The protein conformation and a zinc-binding domain of an autoantigen from mouse seminal vesicle.

The protein conformation of a mouse seminal vesicle autoantigen was studied by circular dichroism spectroscopy. At pH 7.4, the spectrum in the UV region appears as one negative band at 217 nm and one positive band at 200 nm. This together with the predicted secondary structures indicates no helices but a mixture of beta form, beta turn, and unordered form in the protein molecule. The conformation is stable even at pH 10.5 or 3.0. The spectrum in the near-UV region consists of fine structures that are disturbed in acidic or alkaline solution. The environments around Trp2 and Trp82 of this protein were studied by intrinsic fluorescence and solute quenching. They give an emission peak at 345 nm, and about 87% of them are accessible to quenching by acrylamide. Correlating the quenching effect of CsCl and Kl on the protein fluorescence to the charged groups along the polypeptide chain suggests the difference in the "local charge" around the two tryptophan residues. The presence of ZnCl2 in the protein solution effects no change in the circular dichroism but perturbs the fluorescence due to Trp82. Analysis of the fluorescence data suggests a Zn(2+)-binding site on the protein, which cannot coordinate with both Ca2+ and Mg2+. The association constant for the complex formation is 1.35 x 10(5) +/- 0.04 x 10(5) M-1 at pH 7.4.     

Predissociated dimers and molten globule monomers in the equilibrium unfolding of yeast glutathione reductase

The equilibrium unfolding of dimeric yeast glutathione reductase (GR) by guanidine hydrochloride (GdnHCl) was investigated. Unfolding was monitored by a variety of techniques, including intrinsic fluorescence emission, anisotropy and iodide quenching measurements, far-ultraviolet circular dichroism and thiol reactivity measurements. At 1 M GdnHCl, one thiol group of GR became accessible to modification with 5,5′-dithiobis-(2-nitrobenzoic) acid (DTNB), whereas no changes could be detected in the spectroscopic properties (fluorescence, circular dichroism) of the protein. Between 2 and 3 M GdnHCl, two partially folded intermediate states possessing flexible tertiary structures (revealed by fluorescence data) but compact secondary structures (as indicated by circular dichroism measurements) were identified. The quaternary structure of GR in the presence of GdnHCl was also investigated by size-exclusion liquid chromatography. These results indicated the presence of an expanded predissociated dimer at 2.5 M GdnHCl and partially folded monomers at 3 M GdnHCl. Taken together, these results suggest the existence of two molten-globule-like intermediate species (one dimeric and one monomeric) in the unfolding of GR. The results are discussed in terms of the mechanism of GR folding and dimerization.     

Comparative structural analysis of staphylococcal enterotoxins A and E

Structural analysis of staphylococcal enterotoxins A and E, two functionally and serologically related proteins, has been carried out using circular dichroism, and tryptophan fluorescence quantum yield and quenching. Secondary structures derived from the far-UV circular dichroic spectra revealed that both enterotoxins are in predominantly beta-sheets/beta-turn structures (80-85%). Staphylococcal enterotoxin A has significantly higher alpha-helical content (10.0%) than staphylococcal enterotoxin E (6.5%). Tryptophan fluorescence spectra of both enterotoxins showed maxima at approximately 342 nm, indicating that the fluorescent tryptophan residues are in polar environments. However, the tryptophan fluorescence quantum yields indicated that tryptophan residues are approximately 41% more fluorescent in staphylococcal enterotoxin A than in staphylococcal enterotoxin E. Tryptophan fluorescence quenching by a surface quencher, I-, and a neutral quencher, acrylamide, indicated that at least 1 of the 2 tryptophan residues in both staphylococcal enterotoxins A and E is located on the outer surface of the proteins. This tryptophan residue is in significantly different environments in the two enterotoxins. Six antigenic sites are predicted from the hydrophilicity and secondary structure information; at least four sites are identical. In general, staphylococcal enterotoxins A and E have some structural similarities which are compatible with their common biological activities.     

Spectroscopic characterization of thioredoxin covalently modified with monofunctional organoarsenical reagents

Thioredoxin upon reduction with mercaptoethylamine was subjected to covalent modification by the monofunctional organoarsenical reagents H2NPhAsO and HO(CH2)4AsCl2. The degree of modification was monitored by the percentage loss in free thiol content as measured by the reaction with the thiol reagent 5,5'-dithiobis(2-nitrobenzoic acid). The modification results in the formation of a stable 15-membered cyclic dithioarsenite ring that readily extrudes the arsenic moiety upon the addition of 2,3-dimercaptopropanol. The conformational effects of this modification were monitored by steady-state fluorescence and circular dichroism. On the basis of circular dichroic spectra, it appeared that the protein experiences no significant backbone conformational change from this modification. The degree of conformational change was found to be within the range observed upon reduction of the oxidized thioredoxin. Steady-state fluorescence revealed that the arsenicals caused strong quenching of the tryptophan fluorescence. Stern-Volmer titrations revealed that the quenching was a function of both the nature of the organic group and its covalent attachment to the "spatially close" thiols. The analysis of the spectroscopic results obtained with the arsenical reagents provides further insight into the nature of the conformational change that has been observed upon reduction of thioredoxin.     

Optical studies of complexes of quinacrine with DNA and chromatin: implications for the fluorescence of cytological chromosome preparations

The fluorescence and circular dichroism of quinacrine complexed with nucleic acids and chromatin were measured to estimate the relative magnitudes of factors influencing the fluorescence banding patterns of chromosomes stained with quinacrine or quinacrine mustard. DNA base composition can influence quinacrine fluorescence in at least two ways. The major effect, evident at low ratios of quinacrine to DNA, is a quenching of dye fluorescence, correlating with G-C composition. This may occur largely prior to relaxation of excited dye molecules. At higher dye/DNA saturations, which might exist in cytological chromosome preparations stained with high concentrations of quinacrine, energy transfer between dye molecules converts dyes bound near G-C base pairs into energy sinks. In contrast to its influence on quinacrine fluorescence, DNA base composition has very little effect on either quinacrine binding affinity or the circular dichroism of bound quinacrine molecules. The synthetic polynucleotides poly(dA-dT) and poly(dA)-poly(dT) have a similar effect on quinacrine fluorescence, but differ markedly in their affinity for quinacrine and in the circular dichroism changes associated with quinacrine binding. Quinacrine fluorescence intensity and lifetime are slightly less when bound to calf thymus chromatin than when bound to calf thymus DNA, and minor differences in circular dichroism between these complexes are observed. Chromosomal proteins probably affect the fluorescence of chromosomes stained with quinacrine, although this effect appears to be much less than that due to variations in DNA base composition. The fluorescence of cytological chromosome preparations may also be influenced by fixation effects and macroscopic variations in chromosome coiling.     

Effect of a zwitterionic surfactant (HPS) on the conformation and hemolytic activity of St I and St II,two isotoxins purified from Stichodactyla helianthus

N-hexadecyl-N-N-dimethyl-3-ammonio-1-propane-sulfonate (HPS) is a zwitterionic surfactant that readily binds to sticholysins I and II, two sea toxins isolated from Stichodactyla helianthus. The binding constants, evaluated from changes in fluorescence intensities elicited by the surfactant, are 0.5–0.7 M^–1. The binding of the surfactant changes the conformation of the tertiary protein, without significant changes in its secondary structure, as reported from far-ultraviolet circular dichroism spectra. The changes elicited by HPS lead to loss of the native conformation (as reported from near-ultraviolet circular dichroism spectra) and to a shift of the intrinsic protein fluorescence toward longer wavelengths, an increase in fluorescence intensities and lifetimes, and a faster quenching by acrylamide. All these changes are indicative of a more expanded tertiary conformation. Despite this, the toxins fully retain their hemolytic activities, indicating that spectroscopic changes can be poor predictors of toxin activity.     

Ligand-induced conformational changes in cytosolic protein kinase C

The changes in intrinsic spectral properties of protein kinase C were monitored upon association with its divalent cation and lipid activators in a model membrane system. The enzyme demonstrated changes in both its intrinsic fluorescence and far ultraviolet circular dichroism spectra upon association with lipid vesicles in the absence of calcium. The acidic phospholipid, phosphatidylserine, significantly quenched the intrinsic tryptophan fluorescence and was also the most potent lipid support for the phosphorylating activity of the enzyme. The enzyme was fully activated by a number of Ca2(+)-lipid combinations which correlated with maximal fluorescence quenching (40-50%) of available tryptophan residues in hydrophobic domains. The circular dichroism structure of the associated active-protein Ca2(+)-lipid complexes suggested different active enzyme secondary structures. However, the Ca2(+)-dependent changes in fluorescence and circular dichroism spectra were observed only after the enzyme associated with the lipid vesicles. These data suggest that protein kinase C has the properties of a complex multidomain protein and provides an additional perspective into the mechanism of protein kinase C activation.     

A spectroscopic and conformational study of pertussis toxin

The conformation of native pertussis toxin has been investigated by secondary structure prediction and by circular dichroism, fluorescence and second-derivative ultraviolet absorption spectroscopy. The far-ultraviolet circular dichroic spectrum is characteristic of a protein of high beta-sheet and low alpha-helix content. This is also shown by an analysis of the circular dichroic spectrum with the Contin programme which indicates that the toxin possesses 53% beta-sheet, 10% alpha-helix and 37% beta-turn/loop secondary structure. Second-derivative ultraviolet absorption spectroscopy suggests that 34 tyrosine residues are solvent-exposed and quenching of tryptophan fluorescence emission has shown that 4 tryptophan residues are accessible to iodide ions. One of these tryptophans appears to be in close proximity to a positively charged side-chain, since only 3 tryptophans are accessible to caesium ion fluorescence quenching. When excited at 280 nm, the emission spectrum contains a significant contribution from tyrosine fluorescence, which may be a consequence of the high proportion (55%) of surface-exposed tyrosines. No changes in the circular dichroic spectra of the toxin were found in the presence of the substrate NAD. However, NAD did quench both tyrosine and tryptophan fluorescence emission but did not change the shape of the emission spectrum, or the accessibility of the tryptophans to either the ionic fluorescence quenchers or the neutral quencher acrylamide.     

Investigations on the interactions between naphthalimide‐based anti‐tumor drugs and human serum albumin by spectroscopic and molecular modeling methods

The interactions between the three kinds of naphthalimide‐based anti‐tumor drugs (NADA, NADB, NADC) and human serum albumin (HSA) under simulated physiological conditions were investigated by fluorescence spectroscopy, circular dichroism spectroscopy and molecular modeling. The results of the fluorescence quenching spectroscopy showed that the quenching mechanisms for different drugs were static and their affinity was in a descending order of NADA > NADB > NADC. The relative thermodynamic parameters indicated that hydrophobic force was the predominant intermolecular force in the binding of NAD to HSA, while van der Waals interactions and hydrogen bonds could not be ignored. The results of site marker competitive experiment confirmed that the binding site of HSA primarily took place in site I. Furthermore, the molecular modeling study was consistent with these results. The study of circular dichroism spectra demonstrated that the presence of NADs decreased the α‐helical content of HSA and induced the change of the secondary structure of HSA. Copyright © 2015 John Wiley & Sons, Ltd.     

Differential scanning calorimetric studies of aqueous dispersions of phosphatidylcholines containing two polyenoic chains

The structure of the lectin discoidin I has been studied by circular dichroism and fluorescence spectroscopy. A positive ellipticity band at 224 nm is detected in the CD spectrum of discoidin I. The fluorescence spectra show a defined shoulder at 325 nm that through acrylamide quenching has been associated with a displaced tryptophan residue partly buried in the discoidin I molecule. This tryptophan could also be responsible for the 224 nm positive band of the CD spectrum. These spectroscopic characteristics of discoidin I indicate the existence of structural homologies with fibronectin, where the optical activity of aromatic chromophores has been associated with the positive ellipticity band at 227 nm. The CD adjust parameters and theoretical secondary structure predictions show that discoidin I is a molecule with a low content of alpha-helix and beta-strand and high content of beta-turn structures, similar to other lectins.     

Spectroscopic studies on the structural organization of the lectin discoidin I: homologies with fibronectin

The structure of the lectin discoidin I has been studied by circular dichroism and fluorescence spectroscopy. A positive ellipticity band at 224 nm is detected in the CD spectrum of discoidin I. The fluorescence spectra show a defined shoulder at 325 nm that through acrylamide quenching has been associated with a displaced tryptophan residue partly buried in the discoidin I molecule. This tryptophan could also be responsible for the 224 nm positive band of the CD spectrum. These spectroscopic characteristics of discoidin I indicate the existence of structural homologies with fibronectin, where the optical activity of aromatic chromophores has been associated with the positive ellipticity band at 227 nm. The CD adjust parameters and theoretical secondary structure predictions show that discoidin I is a molecule with a low content of α-helix and β-strand and high content of β-turn structures, similar to other lectins.     

Alkalin titrations of human somatotropin, human choriomammotropin and ovine prolactin by circular dichroism and fluorescence.

Structural transitions occurring during the alkalin titration of human somatotropin, human choriomammotropin, and ovine prolactin have been investigated by means of circular dichroism and fluorescence emission spectra. Human somatotropin exhibited an isodichroic point at 287 nm, with all spectral changes being reversed upon back titration from pH 12.50 to pH 8.0. Fluorescence quenching as a function of pH produced a simple sigmoidal curve. Human choriomammotropin exhibited an isodichroic point at 288 nm. The fluorescence and circular dichroism spectra of this protein were found to be reversible between pH 8.0 and 11.0. However, on titration above pH 11, the isodichroic point and the reversibility of the circular dichroism spectra were lost. This conformational transition was accompanied by a sharp increase in fluorescence quantum yield. The circular dichroism spectra of ovine prolactin showed essentially no change on titration to pH 11.0. However, between pH 11.0 and 12.0, a sharp conformational transition was observed similar to that seen in human choriomammotropin, but not exhibiting the same increase in fluorescence quantum yield. The fluorescence titration of prolactin was found to be essentially reversible upon back titration from pH 12.5, although the circular dichroism spectra were not reversible from this pH.     

Combined multispectroscopic and molecular docking investigation on the interaction between delphinidin‐3‐O‐glucoside and bovine serum albumin

Anthocyanin is one of the flavonoid phytopigments with specific health benefits. The interaction between delphinidin‐3‐O‐glucoside (D3G) and bovine serum albumin (BSA) was investigated by fluorescence spectroscopy, synchronous fluorescence spectroscopy, three‐dimensional fluorescence spectroscopy, ultraviolet‐visible absorption spectroscopy, circular dichroism spectroscopy and molecular modeling. D3G effectively quenched the intrinsic fluorescence of BSA via static quenching. The number of binding sites and binding constant K_a were determined, and the hydrogen bonds and van der Waals forces played major roles in stabilizing the D3G–BSA complex. The distance r between donor and acceptor was obtained as 2.81 nm according to Förster's theory. In addition, the effects of pH and metal ions on the binding constants were discussed. The results studied by synchronous fluorescence, three‐dimensional fluorescence and circular dichroism experiments indicated that the secondary structures of the protein has been changed by the addition of D3G and the α‐helix content of BSA decreased (from 56.1% to 52.4%). Furthermore, the study of site marker competitive experiments and molecular modeling indicated that D3G could bind to site I of BSA, which was in the large hydrophobic cavity of subdomain IIA. Copyright © 2014 John Wiley & Sons, Ltd.     

Spectroscopic study of the interaction between lycopene and bovine serum albumin

The interaction of lycopene with bovine serum albumin (BSA) in aqueous solution was studied by fluorescence quenching, three‐dimensional fluorescence and circular dichroism spectroscopy. The data showed that the fluorescence of BSA was quenched by lycopene at different temperatures through a dynamic mechanism. The evaluation of three‐dimensional fluorescence spectra revealed a conformational modification of BSA induced by coupling with lycopene and an increase in protein diameter as a consequence of the ligand–protein interaction. Moreover, the information obtained from evaluation of the effect of lycopene on BSA conformation by circular dichroism strongly supported the existence of a slight unfolding of BSA induced by coupling to lycopene. Copyright © 2012 John Wiley & Sons, Ltd.     

Spectral studies on two genetic forms of the human serum proteinase inhibitor, alpha-1-antitrypsin.

alpha-1-antitrypsin, the major inhibitor of proteolytic enzymes in human serum, was isolated from normal individuals (protease inhibitor type MM) and from those with an inherited deficiency (protease inhibitor type ZZ) of circulatory protein. The two proteins were compared by circular dichroism spectroscopy, and by fluorescence quenching experiments using anionic (I-), and neutral (acrylamide) probes. Both proteins share a similar secondary structure, i.e. approximately 45--50% alpha-helix and 15--20% beta-structure. Evidence was accumulated to show that the microenvironment in the vicinity of the three tryptophanyl residues is altered in Z form as compared to the M form as shown by (a) the absence of the positive dichroic band in the region 290--300 nm of the circular dichroism spectra, (b) a greater than 50% increase in quantum yield in the tryptophanyl fluorescence emission spectra, (c) an increased accessibility of tryptophan to quenching by iodide, and (d) acrylamide quenching experiments which indicate that all tryptophanyl residues in the Z protein are quenched equally or that quenching is dominated by a single residue, while in the M protein, heterogeneous quenching occurs. The potential significance of these findings in terms of alpha-1-antitrypsin deficiency state are discussed.     

Probing the Interaction of Mutiwalled Carbon Nanotubes and Catalase: Mutispectroscopic Approach

In this study, the mechanism of the interaction between multiwalled carbon nanotubes (MWCNTs) and catalase was investigated by fluorescence, UV–vis, and circular dichroism (CD) spectroscopy under physiological conditions. The fluorescence quenching mechanism of catalase by MWCNTs was shown to be a static quenching procedure and was a result of the formation of a catalase–MWCNT complex. The secondary structure and conformation of the catalase adsorbed on MWCNTs was determined by CD and UV‐vis spectroscopy, and the results indicate that the catalase in this complex is partially unfolded with its lost in α‐helical content and obtainment in β‐sheet content. Moreover, binding of MWCNTs to catalase inhibited the enzymatic activity, which may trigger some toxic effects and undesirable physiological consequences. © 2012 Wiley Periodicals, Inc. J Biochem Mol Toxicol 26:493‐498, 2012;Viewthis article online at wileyonlinelibrary.com . DOI 10.1002/jbt.21454     

Conformational alteration of bradykinin in presence of GM1 micelle

We report here the interaction of bradykinin with ganglioside GM1 by circular dichroism, steady-state fluorescence, and one-dimensional 1H NMR spectroscopy. Circular dichroism spectroscopy is indicative of a turn formation of bradykinin backbone in the presence of GM1 micelle. The fluorescence quenching efficiencies of iodide and acrylamide are substantially reduced, indicating a shielding of phenylalanine residue of bradykinin from aqueous environment. Significant line broadening of NMR resonances of bradykinin, suggestive of motional restriction, is observed.     

Bacterial expression and characterization of the ligand-binding domain of the vitamin D receptor

The ligand-binding domain of the rat vitamin D receptor (amino acids 115-423) was expressed as an amino-terminal His-tagged protein in a bacterial expression system and purified over Ni-nitrilotriacetic acid resin and a Mono S column. The purified protein bound its ligand, 1,25-dihydroxyvitamin D3, with high affinity, similar to that of the full-length protein. Saturation of the protein with ligand quenched 90% of the tryptophan fluorescence, consistent with the purified protein being uniformly able to bind ligand. Addition of ligand produced no change in the tryptophan fluorescence lifetime, suggesting static quenching as the mechanism of fluorescence decrease. The near-UV circular dichroism spectrum showed a large increase in signal following the addition of ligand, consistent with a change in the environment of aromatic amino acid side chains. The far-UV circular dichroism spectrum was consistent with a protein of high alpha-helical content. Sedimentation equilibrium experiments demonstrated that the protein formed higher-order complexes, and the distribution of the protein among these complexes was significantly shifted by addition of ligand.     

Divalent cation-induced changes in conformation of protein kinase C

Using physical techniques, circular dichroism and intrinsic and extrinsic fluorescence, the binding of divalent cations to soluble protein kinase C and their effects on protein conformation were analyzed. The enzyme copurifies with a significant concentration of endogenous Ca2+ as measured by atomic absorption spectrophotometry, however, this Ca2+ was insufficient to support enzyme activity. Intrinsic tryptophan fluorescence quenching occurred upon addition to the soluble enzyme of the divalent cations, Zn2+, Mg2+, Ca2+ or Mn2+, which was irreversible and unaffected by monovalent cations (0.5 M NaCl). Far ultraviolet (200-250 nm) circular dichroism spectra provided estimations of secondary structure and demonstrated that the purified enzyme is rich in alpha-helices (42%) suggesting a rather rigid structure. At Ca2+ or Mg2+ concentrations similar to those used for fluorescence quenching, the enzyme undergoes a conformational transition (42-24% alpha-helix, 31-54% random structures) with no significant change in beta-sheet structures (22-26%). Maximal effects on 1 microM enzyme were obtained at 200 microM Ca2+ or 100 microM Mg2+, the divalent cation binding having a higher affinity for Mg2+ than for Ca2+. The Ca2(+)-induced transition was time-dependent, while Mg2+ effects were immediate. In addition, there was no observed energy transfer for protein kinase C with the fluorescent Ca2(+)-binding site probe, terbium(III). This study suggests that divalent cation-induced changes in soluble protein kinase C structure may be an important step in in vitro analyses that has not yet been detected by standard biochemical enzymatic assays.     

Reversible unfolding of the gelatin-binding domain of fibronectin: structural stability in relation to function

Fibronectin, a large multidomain glycoprotein, binds denatured collagen (gelatin) and mediates cell attachment and spreading on collagen-coated surfaces. Despite the high affinity, binding to gelatin is disrupted by relatively mild conditions. We have examined the effects of denaturants on the structure and function of a 42-kDa gelatin-binding fragment (GBF) isolated from chymotryptic and thermolytic digests of the parent protein. Application of linear gradients to GBF-loaded gelatin-agarose columns resulted in peak elution of the fragment at pH 5.2 or 10.2, at 0.4 M dimethylformamide, 0.9 M GdmCl, or 2.0 M urea, conditions far short of those required to induce structural changes detectable by fluorescence or circular dichroism. Solvent perturbation, fluorescence quenching, and chemical modification experiments indicate that about half of the 8 tryptophans, one-third of the 21 tyrosines, and all of the 9 lysine residues are solvent-exposed in the native protein and that 1 or more of the latter are directly involved in binding to gelatin, most likely through a hydrogen-bonding mechanism. Titration with GdmCl produced a single unfolding transition centered near 2.5 M GdmCl as monitored by changes in fluorescence and circular dichroism. This transition was fully reversible with complete recovery of structural parameters and gelatin binding. Treatment with disulfide reducing agents caused rapid irreversible changes in structure similar to those produced by GdmCl with concomitant loss of gelatin binding. Thus, tertiary and secondary structures are important for binding, but binding can be disrupted without perturbing those structures.