Conformation of concanavalin A and its fragments in aqueous solution and organic solvent-water mixtures

Potentized Mercuric chloride and Mercuric iodide enhance alpha-amylase activity in vitro

Mercuric chloride 30c and Mercuric iodide 30c were prepared by successive dilution in 30 steps of 1:100 followed by sonication at 20KHz for 30s at each step. Both were prepared in two media: 90% ethanol and distilled water. Three preparations of Mercuric chloride 30 in water were used: 12-month old, 1-month old and 4-day old. The controls for the water and ethanol-water preparations were pure water 30c and 90% ethanol 30c, respectively. For the three water preparations there were three matched controls of water 30c of the same ages. Each potentized substance or its control was mixed with distilled water 1:100 before testing. Hydrolysis of starch by alpha-amylase was measured by the standard procedure after incubation for 15 min at 27 degrees C. Mercuric chloride 30c and Mercuric iodide 30c in both water and aqueous ethanol media, enhanced enzyme activity significantly, compared to their respective controls. Mercuric chloride 30c, prepared in water 12 months previously, produced no significant change in the enzyme activity compared to its control. We hypothesize that the structure of the active molecule imprinted on water polymers during the process of dynamization. The specifically structured water interacts with the active sites of alpha-amylase, modifying its activity. Ethanol molecules have large non-polar part stabilizing the water structure and thus retaining activity for a longer time.

DNA converts cellular prion protein into the beta-sheet conformation and inhibits prion peptide aggregation

The main hypothesis for prion diseases proposes that the cellular protein (PrP(C)) can be altered into a misfolded, beta-sheet-rich isoform (PrP(Sc)), which in most cases undergoes aggregation. In an organism infected with PrP(Sc), PrP(C) is converted into the beta-sheet form, generating more PrP(Sc). We find that sequence-specific DNA binding to recombinant murine prion protein (mPrP-(23-231)) converts it from an alpha-helical conformation (cellular isoform) into a soluble, beta-sheet isoform similar to that found in the fibrillar state. The recombinant murine prion protein and prion domains bind with high affinity to DNA sequences. Several double-stranded DNA sequences in molar excess above 2:1 (pH 4.0) or 0.5:1 (pH 5.0) completely inhibit aggregation of prion peptides, as measured by light scattering, fluorescence, and circular dichroism spectroscopy. However, at a high concentration, fibers (or peptide aggregates) can rescue the peptide bound to the DNA, converting it to the aggregating form. Our results indicate that a macromolecular complex of prion-DNA may act as an intermediate for the formation of the growing fiber. We propose that host nucleic acid may modulate the delicate balance between the cellular and the misfolded conformations by reducing the protein mobility and by making the protein-protein interactions more likely. In our model, the infectious material would act as a seed to rescue the protein bound to nucleic acid. Accordingly, DNA would act on the one hand as a guardian of the Sc conformation, preventing its propagation, but on the other hand may catalyze Sc conversion and aggregation if a threshold level is exceeded.

Effects of organic solvents on protein structures: observation of a structured helical core in hen egg-white lysozyme in aqueous dimethylsulfoxide

A partly folded state of hen egg-white lysozyme has been characterized in 50% DMSO. Low concentrations of DMSO (< 10%) have little effect on the overall folded conformation of lysozyme as seen from 1H NMR chemical shift dispersion. At increasing DMSO concentrations (> 10%) a cooperative transition of the structure to a new, partially folded state is observed. This transition is essentially complete by approximately 50% DMSO. NMR studies show an overall decrease in chemical shift dispersion with marked broadening of many resonances. A substantial number of backbone and side chain-side chain NOEs suggests the presence of secondary and tertiary interactions in the intermediate state. Tertiary organization of the aromatic residues is also demonstrated by enhanced near-UV circular dichroism and limited exposure of tryptophans as monitored by iodide quenching of fluorescence. The intermediate state exhibits enhanced binding to hydrophobic dyes. Further, the structural transition from this state to a largely unfolded conformation is cooperative. H/D exchange rates of several amide protons and four indole protons of tryptophans (W28, W108, W111, and W123), measured by refolding from 50% DMSO at different time intervals reveal that protection factors are high for the helical domain, whereas NH groups in the triple stranded antiparallel beta-sheet domain are largely solvent-exposed. An ordered hydrophobic core in the intermediate state comprising of helix A, helix B, and helix D is consistent with the high protection factors observed. The structured intermediate in 50% DMSO resembles the early kinetic intermediate observed in the refolding of hen egg white lysozyme, as well as a molten globule state of equine lysozyme at low pH. The results demonstrate the potential use of non-aqueous structure perturbing solvents like DMSO to stabilize partially folded conformations of proteins.

Conformation of bilirubin oxidase in native and denatured states

The conformation of bilirubin oxidase (EC 1.3.3.5) from Myrothecium verrucaria was studied by circular dichroism (CD). The far-UV CD spectrum showed a single minimum at 215 nm and a maximum near 198 nm, suggesting the dominance of beta-sheets. There was another negative band at 187 nm that is absent from the spectra of model alpha-helix or beta-sheet. CD analysis by the method of Chang et al. agreed well with the estimates based on the Chou and Fasman sequence-predictive method, but the Provencher-Glöckner method of CD analysis agreed well with the sequence-predictive method of Garnier et al. At pH 12 the 215- and 187-nm bands completely disappeared and the protein was denatured. This denaturation was accompanied by the appearance of a large positive band at 250 nm, probably due to ionization of tyrosine residues. In 20 mM sodium dodecyl sulfate the magnitude of the 215-nm band increased, but the spectrum transformed to that of partial helices after heating at 100 degrees C. In 6 M guanidine hydrochloride the far-UV CD spectrum was monotonic and became more negative at the lower wavelength limit (near 212 nm), suggesting that the secondary structure of the protein was disrupted. However, the near-UV CD spectrum retained residual aromatic bands even after heating at 100 degrees C. Thus, our denaturation studies suggest that bilirubin oxidase has a rigid tertiary structure.

Conformation of the abortifacient protein pinellin: a circular dichroic study

The conformation of pinellin was studied by circular dichroism, which showed a minimum at 223 nm and a double maximum at 198-200 nm. The protein was rich in beta-sheet (about 40%) with little alpha-helix, based on current CD analyses. It was stable between pH4 and 10 beyond which it unfolded reversibly, but in alkaline solution, prolongly stored at, say, pH 12, it became irreversibly denatured. Thermal denaturation indicated a transition between 55 degrees and 68 degrees C; the solution at 80 degrees C was partially renatured upon air-cooling back to room temperature. Addition of sodium dodecyl sulfate caused a sharp increase in alpha-helix, which leveled off at 0.25 mM surfactant.

Conformation and activity of Phaseolus coccineus var. rubronanus lectin

The conformation of native and denatured Phaseolus coccineus var. rubronanus lectin was studied by circular dichroism (CD) and correlated to the hemagglutinating activity. The far-UV CD spectrum at 25 degrees C showed a broad, negative band around 223 nm and a positive one at 196 nm. CD data analysis of the lectin indicated a beta-sheet-rich protein. At high temperatures, the spectrum was blue-shifted with increasing magnitude; these changes correlated well with the loss of the activity. The conformation of lectin between pH 2 and 10 remained essentially unchanged. At pH 13 the CD spectrum resembled that of unordered form with a negative band near 200 nm and the activity was completely lost. The denatured lectin in 6 M guanidine hydrochloride would be renatured upon diluting the denaturant to 0.75 M; the changes in CD spectrum again correlated well with the loss of the activity. The effect of sodium dodecyl sulfate on the lectin was drastic; it sharply increased the alpha-helix at the expense of the beta-sheet and reduced the activity; the changes reached a plateau above 20 mM surfactant.

Conformation and activity of mannose- and N-acetylgalactosamine-specific lectins from Vicia villosa seeds

The conformation of two Vicia villosa lectins specific for mannose and N-acetylgalactosamine, respectively, was studied by circular dichroism. Both showed a broad negative CD band around 220 nm and a positive one above 190 nm. CD data analysis indicated that they were rich in beta-sheet. However, they differed in conformational stability against extreme pH, at elevated temperature, and in guanidine hydrochloride and sodium dodecyl sulfate solutions. The unusual feature was that the conformation of N-acetylgalactosamine-specific lectin was virtually unaltered in 6 M guanidine hydrochloride and 7.5 mM surfactant.