Hydrophobic Dye Binding Research Articles

Refolding Mechanism of Ovalbumin: INVESTIGATION BY USING A STARTING UREA-DENATURED DISULFIDE ISOMER WITH MISPAIRED CYS367-CYS382

Ovalbumin, a member of the serpin superfamily, contains one cystine disulfide (Cys73-Cys120) and four cysteine sulfhydryls (Cys11, Cys30, Cys367, and Cys382) in the native state. To investigate the folding mechanism of ovalbumin, a urea-denatured disulfide isomer with a mispaired disulfide Cys367-Cys382 (D[367-382]) and its derivative (D[367-382/CM-73]) in which a native cystine counterpart of Cys73 is blocked by carboxymethylation were produced. Both the denatured isomers refolded within an instrumental dead time of 4 ms into an initial burst intermediate IN with partially folded conformation. After the initial burst phase, most of the D[367-382] molecules further refolded into the native form. In contrast, upon dilution of D[367-382/CM-73] with the refolding buffer, the protein stayed in the IN state as a stable form, which displayed a partial regain of the native secondary structure and a compact conformation with a similar Stokes radius to the native form. The structural characteristics of IN were clearly differentiated from those of an equilibrium intermediate IA that was produced by dilution with an acidic buffer of urea-denatured ovalbumin; IA showed much more hydrophobic dye binding and a larger Stokes radius than the IN state, despite their indistinguishable far-UV circular dichroic spectra. The non-productive nature of IA highlighted the importance of a compact conformation of the IN state for subsequent native refolding. These observations were consistent with a refolding model of ovalbumin that includes the regain of the partial secondary structure and of the compactness of overall conformation in an initial burst phase before the subsequent native refolding.

Amyloid Fibril Formation of the Mouse VL Domain at Acidic pH

The recombinant V(L) domain that represents the variable part of the light chain (type kappa) of mouse monoclonal antibody F11 directed against human spleen ferritin was found to form amyloid fibrils at acidic pH as evidenced by electron microscopy, thioflavin T binding, and apple-green birefringence after Congo red staining. This is the first demonstration of amyloid fibril formation of the mouse V(L) domain. To understand the mechanism of acidic pH-induced amyloid fibril formation, conformational changes of the V(L) domain were studied by one-dimensional NMR, differential scanning calorimetry, analytical ultracentrifugation, hydrophobic dye binding, far-UV circular dichroism, and tryptophan fluorescence. The results indicated accumulation of two intermediate states during acid unfolding, which might be responsible for amyloid fibril formation. The more structured intermediate that exhibited maximal accumulation at pH 3 retained the nativelike secondary structure and a hydrophobic core, but exposed hydrophobic surfaces that bind 8-anilino-1-naphthalenesulfonate. Below pH 2, a more disordered intermediate with dequenched tryptophan fluorescence but still retaining the beta-sheet structure accumulated. The optimal pH of amyloid fibril formation (i.e., pH 4) was close to the optimal pH of the accumulation of the nativelike intermediate, suggesting that the amyloid fibrils might be formed through this intermediate.

Effects of Amino Acid Substitution on the Physicochemical Properties of Artificial Proteins with Random Sequences

Physicochemical properties of four random proteins, each consisting of about 150 amino acid residues with different sequence identity, were compared to know the correlation between the physicochemical properties and its sequence. The results showed that the extent of the sequence alterations correlated well with the extent of differences in CD spectra, roughly with those in pH-solubility profiles and sedimentation velocity, and not with that in the binding of a hydrophobic fluorescent dye (ANS). Therefore, proteins with similar sequences can have different physicochemical properties, indicating that the extent of mutational effects varies in response to the sequence being altered. This warrants the evolution of a protein in a sequence-specific manner.

Characterization of acid-induced unfolding intermediates of glucose/xylose isomerase.

Acid-induced unfolding of the tetrameric glucose/xylose isomerase (GXI) from Streptomyces sp. NCIM 2730 has been investigated using intrinsic fluorescence, fluorescence quenching, second derivative spectroscopy, hydrophobic dye (1-anilino-8-naphthalene-sulfonate) binding and CD techniques. The pH dependence of tryptophanyl fluorescence of GXI at different temperatures indicated the presence of two stable intermediates at pH 5.0 and pH 3.0. The pH 3.2 intermediate was a dimer and exhibited molten globule-like characteristics, such as the presence of native-like secondary structure, loss of tertiary structure, increased exposure of hydrophobic pockets, altered microenvironment of tyrosine residues and increased accessibility to quenching by acrylamide. Fluorescence and CD studies on GXI at pH 5.0 suggested the involvement of a partially folded intermediate state in the native to molten globule state transition. The partially folded intermediate state retained considerable secondary and tertiary structure compared to the molten globule state. This state was characterized by its hydrophobic dye binding capacity, which is smaller than the molten globule state, but was greater than that of the native state. This state shared the dimeric status of the molten globule state but was prone to aggregate formation as evident by the Rayleigh light scattering studies. Based on these results, the unfolding pathway of GXI can be illustrated as: N-->PFI-->MG-->U; where N is the native state at pH 7.5; PFI is the partially folded intermediate state at pH 5.0; MG is the molten globule state at pH 3.2 and U is the monomeric unfolded state of GXI obtained in the presence of 6 M GdnHCl. Our results demonstrate the existence of a partially folded state and molten globule state on the unfolding pathway of a multimeric alpha/beta barrel protein.

Development of an optimized feeding technology for dairy cows: improvement in resistance to ruminal proteases in the de novo-designed protein MB-1.

We have previously reported on MB-1, a designer protein with potential application in animal nutrition. Having a high content of selected essential amino acids, MB-1 should provide limiting nutrients for animals and promote growth and production. However, the protein was found to have marginal conformational and proteolytic stability, and, thus, strategies for stabilizing MB-1 were elaborated. We discuss the synthesis of MB-1-Cys dimer, a protein with an intermolecular disulfide bridge. This mutant was exposed to Pronase E protease preparation as well as to proteases extracted from ruminal microbes. It was found that in both cases, MB-1-Cys dimer had a better resistance to proteolytic degradation than MB-1. Denaturation and hydrophobic dye binding studies revealed that this enhanced stability was not owing to conformational stabilization, but rather to changes in surface exposure as a consequence of dimerization. In particular, it was found that binding of ANSA to MB-1-Cys dimer was comparable to that observed for native, compact, natural proteins. We discuss the implications of these results for the design of transgenic protein production systems.

An isoleucine zipper peptide forms a native-like triple stranded coiled coil in solution.

Recent studies in the field of de novo protein design have focused on the construction of native-like structures. Here we describe the design and characterization of an isoleucine zipper peptide intended to form a parallel triple-stranded coiled coil. To obtain the native-like structural uniqueness, the hydrophobic interface of the peptide consists of beta-branched Ile residues for complementary side chain packing. The peptide forms a stable triple-stranded coiled coil, as determined by circular dichroism and sedimentation equilibrium analyses. A fluorescence quenching assay after the incorporation of acridine revealed a parallel orientation of the peptides. The structural uniqueness of the coiled coil was confirmed by proton-deuterium amide hydrogen exchange and hydrophobic dye binding. The peptide contains amide protons with hydrogen exchange rates that are approximately an order of magnitude slower than those expected if the exchange occurred via global unfolding. A hydrophobic dye does not bind to the peptide. These results strongly suggest that the peptide folds into a well-packed structure that is very similar to the native state of a natural protein. Thus, Ile residues in the hydrophobic interface can improve the side chain packing, which can impart native-like structural uniqueness to the designed coiled coil.

Solid-Phase Immunoassays for HCV Antibodies in Gamimune® N

Background and objectives: Occasional false-positive results for the presence of HCV antibodies occur when testing pH 4 Gamimune® N immune globulin intravenous (human) (IGIV) using commercially available immunoassay kits. We investigated the causes. Materials and methods: EIA test results were compared with Nile red hydrophobic dye binding. Results: There was a strict correlation of reactive EIA results with a larger relative proportion of molecules in a low pH-dependent hydrophobic conformation. Conversely, the greater the hydrophilic contribution to the population of IgG molecules (favored at neutral pH), the more nonreactive the EIA test results became for the same lots. An IGIV test preparation procedure consisting of pH neutralization followed by 48-hour incubation at 37 °C decreased positive test result outcomes in four different immunoassay formats by shifting the IgG population to a more hydrophilic conformation. Conclusions: The hydrophobic conformation of IgG favored at low pH appears to give rise to significant levels of nonspecific binding in solid phase immunoassays.

Solid‐Phase Immunoassays for HCV Antibodies in Gamimune® N

Abstract Background and objectives: Occasional false‐positive results for the presence of HCV antibodies occur when testing pH 4 Gamimune® N immune globulin intravenous (human) (IGIV) using commercially available immunoassay kits. We investigated the causes. Materials and methods: EIA test results were compared with Nile red hydrophobic dye binding. Results: There was a strict correlation of reactive EIA results with a larger relative proportion of molecules in a low pH‐dependent hydrophobic conformation. Conversely, the greater the hydrophilic contribution to the population of IgG molecules (favored at neutral pH), the more nonreactive the EIA test results became for the same lots. An IGIV test preparation procedure consisting of pH neutralization followed by 48‐hour incubation at 37°C decreased positive test result outcomes in four different immunoassay formats by shifting the IgG population to a more hydrophilic conformation. Conclusion: The hydrophobic conformation of IgG favored at low pH appears to give rise to significant levels of nonspecific binding in solid phase immunoassays.

Physicochemical characterization of progressive changes in the Xenopus laevis egg envelope following oviductal transport and fertilization

Previous studies have shown that the Xenopus laevis egg envelope exists in three forms with differing ultrastructural, macromolecular, and sperm penetrability properties. The coelomic envelope (CE) is derived from eggs released from the ovary into the body cavity of the female, the vitelline envelope (VE) from eggs which have passed through the oviduct, and the fertilization envelope (FE) from fertilized eggs. In the present study, the physicochemical characteristics of these three envelope types were differentiated. Investigation of envelope solubility, deformability, sulfhydryl reactivity, and hydrophobic dye and ferritin binding capacity demonstrated that profound physicochemical changes occur in envelope conversions CE----VE----FE. The physical strength of the envelopes, as evidenced by deformability studies, ranked FE greater than CE greater than VE. These differences were not accountable by differences in the number of disulfide bonds, although the CE sulfhydryl groups were significantly less accessible than those in the VE or FE. All three envelope forms were hydrophilic in nature, exhibiting little ability to bind 1-anilino-8-naphthalenesulfonic acid. The CE bound greater amounts of ferritin in comparison to the VE and FE, indicating the presence of a basic domain, presumably in the 43-kDa glycoprotein, which is lost upon proteolysis to 41 kDa during the CE----VE conversion. The envelope integrity of all three forms was maintained by both noncovalent and covalent (disulfide) bonds. Measurements of the effect of pH on envelope solubilization indicated the involvement of an ionizable group with pKa of 8.0 in maintaining envelope structure.