Circular dichroism spectroscopic assessment of structural changes upon protein thermal unfolding at contrasting pH: Comparison with molecular dynamics simulations.

In most instances, the usual fastness of protein unfolding events hinders determining changes in secondary structures associated with this process because these determinations rely on the recording of high-resolution circular dichroism (CD) spectra. In this work, far-UV CD spectra, recorded at ten-minute intervals, were used to evaluate the time course followed by four classes of secondary structures in the slow temperature-induced unfolding of yeast triosephosphate isomerase (yTIM) under distinct pH conditions. CONTIN-LL and SELCON3 algorithms were used for the deconvolution of spectra. Both algorithms furnished helix and unordered structure contents that changed according to first-order kinetics, agreeing with the behavior shown by CD data at specific wavelengths. Analyses of unfolded yTIM spectra, using a dataset that includes spectra of unfolded proteins and either one of the two algorithms, clearly showed a more unordered protein structure at high pH; this finding was corroborated with analysis of the difference spectra. Molecular dynamics (MD) simulations performed with AMBER and OPLS force fields resulted in more extensive loss of helices and gain in coils at high pH, in agreement with spectroscopic results. However, structural differences between low- and high-pH unfolded yTIM were relatively small. Comparison of results from CD and MD thus point to the need of fine-tuning of MD procedures.

Discovery of a new non-substrate inhibitor of the 26.5 kDa glutathione transferase from Taenia solium by virtual screening.

The inappropriate use of anthelmintics, such as praziquantel and albendazole, has generated resistance and the need to develop new drugs. Glutathione transferases, GSTs, are bisubstrate dimeric enzymes that constitute the main detoxification mechanism against electrophiles, drugs and oxidative damage in Taenia solium. Therefore, GSTs are important targets for the development of new anthelmintics. In this work, we reported a successful virtual screen aimed at the identification of novel inhibitors of a 26.5 kDa GST from T. solium (TsGST26). We found that a compound, i7, able to inhibit selectively TsGST26 concerning human GSTs, showing a non-competitive inhibition mechanism towards substrate glutathione with a Ki (GSH) of 55.7 µM and mixed inhibition towards the electrophilic substrate 1-chloro-2,4-dinitrobenzene with a Ki (CDNB) of 8.64 µM. These results are in agreement with those of docking simulations, which showed i7 binds a site adjacent to the electrophilic site and furthest from the glutathione site.

Complex kinetics and residual structure in the thermal unfolding of yeast triosephosphate isomerase.

BACKGROUND: Saccharomyces cerevisiae triosephosphate isomerase (yTIM) is a dimeric protein that shows noncoincident unfolding and refolding transitions (hysteresis) in temperature scans, a phenomenon indicative of the slow forward and backward reactions of the native-unfolded process. Thermal unfolding scans suggest that no stable intermediates appear in the unfolding of yTIM. However, reported evidence points to the presence of residual structure in the denatured monomer at high temperature. RESULTS: Thermally denatured yTIM showed a clear trend towards the formation of aggregation-prone, ß-strand-like residual structure when pH decreased from 8.0 to 6.0, even though thermal unfolding profiles retained a simple monophasic appearance regardless of pH. However, kinetic studies performed over a relatively wide temperature range revealed a complex unfolding mechanism comprising up to three observable phases, with largely different time constants, each accompanied by changes in secondary structure. Besides, a simple sequential mechanism is unlikely to explain the observed variation of amplitudes and rate constants with temperature. This kinetic complexity is, however, not linked to the appearance of residual structure. Furthermore, the rate constant for the main unfolding phase shows small, rather unvarying values in the pH region where denatured yTIM gradually acquires a ß-strand-like conformation. It appears, therefore, that the residual structure has no influence on the kinetic stability of the native protein. However, the presence of residual structure is clearly associated with increased irreversibility. CONCLUSIONS: The slow temperature-induced unfolding of yeast TIM shows three kinetic phases. Rather than a simple sequential pathway, a complex mechanism involving off-pathway intermediates or even parallel pathways may be operating. ß-strand-type residual structure, which appears below pH 8.0, is likely to be associated with increased irreversible aggregation of the unfolded protein. However, this denatured form apparently accelerates the refolding process.

Antioxidant capacity and structural changes of human serum albumin from patients in advanced stages of diabetic nephropathy and the effect of the dialysis.

Changes in the antioxidant capacity of albumin and alterations of the albumin structural conformation were examined in patients in advanced stages of diabetes nephropathy. Human serum albumin was purified from diabetic patients in pre-dialysis (glomerular filtration rate [GFR] between 15 and 29 ml min(-1) 1.73 m(-2)) and those in dialysis (GFR ≤ 15 ml min(-1) 1.73 m(-2)) and then compared with albumin from patients with a normal GFR (>90 ml min(-1) m(-2)). We evaluated the antioxidant capacity of albumin using an enhanced chemiluminescence-based assay and thiol group content, and the structural changes were evaluated by circular dichroism and fluorescence spectroscopy. The antioxidant capacity and thiol content of albumin from patients in advanced stages of diabetic nephropathy were markedly reduced. The circular dichroism spectra showed a mean albumin α-helix content reduction from 44 to 37 % and from 44 to 30 % between the control group and pre-dialysis and dialysis patients, respectively. Additionally, the fluorescence intensity was reduced by 4.2 and 13 % for the groups 4 and 5, respectively, in relation with the control. These data provide evidence for the partial denaturation of albumin and exacerbated oxidative stress among patients in advanced stages of diabetes nephropathy before and even after dialysis.

α-Lactalbumin nanoparticles prepared by desolvation and cross-linking: structure and stability of the assembled protein.

A key step in the preparation of cross-linked protein nanoparticles involves the desolvation of proteins with an organic solvent, which is thought to act by modulating hydrophobic interactions. However, to date, no study has examined the conformational changes that proteins undergo during the assembly process. In this work, by using several biophysical techniques (CD spectroscopy, DSC, TEM, etc.), we studied spheroidal nanoparticles made from bovine α-lactalbumin cross-linked with glutaraldehyde in the presence of acetone. Within the nanoparticle, the polypeptide chain acquires a ß-strand-like conformation (completely different from the native protein in secondary and tertiary structure) in which several side chains likely become available for reacting with glutaraldehyde. A multiplicity of cross-linking sites, together with the polymeric nature of glutaraldehyde, may thus explain the low dry-weight fraction of protein that was found in the nanoparticles. Although covalent bonds undoubtedly constitute the main source for nanoparticle stability, noncovalent interactions also appear to play a role in this regard.

Additive effect of single amino acid replacements on the kinetic stability of ß-glucosidase B.

Previously, we applied in vitro evolution to generate the thermoresistant triple mutant H62R/N223Y/M319I of ß-glucosidase B (BglB) from Paenibacillus polymyxa. In order to dissect the energetic contributions to protein stabilization achieved by these mutations, we measured the kinetic constants of the heat denaturation of wild type BglB, the triple mutant and the three single mutants (H62R, N223Y, M319I) by circular dichroism at various temperatures. Our results show that all four mutants delayed the denaturation process. Based on the Transition State theory, the increase of the activation barrier for the thermal denaturation of the triple mutant (ΔΔG ( N→TS )) is equivalent to that produced by the sum of the contributions from the three single mutants, whose C ( ß ) s are located at least 18 Å apart. This analysis provides a formal demonstration of the generally accepted idea that protein thermal stability can be increased through sequential addition of individual mutations. Each of the mutations described here contribute in part to the overall effect, which in this case affects the unfolding barrier.

Thermal denaturation of ß-glucosidase B from Paenibacillus polymyxa proceeds through a Lumry-Eyring mechanism.

ß-glucosidase B (BglB), 1,4-ß-D: -glucanohydrolase, is an enzyme with various technological applications for which some thermostable mutants have been obtained. Because BglB denatures irreversibly with heating, the stabilities of these mutants are assessed kinetically. It, therefore, becomes relevant to determine whether the measured rate constants reflect one or several elementary kinetic steps. We have analyzed the kinetics of heat denaturation of BglB from Paenibacillus polymyxa under various conditions by following the loss of secondary structure and enzymatic activity. The denaturation is accompanied by aggregation and an initial reversible step at low temperatures. At T ≥ T ( m ), the process follows a two-state irreversible mechanism for which the kinetics does not depend on the enzyme concentration. This behavior can be explained by a Lumry-Eyring model in which the difference between the rates of the irreversible and the renaturation steps increases with temperature. Accordingly, at high scan rates (≥1 °C min(-1)) or temperatures (T ≥ T ( m )), the measurable activation energy involves only the elementary step of denaturation.

Effect of a new ionic pair on the unfolding activation barrier of beta-glucosidase B.

Thermal unfolding kinetics of beta-glucosidase B from Paenibacillus polymyxa and its thermoresistant mutant H62R were determined from far-UV circular dichroism (CD) measurements at different temperatures. The unfolding of both enzymes followed simple two-state kinetics. The new ionic pair formed between Arg62 and Glu429 in the H62R variant did not change substantially the enzyme structure as judged by far-UV CD and fluorescence spectra, but produced an increase in the unfolding activation barrier of 0.95 +/- 0.10 kcal mol(-1), in good agreement with the energetic contribution reported for surface salt bridges in proteins. Eyring's analysis of the unfolding kinetic constants showed that the activation enthalpies for thermal denaturation of both enzymes were essentially the same. Thus, the greater kinetic stability rendered by the salt bridge seems to be due to a reduction in the activation entropy.