Addition Of Guanidine Hydrochloride Research Articles

Unfolding of Helical Poly(L-Glutamic Acid) in N,N-Dimethylformamide Probed by Pyrene Excimer Fluorescence (PEF).

The denaturation undergone by α–helical poly(L-glutamic acid) (PLGA) in N,N-dimethylformamide upon addition of guanidine hydrochloride (GdHCl) was characterized by comparing the fluorescence of a series of PLGA constructs randomly labeled with the dye pyrene (Py-PLGA) to that of a series of Py-PDLGA samples prepared from a racemic mixture of D,L-glutamic acid. The process of pyrene excimer formation (PEF) was taken advantage of to probe changes in the conformation of α–helical Py-PLGA. Fluorescence Blob Model (FBM) analysis of the fluorescence decays of the Py-PLGA and Py-PDLGA constructs yielded the average number (<Nblob>) of glutamic acids located inside a blob, which represented the volume probed by an excited pyrenyl label. <Nblob> remained constant for randomly coiled Py-PDLGA but decreased from ~20 to ~10 glutamic acids for the Py-PLGA samples as GdHCl was added to the solution. The decrease in <Nblob> reflected the decrease in the local density of PLGA as the α–helix unraveled in solution. The changes in <Nblob> with GdHCl concentration was used to determine the change in Gibbs energy required to denature the PLGA α–helix in DMF. The relationship between <Nblob> and the local density of macromolecules can now be applied to characterize the conformation of macromolecules in solution.

Hemoglobin and myoglobin stabilization by heme-fluoride complexes

Under physiological conditions, hemoglobin (Hb) and myoglobin (Mb) are subject to autoxidation, leading to the formation of ferric heme proteins with weakened globular structures and resulting in the loss of the heme cofactor. To gain further insights into the role of the heme pocket in the stabilization of the heme-containing proteins (holo-Mb and holo-Hb), the relative stabilities of heme-bound fluoride complexes (Mb-F and Hb-F) were examined under denaturing conditions. The electronic spectra of the heme proteins were followed upon addition of guanidine hydrochloride (GuHCl) and under denaturation-induced acidification. In the presence of ~ 2 M GuHCl, the heme-bound fluoride complexes are 27 – 46% more stable than metaquo Mb and Hb and about 50% more stable under acidic conditions. Mb and Hb denaturation equilibria at 25 and 40 °C were analyzed by using two-state and three-state models, respectively. Under GuHCl-induced and acid-induced denaturations, Mb-F and Hb-F behave as a two-state process. In addition, the affinity for fluoride under these denaturing conditions were determined. The dissociation constants (Kd) for fluoride binding in Hb and Mb under 1.5 M GuHCl are slightly greater than the measured Kd without GuHCl, which we attribute to the presence of molten-globular holo protein intermediates that are not favorable for fluoride binding. This study shows that the measured fluoride affinities in the presence of GuHCl at various temperatures and the effects of pH on the Kd can provide additional thermodynamic properties of Mb and Hb denaturation processes at low pH.

Hemoglobin and Myoglobin Stabilization by Heme-Fluoride Complexes

Under physiological conditions, hemoglobin (Hb) and myoglobin (Mb) are subject to autoxidation, leading to the formation of ferric heme proteins with weakened globular structures and resulting in the loss of the heme cofactor. To gain further insights into the role of the heme pocket in the stabilization of the heme-containing proteins (holo-Mb and holo-Hb), the relative stabilities of heme-bound fluoride complexes (Mb-F and Hb-F) were examined under denaturing conditions. The electronic spectra of the heme proteins were followed upon addition of guanidine hydrochloride (GuHCl) and under denaturation-induced acidification. In the presence of ~2M GuHCl, the heme-bound fluoride complexes are 27 – 46% more stable than ferric Hb and Mb. In addition, the affinity for fluoride under these denaturing conditions were determined. The dissociation constants ( K d ) for fluoride binding in Hb and Mb under 1.5 M GuHCl are slightly greater than the measured K d without GuHCl, which we attribute to the presence of molten-globular holo protein intermediates that are not favorable for fluoride binding. Under acidic denaturation, the acid-induced denaturing curves of Mb-F and Hb-F are -0.3 and -0.5 pH units shifted relative to ferric Hb and Mb, which show that the heme-bound fluoride proteins are more resistant to acid denaturation. This study shows that the measured fluoride affinities in the presence of GuHCl at various temperatures and the effects of pH on the K d can provide additional thermodynamic properties of Hb and Mb denaturation processes at low pH, where interactions between the heme pocket and the heme-bound fluoride are much stronger.

Solution effects on the self-association of a water-soluble peptoid.

A desire to replicate the structural and functional complexity of proteins with structured, sequence-specific oligomers motivates study of the structural features of water-soluble peptoids (N-substituted glycine oligomers). Understanding the molecular-level details of peptoid self-assembly in water is essential to advance peptoids' application as novel materials. Peptoid 1, an amphiphilic, putatively helical peptoid previously studied in our laboratory, shows evidence of self-association in aqueous solution. In this work, we evaluate how changes to aqueous solution conditions influence the self-association of 1. We report that changes to pH influence the fluorescence and CD spectroscopic features as well as the peptoid's interaction with a solvatochromic fluorophore and its apparent size as estimated by size exclusion chromatography. Addition of guanidine hydrochloride and ammonium sulfate also modulate spectroscopic features of the peptoid, its interaction with a solvatochromic fluorophore, and its elution in size exclusion chromatography. These data suggest that the ordering of the self-assembly changes in response to pH and with solvent additives and is more ordered at higher pH and in the presence of guanidine hydrochloride. The deeper understanding of the self-association of 1 afforded by these studies informs the design of new stimuli-responsive peptoids with stable tertiary or quaternary structures.

Comparison of parasite loads in serum and blood samples from patients in acute and chronic phases of Chagas disease - CORRIGENDUM.

Molecular methods have been developed for the detection and quantification of Trypanosoma cruzi DNA in blood samples from patients with Chagas disease. However, aspects of sample processing necessary for quantitative real-time PCR (qPCR), such as the addition of guanidine hydrochloride to whole blood samples, may limit timely access to molecular diagnosis. We analysed 169 samples from serum and guanidine-EDTA blood (GEB) obtained from patients in acute and chronic phases of Chagas disease. We applied qPCR targeted to the satellite DNA region. Finally, we compared the parasite loads and cycle of threshold values of the qPCR. The results confirmed the usefulness of serum samples for the detection and quantification of parasite DNA in patients with Chagas disease, especially in the acute phase. However, the parasite loads detected in serum samples from patients in the chronic phase were lower than those detected in GEB samples. The epidemiological implications of the findings are herein discussed.

A New Biodegradable Injection Moulded Bioplastic from Modified Soy Meal and Poly (butylene adipate-co-terephthalate): Effect of Plasticizer and Denaturant

Soy meal, a co-product of the soy oil-based biodiesel industry, has up to 50 % protein content. The main aim of this work was to develop value-added application for soy meal. Soy meal was plasticized by glycerol and water, denatured by the addition of guanidine hydrochloride (GHCl), and then blended with poly (butylene adipate-co-terephthalate) (PBAT), petroleum based tough biodegradable polymer. Characterization by FTIR spectroscopy confirmed that soy meal was plasticized and denatured. The blends of PBAT/soy meal (SM), PBAT/plasticized soy meal and PBAT/GHCl modified plasticized soy meal (mPSM) were fabricated by industry prevalent extrusion and injection molding process. The developed bioblends were characterized by thermal and mechanical testing. One of the important outcomes of this research was that elongation of the bioblend was found to increase by 80 % after plasticization and denaturation of soy meal. Scanning electron microscope analysis showed that PBAT/mPSM blends have smoother surfaces and better internal structures than the other two.

Self-Assembly, Foaming, and Emulsifying Properties of Sodium Alkyl Carboxylate/Guanidine Hydrochloride Aqueous Mixtures

Unsaturated fatty acids may be extracted from various agricultural resources and are widely used as soaps in the industry. However, there also exist a large variety of saturated and hydroxy fatty acids in nature, but their metal salts crystallize at room temperature in water, hampering their use in biological and chemical studies or for industrial applications. Addition of guanidine hydrochloride (GuHCl) to sodium salt of myristic acid has been shown to prevent its crystallization in water, forming stable flat bilayers at room temperature. Herein, we extend this finding to two other saturated fatty acids (palmitic and stearic acids) and two hydroxyl fatty acids (juniperic and 12 hydroxy stearic acids) and study more deeply (by using small angle neutron scattering) the supramolecular assemblies formed in both saturated and hydroxyl fatty acid systems. In addition, we take the advantage that crystallization no longer occurs at room temperature in the presence of GuHCl to study the foaming and emulsifying properties of those fatty acid dispersions. Briefly, our results show that all fatty acids, even juniperic acid, which is a bola lipid, are arranged in a bilayer structure that may be interdigitated. Depending on the nature of the fatty acid, the systems exhibit good foamability and foam stability (except for juniperic acid), and emulsion stability was good. Those findings should be of interest for using saturated long chain (and hydroxyl) fatty acids as surfactants for detergency or even materials chemistry.

Spectroscopic studies reveal conformational flexibility of intrinsically unstructured protein HYPK

The chaperone-like huntingtin-interacting protein, HYPK, has unusual biophysical behavior like an intrinsically unstructured protein (IUP). The protein exists as a (pre-) molten globule with ~37% residual structure and shows com- paction in presence of Ca++. HYPK contains no intrinsic fluorophore other than a single tyrosine and displays an anomalous fluorescence peak at around 340 nm. The anomalous peak is re- duced to 303 nm by the addition of guanidine hydrochloride and at low pH, concomitant with the emission spectrum of L-tyrosine. At high pH the peak is shifted to ~350 nm with a reduction in intensity. In presence of sodium perchlorate there is no shift in HYPK fluorescence emission peak from ~340 nm suggesting localization of the lone tyrosine residue in helical regions. In CD experiments, however, a shift in local secondary structure is noticed upon perchlorate treatment. Acrylamide quenching experiments at different Ca++ concentrations demonstrate that Ca++ does not alter the accessibility of the tyro- sine to acrylamide. In the absence of any tryp- tophan contamination, these observations vali- date that, in vitro, HYPK possesses a loosely associated (pre-) molten globule like conforma- tion with the lone tyrosine being situated within an α-helix.

Kinetic models of guanidine hydrochloride-induced curing of the yeast [PSI+] prion

A population of [PSI+] Saccharomyces cerevisiae cells can be cured of the [PSI+] prion by the addition of guanidine hydrochloride (GdnHCl). In this paper we extend existing nucleated polymerisation simulation models to investigate the mechanisms that might underlie curing. Our results are consistent with the belief that prions are dispersed through the cells at division following GdnHCl addition. A key feature of the simulation model is that the probability that a polymer is transmitted from mother to daughter during cell division is dependent upon the length of the polymer. The model is able to reproduce the essential features of data from several different experimental protocols involving addition and removal of GdnHCl.

Monitoring the structural alterations induced in β-lactoglobulin during ultrafiltration: learning from chemical and thermal denaturation phenomena

This work aims to identify of non-reversible structural changes induced in β-lactoglobulin by permeation through porous ultrafiltration membranes. The evaluation of these structural changes is performed using a fluorescence methodology, which combines the use of three different, complementary, fluorescence techniques: steady-state fluorescence, picosecond time-resolved fluorescence and steady-state fluorescence anisotropy. The identification of the nature of the structural changes induced upon permeation is possible through comparison of the fluorescence responses obtained for β-lactoglobulin solutions collected after permeation (permeates and retentates) with those induced by chemical (addition of Guanidine hydrochloride, GndHCl) and thermal denaturation of β-lactoglobulin. The fluorescence approach used allowed to identify irreversible losses of structural integrity of β-lactoglobulin in the permeates, while β-lactoglobulin retentates seemed to be unaffected by the ultrafiltration process. The mechanisms that regulate the structural alterations of β-lactoglobulin and the magnitude of these alterations depend on the protein to membrane pore size ratio, λ, being more substantial at higher λ (severe pore constriction). Under these conditions (permeation with a 10 kDa membrane) the structural changes induced in the proteins are dictated by the high shear stress at the membrane pore walls. The increase of the membrane cut-off (30 kDa membrane) induces a decrease in the magnitude of the shear stress and the effect of protein–membrane chemical interactions becomes noticeable.

Value-Added New Materials from Byproduct of Corn Based Ethanol Industries: Blends of Plasticized Corn Gluten Meal and Poly(ε-caprolactone)

This study attempts to explore the value-added applications of corn gluten meal (CGM), the inexpensive byproduct from corn based ethanol industries. The byproducts, CGM, was plasticized using glycerol/ethanol mixture, denatured by the addition of guanidine hydrochloride (GHCl), and then blended with poly(e-caprolactone), PCL, a synthetic commercial biodegradable polymer. Extrusion followed by injection molding was adopted to fabricate the newly blended green materials. The processing conditions affected the performance of the blends. The GHCl modified corn gluten meal was characterized by IR spectroscopy. The developed materials were characterized through their thermomechanical, tensile, and Izod impact strength measurements. The effects of processing conditions on properties of blends were investigated. One of the promising outcomes of this research was that the GHCl modified corn gluten meal based bioplastic, on blending with PCL had a substantially higher percent elongation. Scanning electron microscop...

Second derivative tryptophan fluorescence spectroscopy as a tool to characterize partially unfolded intermediates of proteins

The application of second derivative tryptophan (Trp) fluorescence spectroscopy to characterize partially unfolded intermediates of proteins relevant to protein formulation was investigated. The second derivatives of the normalized emission scans of N-acetyl tryptophanamide (NATA), single-Trp containing proteins, somatostatin and human serum albumin (HSA), and two-Trp containing proteins previously shown to form partially unfolded intermediates, β-lactoglobulin (βLg) and interferon α-2a (IFNα2a), were studied in solution. The second derivative of NATA in water showed three bands at 340, 348 and 367 nm. The 340 nm band showed a blue shift, whereas the intensity of all three bands was affected by a decrease in solution polarity. Second derivative of single-Trp containing proteins, somatostatin and HSA, showed three negative bands, whereas, the second derivative of the two-Trp containing proteins, βLg and IFNα2a, showed four bands, two of which lie in the 320–340 nm range. These two bands were attributed to the presence of the Trps in different microenvironments. The characteristic changes in the intensities of these two bands on addition of guanidine hydrochloride (βLg) and with a decrease in solution pH (IFNα2a) were related to the presence of partially unfolded intermediates of these proteins. Thus, second derivative Trp fluorescence spectroscopy can be used as an important tool to identify partially unfolded states of proteins during formulation utilizing order of magnitude lower concentrations compared to such other technique as near UV CD.

Mechanisms of beta cell death during restricted and unrestricted enterovirus infection

Coxsackie B virus (CVB-5) infections potentially trigger and accelerate pancreatic beta cell damage leading to type 1 diabetes. In vivo, all viruses face natural resistance mediated by various host factors which restrict the progression of infection. Thus, the aims of this study were to generate a tissue culture model of restricted coxsackie B virus infection in primary islet cells by preventing the production of viral progeny with a selective inhibitor of viral RNA replication and to investigate the mechanisms of virus-induced islet cell death during productive and restricted infective conditions. Cultured foetal porcine islet cells were infected effectively with the prototype strain of coxsackievirus B5 (CVB-5). Nuclear viability stainings and electron microscopy showed productive infection to result in dominantly necrotic cell death with additional slight induction of apoptosis during the 7 days of follow-up. The restricted conditions were created by addition of guanidine-hydrochloride (G-HCl) into culture medium. At 1 mM concentration, it significantly protected the infected cells from necrosis and thus maintained high viability. This was associated with increased significantly apoptosis. In perifusion analysis, the cellular ability to release insulin was reduced, although the metabolic integrity was preserved as shown by MTT-analysis and cellular ATP levels. These data show that restriction of CVB-5 replication with G-HCl protects islet cells against virus-induced necrosis. However, restriction of viral replication shifts the mechanism of cell death from necrosis toward apoptosis. A slowly progressing subclinical infection of islets could thus lead to increased beta-cell apoptosis.

Study on Escherichia coli alkaline phosphatase conformation by phosphorimetry in the presence of denaturant

The influence of different denaturants on the phosphorescence spectrum and lifetime decay of Escherichia coli alkaline phosphatase (AP) was investigated. Phosphorescence intensity and lifetime of tryptophan residue (Trp-109) decrease upon addition of guanidine hydrochloride, ethylene diamine tetraacetic acid, and urea or decreasing acidity. The experiments show that AP undergoes different pathways with different denaturants and that the activation energy data, Δ S° ≠ and Δ H° ≠ further confirm that there is a stable intermediate state between the folded and unfolded AP states in solution.

Salt-dependent monomer-dimer equilibrium of bovine beta-lactoglobulin at pH 3.

Although bovine beta-lactoglobulin assumes a monomeric native structure at pH 3 in the absence of salt, the addition of salts stabilizes the dimer. Thermodynamics of the monomer-dimer equilibrium dependent on the salt concentration were studied by sedimentation equilibrium. The addition of NaCl, KCl, or guanidine hydrochloride below 1 M stabilized the dimer in a similar manner. On the other hand, NaClO(4) was more effective than other salts by about 20-fold, suggesting that anion binding is responsible for the salt-induced dimer formation, as observed for acid-unfolded proteins. The addition of guanidine hydrochloride at 5 M dissociated the dimer into monomers because of the denaturation of protein structure. In the presence of either NaCl or NaClO(4), the dimerization constant decreased with an increase in temperature, indicating that the enthalpy change (DeltaH(D)) of dimer formation is negative. The heat effect of the dimer formation was directly measured with an isothermal titration calorimeter by titrating the monomeric beta-lactoglobulin at pH 3.0 with NaClO(4). The net heat effects after subtraction of the heat of salt dilution, corresponding to DeltaH(D), were negative, and were consistent with those obtained by the sedimentation equilibrium. From the dependence of dimerization constant on temperature measured by sedimentation equilibrium, we estimated the DeltaH(D) value at 20 degrees C and the heat capacity change (DeltaC(p)) of dimer formation. In both NaCl and NaClO(4), the obtained DeltaC(p) value was negative, indicating the dominant role of burial of the hydrophobic surfaces upon dimer formation. The observed DeltaC(p) values were consistent with the calculated value from the X-ray dimeric structure using a method of accessible surface area. These results indicated that monomer-dimer equilibrium of beta-lactoglobulin at pH 3 is determined by a subtle balance of hydrophobic and electrostatic effects, which are modulated by the addition of salts or by changes in temperature.

Enhanced recovery and catalytic activity ofRhizopus delemar lipase in an AOT microemulsion system with guanidine hydrochloride

The efficacy of guanidine hydrochloride (GuHCl) addition on the recovery and catalytic activity of Rhizopus delemar lipase was investigated in an AOT microemulsion system. The activity yield of lipase was markedly increased by the addition of GuHCl, and was maximum at a GuHCl concentration of ca 0.08 mol dm−3. Addition of GuHCl was similarly effective in enhancing enzyme recovery after the hydrolysis of triolein. A kinetic study of the hydrolysis reaction was made as a function of GuHCl concentration. The reaction followed a non-competitive inhibition mechanism. The Km remained constant at GuHCl concentrations from 0 to 0.12 mol dm−3, while the maximum reaction rate at a GuHCl concentration of 0.08 mol dm−3 was only 30% lower than that in a GuHCl-free system. © 1999 Society of Chemical Industry

Conformational unfolding studies of three-disulfide mutants of bovine pancreatic ribonuclease A and the coupling of proline isomerization to disulfide redox reactions.

The equilibrium stability and conformational unfolding kinetics of the [C40A, C95A] and [C65S, C72S] mutants of bovine pancreatic ribonuclease A (RNase A) have been studied. These mutants are analogues of two nativelike intermediates, des[40-95] and des[65-72], whose formation is rate-limiting for oxidative folding and reductive unfolding at 25 degrees C and pH 8.0. Upon addition of guanidine hydrochloride, both mutants exhibit a fast conformational unfolding phase when monitored by absorbance and fluorescence, as well as a slow phase detected only by fluorescence which corresponds to the isomerizations of Pro93 and Pro114. The amplitudes of the slow phase indicate that the two prolines, Pro93 and Pro114, are fully cis in the folded state of the mutants and furthermore that the 40-95 disulfide bond is not responsible for the quenching of Tyr92 fluorescence observed in the slow unfolding phase, contrary to an earlier proposal [Rehage, A., and Schmid, F. X. (1982) Biochemistry 21, 1499-1505]. The ratio of the kinetic unfolding m value to the equilibrium m value indicates that the transition state for conformational unfolding in the mutants exposes little solvent-accessible area, as in the wild-type protein, indicating that the unfolding pathway is not dramatically altered by the reduction of the 40-95 or 65-72 disulfide bond. The stabilities of the folded mutants are compared to that of wild-type RNase A. These stabilities indicate that the reduction of des[40-95] to the 2S species is rate-limited by global conformational unfolding, whereas that of des[65-72] is rate-limited by local conformational unfolding. The isomerization of Pro93 may be rate-limiting for the reduction of the 40-95 disulfide bond in the native protein and in the des[65-72] intermediate.

NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions.

The isolated N-terminal SH3 domain of the Drosophila adapter protein drk (drkN SH3 domain) exists in a dynamic equilibrium between a folded (F(exch)) and an unfolded (U(exch)) state under native-like buffer conditions [Zhang, O., & Forman-Kay, J. D. (1995) Biochemistry 34, 6784-6794]. The effect of binding a proline-rich peptide derived from the protein Sos, a biological target of the drkN SH3 domain, on this equilibrium has been investigated. The stabilization of the F(exch) folded state upon binding provides an example of the link between binding and protein folding or stabilization. We have compared NMR parameters of the U(exch) state with those of a denatured state in 2 M guanidine hydrochloride (U(Gdn)). Variable-temperature experiments demonstrate that interactions in a region encompassing residues Gln 23-Leu 28 in the U(exch) state are destabilized upon addition of guanidine hydrochloride. Data from an 15N HSQC-NOESY-HSQC experiment as well as recently developed methods provide more unambiguous structural information than described previously, showing the presence of preferential structure in both unfolded states. Backbone NOEs observed in both unfolded states as well as chemical shifts and coupling constants suggest a rapid equilibrium between extended structure and turn-like structures which may play a role in initiation of protein folding. However, differences in detailed structural features between the two unfolded states argue that caution is needed in interpretation of results from structural characterization of protein conformational states generated using denaturing conditions.

Folding of a four-helix bundle: studies of acyl-coenzyme A binding protein.

The refolding from denaturing conditions of a small four-helix bundle, the acyl-coenzyme A binding protein, has been investigated by utilizing an array of fast-reaction techniques. Stopped-flow tryptophan fluorescence for measuring the incorporation of aromatic residues into the protein core and far- and near-ultraviolet circular dichroism to measure the formation of secondary and tertiary structure, respectively, together with the formation of persistent structure measured by hydrogen exchange pulse labeling experiments analyzed by electrospray ionisation mass spectrometry all show that 90% of the acyl-coenzyme A binding protein molecules achieve their fully folded and active, native state with a time constant of less than 5 ms at 25 degrees C and of ca. 30 ms at 5 degrees C. The kinetic parameters measured by the different techniques are closely similar, indicating that the different elements of structure form effectively concomitantly. There is no evidence for a significant population of any partially structured intermediate states, and the kinetics are identical whether refolding occurs from an unfolded state generated either by low pH or by addition of guanidine hydrochloride. The kinetics of both refolding and unfolding are monophasic processes for practically 90% of the molecules, and can be described by a two-state model. The results add to our knowledge of the folding scheme of different structural motifs and are discussed in terms of current views of the mechanisms of protein folding.

Apolipoprotein E self-association in solution studied by non-radiative energy transfer

The self-association of human apolipoprotein E (apoE), isolated from plasma very low density lipoproteins, was studied at apoE concentrations less than 0.6 microM by non-radiative energy transfer. ApoE was separately labeled with a fluorescent donor group i.e. dansyl chloride (apoE/D) and with an acceptor i.e. fluorescein isothiocyanate (apoE/F). Mixed apoE/D:apoE/F complexes were prepared either by incubation or the donor- and of the acceptor-labeled apoE or by renaturation during dialysis of the apoE/D:apoE/F mixture pre-denatured by addition of guanidine hydrochloride or by treatment with sodium cholate. The efficiency of energy transfer E at an equimolar ratio of the donor to acceptor and a ratio of 1.9 mol fluorescein/mol protein amounted to 29.2 +/- 2.6% (n = 3). The E value increased linearly with increasing acceptor fraction in the mixture. The state of self-association of apoE as tetramers within this concentration range was confirmed by cross-linking experiments with a water-soluble bifunctional reagent. This approach can be applied to the study of protein-protein interactions in apolipoprotein-phospholipid recombinants.