative stress. Though GSSG is commercially available, its roles in various GSSG-associated normal/abnormal physiological functions have not been fully delineated due to the reason that GSSG is not cell membrane permeable and a lack of method to specifically increase GSSG in cells. We have developed cationic liposomes that can effectively deliver GSSG into cells. Various concentrations of GSSG liposomes can be conveniently prepared. At 1 mg/mL, the GSSG liposomes effectively increased intracellular GSSG by 27.1±6.9 folds (n=3) in 4 h and led to a significant increase in protein S-glutathionylation confirming that the increased GSSG is functionally effective. The Trypan blue assay demonstrated that GSSG liposomes were not cytotoxic; the cell viability was greater than 95% after cells were treated with the GSSG liposomes for 4 h. A stability study showed that the dry form of the GSSG liposomes were stable for at least 70 days when stored at ?80 °C. Our data demonstrate that the GSSG liposomes can be a valuable tool in studying GSSG-associated physiological/pathological functions.     

Contribution of allosteric disulfide in the structural regulation of membrane-bound tissue factor–factor VIIa binary complex

Abstract

Two distinct populations, active and cryptic forms of tissue factor (TF), reside on the cell surface. Apart from phospholipid contribution, various models have been introduced to explain decryption/encryption of TF. The proposed model, the switching of Cys186–Cys209 bond of TF, has become the matter of controversy. However, it is well accepted that this disulfide has an immense influence upon ligand factor VIIa (FVIIa) for its binding. However, molecular level understanding for this remains unveiled due to lack of detailed structural information. In this regard, we have performed the molecular dynamic study of membrane-bound TF/TF–FVIIa in both the forms (±Cys186–Cys209 allosteric disulfide bond), individually. Dynamic study depicts that disulfide bond provides structural rigidity of TF in both free and ligand-bound forms. This disulfide bond also governs the conformation of FVIIa structure as well as the binding affinity of FVIIa toward TF. Significant differences in lipid–protein interaction profiles of both the forms of TF in the complex were observed. Two forms of TF, oxidized and reduced, have different structural conformation and behave differentially toward its ligand FVIIa. This disulfide bond not only alters the conformation of GLA domain of FVIIa in the vicinity but allosterically regulates the conformation of the distantly located FVIIa protease domain. We suggest that the redox status of the disulfide bond also governs the lipid-mediated interactions with both TF and FVIIa.

Communicated by Ramaswamy H. Sarma     

Proton transfer in and polarizability of hydrogen bonds in proteins. Tyrosine-lysine and glutamic acid-lysine hydrogen bonds — IR investigations

The OH N O^– H⁺N hydrogen bonds formed between tyrosine and lysine, and between glutamic acid and lysine residues are studied by infrared spectroscopy considering the following systems: (l-lys)_n + phenol, copoly (l-lys, l-tyr)_n, (l-lys)_n + (l-tyr)_n and (l-lys)_n + (l-glu)_n. The phenol-lysine hydrogen bonds are largely symmetrical in the average if the pK_a of the protonated lysine is 2.2 units larger than that of the phenols. In the case of the hydrogen bonds between tyrosine and lysine residues in copoly (l-lys, l-tyr)_n and (l-lys)_n + (l-tyr)_n, the weight of the proton limiting structure OH N is 80–90%, and that of the polar O^– H⁺N structure 10–20%. Double minimum proton potentials occur but the proton is preferentially present at the tyrosine residues. In the (l-lys)_n + (l-glu)_n system, the protons are present at the lysine residues. Thus, these hydrogen bonds have very large dipole moments (about 10 D). With the lysine-phenole hydrogen bonds, hydration shifts the proton transfer equilibrium a little in favour of the polar proton limiting structure O^– H⁺N. These hydrogen bonds are broken to a large extent, however, when only about 3 water molecules are present per lysine residue. When less water is present, as in the copoly (l-lys, l-tyr)_n and (l-lys)_n + (l-tyr)_n systems, these hydrogen bonds are, however, formed quantitatively. Thus — as discussed in this paper — the tyrosine-lysine hydrogen bonds can participate in proton conducting hydrogen bonded systems — as, for instance, present in bacteriorhodopsin — performing the proton transport through hydrophobic regions of biological membranes.