Unfolding and refolding of porcine odorant binding protein in guanidinium hydrochloride: equilibrium studies at neutral pH

Probing the role of protein conformational changes in the mechanism of prenylated-FMN-dependent phenazine-1-carboxylic acid decarboxylase

Phenazine-1-carboxylic acid decarboxylase (PhdA) is a prenylated-FMN-dependent (prFMN) enzyme belonging to the UbiD family of decarboxylases. Many UbiD-like enzymes catalyze (de)carboxylation reactions on aromatic rings and conjugated double bonds and are potentially valuable industrial catalysts. We have investigated the mechanism of PhdA using a slow turnover substrate, 2,3-dimethylquinoxaline-5-carboxylic acid (DQCA). Detailed analysis of the pH dependence and solvent deuterium isotope effects associated with the reaction uncovered unusual kinetic behavior. At low substrate concentrations, a substantial inverse solvent isotope effect (SIE) is observed on Vmax/KM of ∼ 0.5 when reaction rates of DQCA in H2O and D2O are compared. Under the same conditions, a normal SIE of 4.15 is measured by internal competition for proton transfer to the product. These apparently contradictory results indicate that the SIE values report on different steps in the mechanism. A proton inventory analysis of the reaction under Vmax/KM and Vmax conditions points to a "medium effect" as the source of the inverse SIE. Molecular dynamics simulations of the effect of D2O on PhdA structure support that D2O reduces the conformational lability of the enzyme and results in a more compact structure, akin to the active, "closed" conformer observed in crystal structures of some UbiD-like enzymes. Consistent with the simulations, PhdA was found to be more stable in D2O and to bind DQCA more tightly, leading to the observed rate enhancement under Vmax/KM conditions.

Odorant-binding proteins of mammals

Odorant-binding proteins (OBPs) of vertebrates belong to the lipocalin superfamily and perform a dual function: solubilizing and ferrying volatile pheromones to the olfactory receptors, and complexing the same molecules in specialized glands and assisting their release into the environment. Within vertebrates, to date they have been reported only in mammals, apart from two studies on amphibians. Based on the small number of OBPs expressed in each species, on their sites of production outside the olfactory area and their presence in biological fluids known to be pheromone carriers, such as urine, saliva and sexual secretions, we conclude that OBPs of mammals are specifically dedicated to pheromonal communication. This assumption is further supported by the observation that some OBPs present in biological secretions are endowed with their own pheromonal activity, adding renewed interest to these proteins. Another novel piece of evidence is the recent discovery that glycosylation and phosphorylation can modulate the binding activity of these proteins, improving their affinity to pheromones and narrowing their specificity. A comparison with insects and other arthropods shows a completely different scenario. While mammalian OBPs are specifically tuned to pheromones, those of insects, which are completely different in sequence and structure, include carriers for general odorants in addition to those dedicated to pheromones. Additionally, whereas mammals adopted a single family of carrier proteins for chemical communication, insects and other arthropods are endowed with several families of semiochemical-binding proteins. Here, we review the literature on the structural and functional properties of vertebrate OBPs, summarize the most interesting new findings and suggest possible exciting future developments.

Biotechnological applications of mammalian odorant-binding proteins

The olfactory system of mammals allows the detection and discrimination of thousands of odors from the environment. In mammals, odorant-binding proteins (OBPs) are considered responsible to carry odorant molecules across the aqueous nasal mucus to the olfactory receptors (ORs). The three-dimensional structure of these proteins presents eight antiparallel β-sheets and a short α-helical segment close to the C terminus, typical of the lipocalins family. The great ability of OBPs to bind differentiated ligand molecules has driven the research to understand the mechanisms underlying the OBP function in nature and the development of advanced biotechnological applications. This review describes the role of mammalian OBPs in the olfactory perception, highlighting the influence of several key parameters (amino acids, temperature, ionic strength, and pH) in the formation of the OBP/ligand complex. The information from the literature regarding OBP structure, affinity, the strength of binding, and stability inspiring the development of several applications herein detailed.

Stability of OBPs

Odorant binding proteins (OBPs) are small proteins, some of which bind odorants with high specificity. OBPs are relatively easy to produce and show a pronounced stability toward thermal and chemical denaturation. This high stability renders OBPs attractive candidates for the development of odorant detections systems. Unfortunately, binding of odorants is not easy to quantify due to lack of spectroscopic signals upon binding. Therefore, a possible approach to detect binding is to employ the shift in thermal or chemical stability upon ligand-protein interaction. Being a rather indirect approach, the experimental setup should be done with care. Here, the experimental results on stability of OBPs are summarized and issues which should be considered when performing stability experiments are discussed.

Effect of electron beam irradiation on the structural characteristics and functional properties of rice proteins

A study of the structural and functional changes of rice proteins (RPs) induced by electron beam irradiation (EBI) at 5 kGy, 10 kGy, 20 kGy, and 30 kGy was performed. The microcosmic surface structures of the RPs were changed and fragmented due to irradiation damage occurring on the RP surfaces. The changes in the UV visible spectra, intrinsic fluorescence spectra, surface hydrophobicity and SH and SS group contents indicated that the RPs unfolded after EBI treatment. In addition, the degree of conformational change was increased with increasing EBI treatment doses. FTIR analysis showed that the secondary structure redistributed, showing decreases in α-helices and concomitant increases in β-sheets, β-turns and random coils. The functional properties, emulsifying abilities, water adsorption capacities and oil adsorption capacities of the irradiated RPs improved dose-dependently, with maximums occurring at 30 kGy. The foaming properties were also enhanced by EBI; however, this effect was not dose-dependent. In contrast, all of the samples irradiated by electron beams presented lower emulsion stability than the control (0 kGy). These results provide a theoretical basis for the application of EBI in improving protein properties in the future.

A study of the structural and functional changes of rice proteins (RPs) induced by electron beam irradiation (EBI) at 5 kGy, 10 kGy, 20 kGy, and 30 kGy was performed.

A possible mechanism for enhancing the antioxidant activity by pulsed electric field on pine nut peptide Glutamine-Tryptophan-Phenylalanine-Histidine

The aim of this study was to investigate the possible mechanism for increasing the antioxidant activity on peptide Glutamine-Tryptophan-Phenylalanine-Histidine (QWFH) from pine nut (Pinus koraiensis) protein by a pulsed electric field (PEF). The antioxidant capacity of PEF-treated QWFH increased significantly (p < 0.05) through 1,1-diphenyl-2-pycryl-hydrazyl radical scavenging and oxygen radical absorbance capacity assays. A series of mechanism exploration methods, including reversed-phase high-performance liquid chromatography, ultraviolet absorption spectroscopy, intrinsic fluorescence spectra, circular dichroism spectroscopy, and 1D and 2D nuclear magnetic resonance spectroscopies, were applied. QWFH chain was not cleaved by the PEF treatment, while more aromatic amino acids (Trp and Phe) were exposed to the polar solvent. In addition, the content of random coil of QWFH in solution was increased and its active hydrogen was changed after the PEF treatment. Moreover, the long-range connectivity between OH (14.234 ppm) on 4-H His, N_α H (7.295 ppm) on 3-H Phe, and N_α H₂ (6.801 ppm) on 1-H Gln disappeared due to the PEF. PRACTICAL APPLICATIONS: Antioxidants have been extensively explored as a potential drug to decrease the risk of certain chronic diseases. Food-derived bioactive compounds are safer than synthetic antioxidants for human health and well-being. And the PEF technology is one of the promising processes for improving the biological activity of food components. Currently, the activity of the antioxidant peptide QWFH increased after a PEF treatment. The basic structure of QWFH did not change, but the unfolding of the secondary structure on the peptide chain and the displacement of the active hydrogen increased the antioxidant activity of the peptide. Thus, the range of application of a PEF has been expanded and it also benefited the development of more functional factors in the functional food industry.

The porcine odorant-binding protein as molecular probe for benzene detection

In recent years, air pollution has been a subject of great scientific and public interests for the strong impact on human health. Air pollution is due to the presence in the atmosphere of polluting substances, such as carbon monoxide, sulfur and nitrogen oxides, particulates and volatile organic compounds (VOCs), derived predominantly from various combustion processes. Benzene is a VOC belonging to group-I carcinogens with a toxicity widely demonstrated. The emission limit values and the daily exposure time to benzene (TLV-TWA) are 5μg/m3 (0.00157 ppm) and 1.6mg/m3 (0.5 ppm), respectively. Currently, expensive and time-consuming analytical methods are used for detection of benzene. These methods require to perform a few preliminary steps such as sampling, and matrices pre-treatments. In addition, it is also needed the support of specialized personnel. Recently, single-walled carbon nanotube (SWNTs) gas sensors with a limit detection (LOD) of 20 ppm were developed for benzene detection. Other innovative bioassay, called bio-report systems, were proposed. They use a whole cell (Pseudomona putida or Escherichia coli) as molecular recognition element and exhibit a LOD of about 10 μM. Here, we report on the design of a highly sensitive fluorescence assay for monitoring atmospheric level of benzene. For this purpose, we used as molecular recognition element the porcine odorant-binding protein (pOBP). 1-Aminoanthracene was selected as extrinsic fluorescence probe for designing a competitive fluorescence resonance energy transfer (FRET) assay for benzene detection. The detection limit of our assay was 3.9μg/m3, a value lower than the actual emission limit value of benzene as regulated by European law.

Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet

Vibrational structure in the near-UV circular dichroism (CD) spectra of proteins is an important source of information on protein conformation and can be exploited to study structure and folding. A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper interpretation of and insight into biophysical and simulation studies of protein dynamics and folding. We have developed new models of the aromatic side chain chromophores toluene, p-cresol and 3-methylindole, which incorporate ab initio calculations of the Franck-Condon effect into first principles calculations of CD using an exciton approach. The near-UV CD spectra of 40 proteins are calculated with the new parameter set and the correlation between the computed and the experimental intensity from 270 to 290 nm is much improved. The contribution of individual chromophores to the CD spectra has been calculated for several mutants and in many cases helps rationalize changes in their experimental spectra. Considering conformational flexibility by using families of NMR structures leads to further improvements for some proteins and illustrates an informative level of sensitivity to side chain conformation. In several cases, the near-UV CD calculations can distinguish the native protein structure from a set of computer-generated misfolded decoy structures.

Characterization of a deswapped triple mutant bovine odorant binding protein

The stability and functionality of GCC-bOBP, a monomeric triple mutant of bovine odorant binding protein, was investigated, in the presence of denaturant and in acidic pH conditions, by both protein and 1-aminoanthracene ligand fluorescence measurements, and compared to that of both bovine and porcine wild type homologues. Complete reversibility of unfolding was observed, though refolding was characterized by hysteresis. Molecular dynamics simulations, performed to detect possible structural changes of the monomeric scaffold related to the presence of the ligand, pointed out the stability of the β-barrel lipocalin scaffold.

The role of water in drug–receptor interactions

The idea that liquid water is not a uniform and random arrangement of molecules has been taken very seriously by the scientific community. Many experimental and computational investigations show that clathrate- or ice-like structures probably exist at a short time scale in solution. We have designed a new program to simulate water structure around solutes. Our model is based on the geometrical constraints of hydrogen bonding in order to be capable of producing clathrate-like structures. Simulations with small molecules and bio-molecules, using the new software, produce networks of water with specific patterns made of small water rings. The water structures built are consistent with the classification of molecules in terms of structure breaking and making. This approach may give insight into, and a more accurate description of, drug-receptor interactions. The results also suggest that water structure may impart sufficient energy to modify the conformational space of organic molecules through hydrogen bonding.

Effect of heat and pH denaturation on the structure and conformation of recombinant human hepatic stimulator substance

Hepatic stimulator substance (HSS) is a novel liver-specific growth-promoting factor. Although HSS has been successfully crystallized, several properties of this protein have yet to be determined. This study shows that recombinant human HSS (rhHSS) is a dimer with a molecular mass of 31 kDa, the protein is weakly acidic and has an isoelectric point (pI) of 4.50. RhHSS was able to protect hepatoma cells from H2O2-induced apoptosis and to stimulate cell growth. The recombinant protein was thermostable up to 80 degrees C and resistant to changes in pH, as determined by synchronous fluorescence and far-UV circular dichroism (CD). Within the range of pH 4.0-10.0, rhHSS assumed a folded conformation identical to the secondary structure of the original, native protein and a native-like far-UV CD spectrum. Denatured rhHSS could be partly reconstituted with respect to its structure, but not its activity. Thus, rhHSS is a structurally stable protein insensitive to thermal and acid-alkaline denaturation.

Three-stage refolding/unfolding of the dual-color β-subunit in R-phycocyanin from Polysiphonia urceolata

The conformational changes during refolding and unfolding of the dual-color beta-subunit in R-phycocyanin (R-PC) were monitored by the spectra, fluorescence anisotropy, and FRET. It was observed that both of the refolding and unfolding of the beta-subunit would undergo a three-stage conformational change, but in a reverse order. During the refolding process, at the first stage, the configuration of the tetrapyrrole chromophores transformed from the cyclohelical to the extended one, suggested by the blue-shifted spectra. At the second stage, recovery of the hydrogen-bond and hydrophobic interaction network fixed the chromophore in a more rigid configuration, suggested by a linear increase in the total fluorescence yield. At the third stage, the increase of the FRET efficiency suggested a protein-framework movement that made the two chromophores closer or/and into a more parallel orientation. The fluorescence anisotropy further confirmed the three-stage model.

Attributes of glycosylation in the establishment of the unfolding pathway of soybean agglutinin

Soybean agglutinin (gSBA) is a tetrameric legume lectin, each of whose subunits are glycosylated. Earlier studies have shown that this protein shows exceptionally high stability in terms of free energy of unfolding when compared to other proteins from the same family. This article deals with the unfolding reactions of the nonglycosylated recombinant form of the protein rSBA and its comparison with the glycosylated counterpart gSBA. The nonglycosylated form features a lower stability when compared to the glycosylated form. Further, the unfolding pathways in the two are widely different. Although the glycosylated form undergoes a simple two-state unfolding, the nonglycosylated species unfolds via a compact monomeric intermediate that is not a molten globule. Representative isothermal and thermal denaturation profiles show that glycosylation accounts for a stabilization of approximately 9 kcal/mol of the tetramer, whereas the difference in T(m) between the two forms is 26 degrees C. Computational studies on the glycan-protein interactions at the noncanonical interface of the protein show that quite a number of hydrogen bond and hydrophobic interactions stabilize the glycoprotein tetramer.

Lipocalins - a family portrait

Lipocalins are a widely distributed group of proteins whose common feature is the presence of six-or eight-stranded beta-barrel in their tertiary structure and highly conservative motifs short conserved region, (SCR) in their amino acid sequences. The presence of three SCRs is typical for kernel lipocalins, while outlier lipocalins have only one or two such regions. Owing to their ability to bind and transport small, hydrophobic molecules, lipocalins participate in the distribution of such substances. However, the physiological significance of lipocalins is not limited to transfer processes. They play an important role in the regulation of immunological and developmental processes, and are also involved in the reactions of organisms to various stress factors and in the pathways of signal transduction. Of special interest is the enzymatic activity found in a few members of the lipocalin family, as well as the interaction with natural membranes, both directly with lipids and through membrane-localized protein receptors.

Oligomerization endows enormous stability to soybean agglutinin: a comparison of the stability of monomer and tetramer of soybean agglutinin

Soybean agglutinin is a tetrameric legume lectin, each of whose subunits are glycosylated. This protein shows a very high degree of stability when compared to the other proteins of the same family. In a previous work, it was shown that the unusual stability of the protein is due to a high degree of subunit interactions. In this study we present the thermodynamic parameters for the stability of soybean agglutinin monomer. The monomeric species is found at pH 2 and below which it is most populated at pH 1.9, as evident from size-exclusion chromatographic and dynamic light scattering studies. The analyses of circular dichroism and fluorescence spectroscopy suggest that the monomer is well folded, and that it has certain characteristic features when compared to its tetrameric counterpart. The conformational stabilities of the tetramer and the monomer at the temperature of their maximum stabilities (310 K) are 59.2 kcal/mol and 9.8 kcal/mol, respectively, indicating that oligomerization contributes significantly to the stability of the native molecule. Also, the T(g) difference for the two forms of the protein is approximately 40 K, whereas the difference in DeltaC(p) is only 1.6 kcal/mol/K. This suggests that the major hydrophobic core is present in the monomer itself, and that oligomerization involves mainly ionic interactions.

Role of the disulphide bridge in folding, stability and function of porcine odorant binding protein: spectroscopic equilibrium studies on C63A/C155A double mutant

Porcine odorant binding protein (pOBP) contains a single disulphide bridge linking residues Cys63 and Cys155. In order to get information on the role played by this crosslink in determining the structural and functional properties of the protein, we substituted these two Cys residues with two Ala residues by site directed mutagenesis and investigated the changes in folding, stability and functional features, as detected by fluorescence and circular dichroism measurements. In particular, we studied both chemical and thermal unfolding/refolding processes under equilibrium conditions, the first induced by guanidinium hydrochloride and the second by raising the temperature from 15 to 90 degrees C. Chemical unfolding curves, as obtained from intrinsic fluorescence and far-UV circular dichroism data, can be fitted by a simple two-state cooperative sigmoidal function; however, their partial overlap (C(1/2)=0.57+/-0.05 from fluorescence and 0.66+/-0.03 from CD) suggests the formation of an intermediate, which lacks tertiary structural features. Thermal unfolding was found to be reversible if the protein was heated up to 65 degrees C, but irreversible above that temperature because of aggregation. The thermodynamic unfolding parameters of this double mutant protein, when compared to those of the wild type protein, clearly point out the important role played by the disulphide bridge on the stability and function of this protein family and probably of many other lipocalins.

Cloning, expression, and refolding of a secretory protein ESAT-6 of Mycobacterium tuberculosis

A DNA encoding the 6-kDa early secretory antigenic target (ESAT-6) of Mycobacterium tuberculosis was inserted into a bacterial expression vector of pQE30 resulting in a 6x His-esat-6 fusion gene construction. This plasmid was transformed into Escherichia coli strain M15 and effectively expressed. The expressed fusion protein was found almost entirely in the insoluble form (inclusion bodies) in cell lysate. The inclusion bodies were solubilized with 8M urea or 6M guanidine-hydrochloride at pH 7.4, and the recombinant protein was purified by Ni-NTA column. The purified fusion protein was refolded by dialysis with a gradient of decreasing concentration of urea or guanidine hydrochloride or by the size exclusion protein refolding system. The yield of refolded protein obtained from urea dialysis was 20 times higher than that from guanidine-hydrochloride. Sixty-six percent of recombinant ESAT-6 was successfully refolded as monomer protein by urea gradient dialysis, while 69% of recombinant ESAT-6 was successfully refolded as monomer protein by using Sephadex G-200 size exclusion column. These results indicate that urea is more suitable than guanidine-hydrochloride in extracting and refolding the protein. Between the urea gradient dialysis and the size exclusion protein refolding system, the yield of the monomer protein was almost the same, but the size exclusion protein refolding system needs less time and reagents.