Showing papers on "Circular dichroism published in 1988"

Secondary Structure of Proteins Through Circular Dichroism Spectroscopy

Abstract: CIRCULAR DICHROISM SPECTROSCOPY .........•.....••......• • 147 Technique .. ...... . . . . .. . . . . . . . . . . . . . . . . . . ...... .... ........ . . . .... 147 Spectrometers.... . . . . . . .... . . . . . . ........ . ...... . . . . . . . . . . . . .... . . . .... . . . ...... . . . . ...... . . . ..... 148 Concentration and Pathlength.. . . . . . . ...... ..... . . . ...... .... ..... . . . .. . . . . ....... .... . . . ... . . . . 149 Noise .. .... . . . . ... . . . . . ....... . . . . . . . . . . . . ... . . ........ ........ ........ . ...... 150 METHODS OF ANALySIS 151 Information Content and Constraints .... . . . . . . . . . . .. . . . .... . ... . . . . ...... ... . ........ . . . . . ... . . 151 Circular Dichroism Spectra for Pure Secondary Structures ...... . . . . . .. . . . . . ... . . . . . . . . . . .. . . . . . 152 Reference Circular Dichroism From Proteins of Known Secondary Structure . . . .... . . . . 154 APPLICATIONS . ......... ..... . . . . . .... . . . . .. . . . ... 159 Analysisfor Secondary Structure......... . . . ..... . . . .. . . . . . ....... .... . . . ....... 159 Proteins With Denatured Circular Dichroism . . . . ..... .. ....... . . . . . . . . .... . 160 Changes in Secondary Structure on Ligand Binding ..... . . . . . . . . . . . . . ... . . . ..... . . ......... 161 Changes in Secondary Structure With Solvent Variation ......... ..... . . ..... . . ..... . ..... . . . ..... 162 Changes in Secondary Structure on Protein Denaturation.... ........ . . . ...... . . .. . . . . . 163 CONCLUSIONS.... ...... ....... ........ 164

Zinc-dependent structure of a single-finger domain of yeast ADR1.

Abstract: In the proposed "zinc finger" DNA-binding motif, each repeat unit binds a zinc metal ion through invariant Cys and His residues and this drives the folding of each 30-residue unit into an independent nucleic acid-binding domain. To obtain structural information, we synthesized single and double zinc finger peptides from the yeast transcription activator ADR1, and assessed the metal-binding and DNA-binding properties of these peptides, as well as the solution structure of the metal-stabilized domains, with the use of a variety of spectroscopic techniques. A single zinc finger can exist as an independent structure sufficient for zinc-dependent DNA binding. An experimentally determined model of the single finger is proposed that is consistent with circular dichroism, one- and two-dimensional nuclear magnetic resonance, and visual spectroscopy of the single-finger peptide reconstituted in the presence of zinc.

Circular-dichroism studies on two murine serum amyloid A proteins

Abstract: C.d. studies have shown that mouse SAA2 (serum amyloid A2) protein has about one-half of the alpha-helix content of the SAA1 (serum amyloid A1) analogue (15 as against 32%), although secondary-structure prediction analyses based on sequence data do not suggest such a large difference between the forms. The decreased helical content may be a reflection or indication of a stronger propensity to aggregation of the SAA2 form compared with SAA1. The main elements of secondary structure in both proteins are beta-sheets/turns. Interactions with Ca2+ are accompanied by small losses in alpha-helix content, whereas binding to chondroitin-6-sulphate in the presence of millimolar Ca2+ also decreases the amount of secondary structure. However, SAA2 binding to heparan sulphate increases its beta-sheet structure, whereas with SAA1 secondary structure is not apparently altered by its interaction with heparan sulphate. Computer-generated surface profiles show slight differences in accessibility, hydrophilicity and flexibility between the proteins. Understanding these differences may help to explain why SAA2 is found in amyloid fibrils whereas SAA1 is not. In particular, a stronger tendency to aggregation might be the reason why SAA2 is deposited exclusively in these fibrils.

Alpha-helix in the carboxy-terminal domains of histones H1 and H5.

Abstract: Although the carboxy-terminal domains of histones H1 and H5 exist as random-coil in aqueous solution, secondary structure prediction suggests that this region has a high potential for alpha-helix formation. We have measured CD spectra in various conditions known to stabilize alpha-helices, to determine whether this potential can be realized in an appropriate environment. Trifluoroethanol increases the helix contents of H1, H5 and their carboxy-terminal fragments, presumably through promotion of axial hydrogen bonding. Sodium perchlorate is also effective and better than sodium chloride, suggesting stabilization by binding of bulky perchlorate ions rather than simple charge screening. Extrapolating from these measurements in solution, and taking into account the occurrence of proline residues throughout the carboxy-terminal domain, we propose that binding to DNA stabilizes helical segments in the carboxy-terminal domains of histones H1 and H5, and that it is this structured form of the domain that is functionally important in chromatin.

Reconstitution of the B873 light-harvesting complex of Rhodospirillum rubrum from the separately isolated alpha- and beta-polypeptides and bacteriochlorophyll a.

Abstract: The light-harvesting complex of Rhodospirillum rubrum was reversibly dissociated into its component parts: bacteriochlorophyll and two 6-kilodalton polypeptides. The dissociation of the complex by n-octyl beta-D-glucopyranoside was accompanied by a shift of the absorbance maximum from 873 to 820 nm (a stable intermediate form) and finally to 777 nm. In the latter state, bacteriochlorophyll was shown to be free from the protein. Complexes absorbing at 820 and 873 nm could be re-formed from the fully dissociated state with over 80% yield by dilution of the detergent. Absorbance and circular dichroism properties of the re-formed B820 complex were essentially identical with those of B820 formed from chromatophores. Phospholipids and higher concentrations of complex were required to obtain the in vivo circular dichroism spectrum for reassociated B873. Reconstitution of the light-harvesting complexes from separately isolated alpha- and beta-polypeptides and bacteriochlorophyll was also demonstrated. Absorbance and circular dichroism spectra of these complexes were identical with those of complexes formed by the reassociation of the dissociated complex. Bacteriochlorophyll and the beta-polypeptide alone formed a complex that had an absorbance at 820 nm, but an 873-nm complex could not be formed without addition of the alpha-polypeptide. The alpha-polypeptide alone with bacteriochlorophyll did not form any red-shifted complex. In preliminary structure-function studies, some analogues of bacteriochlorophyll were also tested for reconstitution.

The membrane as an environment of minimal interconversion. A circular dichroism study on the solvent dependence of the conformational behavior of gramicidin in diacylphosphatidylcholine model membranes.

Abstract: The conformation of gramicidin in diacylphosphatidylcholine model membranes was investigated as a function of the solvent in which peptide and lipid are initially codissolved. By use of circular dichroism it is demonstrated that, upon removal of the solvent and hydration of the mixed gramicidin/lipid film, it is the conformational behavior of the peptide in the organic solvent that determines its final conformation in dimyristoylphosphatidylcholine model membranes. As a consequence, parameters that influence the conformation of the peptide in the solvent also play an essential role, such as the gramicidin concentration and the rate of interconversion between different conformations. Of the various solvents investigated, only with trifluoroethanol is it possible directly to incorporate gramicidin entirely in the beta 6.3-helical (channel) configuration. It is also shown that the conformation of gramicidin in the membrane varies with the peptide/lipid ratio, most likely as a result of intermolecular gramicidin-gramicidin interactions at higher peptide/lipid ratios, and that heat incubation leads to a conformational change in the direction of the beta 6.3-helical conformation. Using lipids with an acyl chain length varying from 12 carbon atoms in dilauroylphosphatidylcholine to 22 carbon atoms in dierucoylphosphatidylcholine, it was possible to investigate the acyl chain length dependence of the gramicidin conformation in model membranes prepared from these lipids with the use of different solvent systems. It is demonstrated for each solvent system that the distribution between different conformations is relatively independent of the acyl chain length but that the rate at which the conformation converts toward the beta 6.3-helical configuration upon heating of the samples is affected by the length of the acyl chain.(ABSTRACT TRUNCATED AT 250 WORDS)

Circular dichroism microscopy of compact forms of DNA and chromatin in vivo and in vitro: cholesteric liquid-crystalline phases of DNA and single dinoflagellate nuclei.

Abstract: Two highly condensed structures of DNA have been analyzed in the circular dichroism (CD) microscope: the cholesteric liquid-crystalline phase of DNA and the nucleus of a dinoflagellate (Prorocentrum micans). In both cases, the DNA shows a helical cholesteric organization, but the helical pitch equals about 2500 nm in the first case and 250 nm in the second one. Since the absorption band of DNA is located at 260 nm, the reflection and absorption bands are well separated in the cholesteric phase of DNA and are overlapping in the dinoflagellate nucleus. However, both structures give a very strong negative CD signal at 265 nm. We show that this very strong signal cannot correspond to a Borrmann effect, i.e., to a superposition of the absorption and reflection bands, but is a differential absorption of left versus right circularly polarized light. This anomalous differential absorption is probably due to a significant scattering of light, inside of the structure, which produces a resonance phenomenon in the absorption band of the chromophore. Therefore, for any helical structure containing a chromophore, the apparent CD can be expressed as CD = [(epsilon L - epsilon R)cl] + (psi L - psi R) + (SL - SR) The first term is true absorption and is located in the absorption band of the chromophore, and the last term is true scattering and is observed at the wavelength corresponding to the helical pitch of the structure. The second term (psi L - psi R) corresponds to the anomalous differential absorption observed in dense superhelical structures of DNA. It superimposes to the first term in the absorption band of the chromophore. psi L - psi R is a measure of the perfection of the helical structure and of the density of chromophores in the material. Intercalative dyes [ethidium bromide and meso-tetrakis(4-N-methylpyridyl)porphine (H2TMpyP-4) and its nickel(II) derivative (NiIITMpyP-4)] were inserted in the dinoflagellate chromatin. The CD signal recorded in their absorption band mimics the signal observed in the absorption band of DNA. In both structures, the negative sign of the CD at 265 nm indicates that the twist occurring between DNA. In both structures, the negative sign of the CD at 265 nm indicates that the twist occurring between DNA molecules is left-handed, and we show that this situation is the most frequently encountered in vivo and vitro.

The enzymatic activity of proteinase K is controlled by calcium

Abstract: The fungal proteinase K (EC 3.4.21.14) is a very potent unusually stable member of the subtilisin family. Its X-ray structure determined at 0.15-nm resolution shows two bound Ca2+ ions. Ca1 is in near-ideal pentagonal bipyramidal configuration with Asp200 carboxylate and Pro175 peptide C = O in an apical, and Val177 peptide C = O and four water molecules in an equatorial position, whereas Ca2 displays incomplete octahedral coordination with the carboxylate of Asp260, the peptide C = O of Val16 and the two water molecules. Scatchard analysis of the titration of Ca2+-free proteinase K with Ca2+ yields a single dissociation constant (7.6 +/- 2.5) x 10(-8) M associated with the tightly bound Ca1 whereas Ca2 is so weakly bound that it cannot be titrated. If proteinase K is depleted of Ca2+ by treatment with EDTA, followed by gel filtration, its enzymatic activity drops within 6 h to 20% of its original value, without autolysis. Addition of excess Ca2+ immediately raises the residual activity to 28%, but full activity is not achieved. Removal of Ca2+ triggers a conformational change of the substrate recognition site because there is a direct connection, via secondary structure hydrogen bonds, between the Ca1 binding site and the substrate-recognition site. This is indicated further by circular dichroism and fluorescence-spectroscopic data, and by reversed-phase FPLC, carried out in the presence and absence of Ca2+, but the overall structure of the enzyme is not affected. Depletion of Ca2+ also influences binding of longer peptide inhibitors of the chloromethane type, it increases the rate of autolysis after about 48 h, it reduces the thermal stability (measured by activity tests from 65 degrees C to 46 degrees C), and it enhances the deactivation by 8 M urea which inactivates to only 65%, whereas sodium dodecyl sulfate totally inactivates at a concentration of 12.5%.

Structure and activity of trypsin in reverse micelles

Abstract: The kinetic properties of trypsin have been studied in reverse micelles formed by two surfactant systems, namely bis(2-ethylhexyl) sodium sulfosuccinate (AOT) in isooctane, and hexadecyltrimethyl ammonium bromide (CTAB) in chloroform/isooctane (1:1, by vol.). Three substrates have been used, namely N alpha-benzoyl-L-Arg ethyl ester, N alpha-benzoyl-L-Phe-L-Val-L-Arg p-nitroanilide (BzPheValArg-NH-Np) in AOT and N alpha-benzyloxycarbonyl-L-Lys p-nitrophenyl ester (ZLysO-Np) in CTAB. One of the main aims of the work was to compare the behaviour of trypsin in reverse micelles with that of alpha-chymotrypsin, for which an enhancement of kcat had been observed with respect to aqueous solutions. The pH profile is not significantly altered in reverse micelles with respect to water, however the kinetic parameters (kcat and Km) differ widely from one another, and are markedly affected by the micellar conditions, in particular by the water content wo (wo = [H2O]/[AOT]). Whereas in the case of BzPheValArg-NH-Np kcat is much smaller than in water, in the case of ZLysO-Np at pH 3.2 (but not at pH 6.0) a slight enhancement with respect to water is observed. On the basis of rapid kinetic spectrophotometry (stopped-flow) and solvent isotope effect studies, this enhancement is ascribed to a change in the rate-limiting step (acylation rather than hydrolysis). As in the case of alpha-chymotrypsin, the maximal activity is found for all substrates at rather small wo values (below 12), which is taken to suggest that the enzyme works better when is surrounded by only a few layers of tightly bound water. Spectroscopic studies [ultraviolet absorption, circular dichroism (CD) and fluorescence] have been carried out as a function of wo. Whereas the absorption properties are practically unchanged, the CD spectrum in AOT micelles has a lower intensity than in water, which is interpreted as a partial unfolding. The intensity is partly restored when Ca2+ ions are added, indicating that the micellar environment may cause a partial denaturation by depleting it of calcium ions. Fluorescence data show that the emission properties of the protein in reverse micelles match those in aqueous solution at around wo = 13 approx., whereas lambda max shifts towards the red by increasing wo, indicating an exposure of the tryptophan residues and probably an unfolding of the whole protein, at wo values above 15. Finally the reaction between trypsin and its specific macromolecular Kunitz inhibitor from soybeans is studied.(ABSTRACT TRUNCATED AT 400 WORDS)

Folding of collagen IV.

Abstract: Collagen IV dimers of two collagen IV molecules connected by their C-terminal globular NC1 domains were isolated by limited digestion with bacterial collagenase from mouse Engelbreth-Holm-Swarm (EHS) sarcoma tissue. The collagenous domains were only 300 nm long as compared to 400 nm of intact collagen IV but the disulfide bonds in the N-terminal region of the major triple helix were retained. Unfolding of the collagenous domains as monitored by circular dichroism occurred in a temperature range of 30 to 44°C with a midpoint at 37°C. The transition is significantly broader than that of the continuous triple helices in collagens I, II and III, a feature which can be explained by the frequent non-collagenous interruptions in the triple-helical domain of collagen IV. Refolding at 25°C following complete unfolding at 50°C was monitored by circular dichroism, selective proteolytic digestion of non-refolded segments and by a newly developed method in which the recovered triple-helical segments were visualized by electron microscopy. Triple-helix formation was found to proceed in a zipper-like fashion from the C-terminal NC1 domains towards the N-terminus, indicating that this domain is essential for nucleations. For collagen IV dimers with intact NC1 domains the rate of triple-helix growth was of comparable magnitude to that of collagen III, demonstrating that the non-collagenous interruptions do not slow down the refolding process where the rate-limiting step is the cis-trans isomerization of proline peptide bonds. Refolding was near to 100% and the refolding products were similar to the starting material as judged by thermal stability and electron microscopic appearance. Removal of the NC1 domains by pepsin or dissociation of their hexametric structures by acetic acid led to a loss of the refolding ability. Instead products with randomly dispersed short triple-helical segments were formed in a slow reaction. In no case, even when the disulfide bonds in the N-terminal region of the triple-helical domain were intact, was refolding from the N- towards the C-terminus observed. Taken together with results in other collagens, this suggests that C to N directionality might be an intrinsic property of triple-helix folding.

Macroorganization of Chlorophyll a/b Light-Harvesting Complex in Thylakoids and Aggregates: Information from Circular Differential Scattering

Abstract: Circular dichroism (CD) and magnetic circular dichroism (MCD) spectra were recorded for spinach thylakoids and for isolated, aggregated chlorophyll a/b light-harvesting pigment-protein complex, in random and magnetically aligned states of orientation at room and low temperatures. The shape and magnitude of the CD signal of most bands strongly depended on the orientation of the thylakoid membranes or the aggregated pigment-protein complex. In both thylakoids and aggregated light-harvesting complexes, however, the MCD spectra of the two different orientations were almost identical. Random and magnetically aligned samples exhibited anomalous, large CD signals outside the bands of pigment absorbance. Lack of similarity between the corresponding MCD and CD spectra showed that the large CD signals are not produced as a distortion of CD of absorbance by light scattering. Instead, these anomalous spectral features are believed to originate in differential selective scattering of circularly polarized light. The results lead to the conclusion that the light-harvesting pigment-protein complex in thylakoid grana forms a helical macroarray with dimensions commensurate with the wavelengths of the anomalous circular dichroism signals. A hypothesis is put forward suggesting a role for these macrodomains in granal organization.

Interactions between DNA and mono-, bis-, tris-, tetrakis-, and hexakis(aminoacridines). A linear and circular dichroism, electric orientation relaxation, viscometry, and equilibrium study

Abstract: The interaction between DNA and a series of mono-, bis-, tris-, tetrakis-, and hexakis-intercalating 9-aminoacridines has been studied with flow linear dichroism (LD), circular dichroism (CD), electric orientation relaxation (EOR) techniques, and with viscometry and equilibrium analyses. The orientation of the 9-aminoacridine ligand relative to the average orientation of the DNA bases, measured by LD, shows that with both 9-aminoacridine and the bis(acridines) the in-plane short axes of the acridine ligands are oriented perfectly parallel to the planes of the DNA bases, as expected for classical intercalation, whereas the long axes are found to be significantly tilted. This is supported by the DNA lengthening measured by EOR, which for 9-aminoacridine is 1.5 base-pair units, compared with 1.0 for ethidium bromide. Also in case of the tris(acridines) LD, CD, viscometry, and equilibrium data indicate that all acridine ligands are intercalated. The binding analysis shows an increasing degree of cooperativity in the sequence 9-aminoacridine < bis(acridines) < tris(acridines), and the corresponding binding densities, 4, 8, and 11–14, respectively, are in good agreement with those expected from the nearest-neighbor exclusion principle. The LD and CD measurements show that the tetrakis- and hexakis(acridines), despite long and flexible links, bind to DNA with only three of the acridine ligands intercalated.