Showing papers on "Circular dichroism published in 1982"

Structure of methylene blue-DNA complexes studied by linear and circular dichroism spectroscopy.

Abstract: Bradley et al. [(1972) Biopolymers11, 645–652] used electro-optical measurements to show that methylene blue (MB), like acridine orange, in its DNA complex is oriented more or less perpendicular to the helix axis as expected if intercalated. High-precision flow linear dichroism (LD) here confirms that MB is coplanar with the DNA bases at low dye/DNA binding ratios and low ionic strengths. CD shows two origins of induced optical activity for the transition of lowest energy (polarized parallel to the long-axis of the dye molecule): at low binding ratios (r 300 mM Na+ or >0.4 mM Mg2+). Nondegenerate coupled-oscillator theory can explain the CD in terms of interactions of transition moments of the dye and the nearest nucleotide bases and indicates a change between two intercalation geometries: a Lerman type of mode, denoted γ−, and an orthogonal mode, denoted γ+. This rotation of MB in the base-pair pocket is accomplished at Na+ and Mg2+ concentrations when the phosphates are effectively screened and the result suggests a more localized bonding of Mg2+ than is expected from simple polyelectrolyte models. The exciton effect at high binding ratios, observed both in CD and in LD, can be interpreted in terms of an interaction between an intercalated and a nonintercalated MB. The geometry of this “accidental” dimer is consistent with a location of the nonintercalated MB in the minor groove, bridging the strands by the positively charged amino groups directed towards phosphate groups. The dihedral angle of the MB pairs, corresponding to a left-handed helix, is opposite to that with acridine orange and proflavine on DNA, indicating that the latter ligands bind to DNA in a different way.

Molecular Optical Activity and the Chiral Discriminations

Abstract: 1. Introduction 2. Optical rotatory dispersion and circular dichroism 3. General mechanisms for optical activity 4. The symmetric chromophore in a chiral molecular environment 5. Inherent dissymmetry 6. Dimers and polymers 7. Chiral transition-metal complexes 8. Vibration optical activity 9. The characterisation of chiral structures 10. Enantiomeric discrimination 11. Chiral energy discrimination.

Protease resistance and conformation of laminin.

Abstract: Laminin, obtained from a tumor basement membrane, was treated with neutral proteases (trypsin, chymotrypsin, elastase, subtilisin, Stuphylococcus aureus protease), which all produced similar fragment patterns upon prolonged digestion. The patterns were different from those obtained for fibronectin, which showed a much higher susceptibility to proteolysis by the same enzymes. Four large fragments could be purified which accounted together for more than half of the mass of laminin. They were found to differ in size, amino acid composition, spectral properties and antigenicity. The largest fragment 1 (Mr 260000-300000) was rich in half-cystine (120 residues/1000) and showed a circular dichroism spectrum indicating the absence of α helix and β structure. Fragment 3 (Mr= 50000) possessed beta; structure and was able to bind onto heparin-Sepharose. Fragments 2 (Mr= 50000) and 4 (Mr= 75000) were related structures and their relative yields depended on the protease used. They showed spectra similar to those of fragment 1. Electron microscopy revealed that fragment 1 consists of three rodlike elements (length 26 nm) connected to each other at one end. The other fragments appeared as globules (fragment 3), short rods (fragment 2) or globules connected to a short rod (fragment 4). Data obtained from limited proteolysis indicated that fragment 1 and 4 (or 2) are in close proximity to each other in the three short arms of laminin, which in its intact form has the shape of an asymmetric cross. The long arm appeared to be readily degraded by proteases. Circular dichroism studies of native laminin indicated about 55%, aperiodic structures, 15%β structure and 30%× helix. The α helix was readily destroyed by proteolysis and showed a sharp, reversible transition at 58° C. Stability of these structures was decreased by reduction of disulfide bonds or by increasing concentrations of guanidine. Heat denaturation rendered laminin susceptible to plasmin, which did not degrade the native protein. Cleavage occurred mainly within the 440000-Mrpolypeptide chain of laminin and was accompanied by a partial loss of the long arm.

Calcium-dependent .alpha.-helical structure in osteocalcin

Abstract: Osteocalcin is an abundant Ca2+-binding protein of bone containing three residues of vitamin K dependent gamma-carboxyglutamic acid (Gla) among its 49 (human, monkey, cow) or 50 (chicken) amino acids. Gla side chains participate directly in the binding of Ca2+ ions and the adsorption of osteocalcin to hydroxylapatite (HA) surfaces in vivo and in vitro. Osteocalcin exhibits a major conformational change when Ca2+ is bound. Metal-free chicken osteocalcin is a random coil with only 8% of its residues in the alpha helix as revealed by circular dichroism. In the presence of physiological levels of Ca2+, 38% of the protein adopts the alpha-helical conformation with a transition midpoint at 0.75 mM Ca2+ in a rapid, reversible fashion which (1) requires an intact disulfide bridge, (2) is proportionally diminished when Gla residues are decarboxylated to Glu, (3) is insensitive to 1.5 m NaCl, and (4) can be mimicked by other cations. Tyr fluorescence, UV difference spectra, and Tyr reactivity to tetranitromethane corroborate the conformational change. Homologous monkey osteocalcin also exhibits Ca2+-dependent structure. Integration of predictive calculations from osteocalcin sequence has yielded a structural model for the protein, the dominant features of which include two opposing alpha-helical domains of 9-12 residues each, connected by a bea turn and stabilized by the Cys23-Cys29 disulfide bond. Cation binding permits realization of the full alph a-helical potential by partial neutralization of high anionic charge in the helical domains. Periodic Gla occurrence at positions 17, 21, and 24 has been strongly conserved throughout evolution and places all Gla side chains on the same face of one alpha helix spaced at intervals of approximately 5.4 A, closely paralleling the interatomic separation of Ca2+ in the HA lattice. Helical osteocalcin has greatly increased affinity for HA; thus, the Ca2+-induced structural transition may perform an informational role related to bone metabolism.

A salt bridge stabilizes the helix formed by isolated C-peptide of RNase A

Abstract: C-peptide, which contains the 13 NH2-terminal residues of RNase A, shows partial helix formation in water at low temperature (1 degree C, pH 5, 0.1 M NaCl), as judged by CD spectra; the helix is formed intramolecularly [Brown, J. E. & Klee, W. A. (1971) Biochemistry 10, 470-476]. We find that helix stability depends strongly on pH: both a protonated histidine (residue 12) and a deprotonated glutamate (residue 9 or 2 or both) are required for optimal stability. This information, together with model building, suggests that the salt bridge Glu-9- ... His-12+ stabilizes the helix. Formation of the helix is enthalpy driven [van't Hoff delta H, - 16Kcal/mol (1 cal = 4.18 J)] and the helix is not observed above 30 degrees C. Proton NMR data indicate that several side chains adopt specific conformations as the helix is formed. These results have two implications for the mechanism of protein folding. First, they indicate that short alpha-helices, stabilized by specific side-chain interactions within the helix, can be stable enough in water to function as folding intermediates. Second, they suggest that similar experiments with peptides of controlled amino acid sequence could be used to catalogue the intrahelix interactions that stabilize or destabilize alpha-helices in aqueous solution. These data might provide the code relating amino acid sequence to the locations of alpha-helices in proteins.

Folding of the mitochondrial proton adenosinetriphosphatase proteolipid channel in phospholipid vesicles.

Abstract: The mitochondrial H+-ATPase proteolipid from Neurospora crassa was incorporated into small unilamellar dimyristoylphosphatidylcholine vesicles and its conformation determined by circular dichroism spectroscopy (CD) While the largely alpha-helical conformation is relatively independent of the method of incorporation into vesicles, ie, rehydration, detergent dialysis, or detergent dilution, the proteolipid conformation was significantly different in detergent micelles and in organic solvents Only very slight changes in the CD spectrum were observed upon binding of the H+-ATPase inhibitor dicyclohexylcarbodiimide to the proteolipid in vesicles, thus suggesting that the inhibitor acts either by blocking the channel or by masking an essential charge group, rather by than causing an overall conformational change in the channel Additionally, very similar CD spectra were obtained for vesicles with different lipid/protein mole ratios, indicating either that no substantial conformational differences exist between monomer and multimers or that monomers self-associate to form stable complexes during incorporation into vesicles This study has provided a physical basis for model-building studies of the proteolipid channel structure

Conformation and aggregation of melittin: dependence on pH and concentration.

Abstract: Melittin, a 26-residue peptide from bee venom, is transformed from a largely random to a largely alpha-helical conformation at elevated pH. At 3 x 10(-5) M melittin, circular dichroism spectra show a transition with a pK near 9.6. At 8 x 10(-5) M, two approximately equal transitions occur with pKs at 7.2 and 9.6. At 6 x 10(-4) M, a single transition is seen with a pK of 6.8, followed by a more gradual increase to at least pH 11. The transitions near pH 7 presumably arise from deprotonation of the alpha-amino group. When the amino groups are acetylated or succinylated, a 60% alpha-helical conformation is adopted at neutral or low pH. The acylated melittins form more stable oligomers than does native melittin.

Conformational states of tubulin liganded to colchicine, tropolone methyl ether, and podophyllotoxin.

Abstract: The conformational effects of colchicine, podophyllotoxin, and tropolone methyl ether binding to tubulin have been studied. Conditions for the stability of the purified calf brain protein were established, and the effects of binding were examined by means of difference absorption spectroscopy, circular dichroism, fluorescence, activation of tubulin GTPase, and tubulin self-association reactions. The tubulin-colchicine complex was isolated and characterized. It displays quenched intrinsic protein fluorescence, ligand fluorescence, and GTPase activity, probably accompanied by minor perturbations in the secondary structure. The conformation of the tubulin-colchicine complex appears to be nonidentical with that of the unliganded protein. Podophyllotoxin was not found to induce any of the mentioned changes. This ligand seems to bind through a hydrophobic interaction of its trimethoxybenzene ring with tubulin, as does colchicine. Binding of tropolone methyl ether, which is the analogue of the other part of the colchicine molecule that binds to tubulin, produced effects consistent with a ligand-linked conformational change. The small perturbation by tropolone methyl ether of the circular dichroism spectrum of tubulin resembles changes induced by colchicine.

Z* DNA, the left-handed helical form of poly[d(G-C)] in MgCl2-ethanol, is biologically active.

Abstract: The interconversion between the right (R) and left (L) helical forms of poly[d(G-C)] occurs at low concentrations of MgCl2 and EtOH, acting together in a highly synergistic manner. Thus, the cooperative R---L transition is induced by only 0.4 mM and 4 MM MgCl2 in combination with 20% and 10% EtOH, respectively. The L form of poly[d(G-C)] formed under these conditions has the spectroscopic properties (absorption, circular dichroism) previously demonstrated under high salt conditions (Pohl and Jovin, 1972) and thought to correspond to the left-handed Z DNA structures recently established by X-ray crystallography (Wang et al., 1979; Drew et al., 1980). However, L DNA formed in Mg2+-EtOH (which we designate as Z* DNA) has unique properties: a) it can be sedimented readily out of solution at low speed, indicative of condensation and intermolecular aggregation; b) it supports the binding of several intercalating (ethidium bromide, actinomycin D) and non-intercalating (mithramycin) drugs, although these interact preferentially with the R (i.e., B) form of DNA; and c) it functions as a template for Escherichia coli RNA polymerase. B and Z* DNAs can be generated under identical ionic conditions and compared in a number of biochemical systems. Our results suggest that left-handed DNA may form under physiological conditions and serve a biological function.

Mn2+ and other transition metals at low concentration induce the right-to-left helical transformation of poly[d(G-C)].

Abstract: The effects of the first-row transition metal ions on the right(B)- to left(Z)-handed helical transition of poly[d(G-C)] have been determined. The Z conformation is induced by MnCl2 at submillimolar concentrations. The forward reaction has a very large activation energy (440 kJ/mol) so that a facile conversion occurs only at temperatures above 45 degrees C. However, the left-handed form remains stable upon cooling. The addition of ethanol (20% v/v) eliminates the requirement for elevated temperature. The transition is highly co-operative and is accompanied by spectral changes (absorption, circular dichroism) characteristic for the B----Z conformational transition. NiCl2 and CoCl2 also induce the B----Z transition in poly[d(G-C)] but the activation energies and thus the temperature requirements for the forward reaction are lower than those observed with MnCl2. The left-handed DNA formed in the presence of Mn2+ is similar to 'Z DNA' previously described in Mg2+-EtOH (van de Sande and Jovin , 1982): (a) it readily sediments out of solution at low speed as a consequence of intermolecular association which, however, is not accompanied by turbidity; and (b) it supports the binding of ethidium bromide although this drug interacts preferentially with the B form of DNA. With Ni2+, the B----Z isomerization step can be separated from the subsequent specific Z----Z* association. Mn2+, Ni2+, and Co2+ also promote the B----Z transition of poly[d(G-m5C)] at substoichiometric concentrations with respect to DNA nucleotide.

Interaction of cis-[Pt(NH3)2(H2O)2](NO3)2 with ribose and deoxyribose diguanosine phosphates

Abstract: The three diguanosine phosphates GpG (4 X 10(-4) M), d(GpG) (10(-5) M), and d(pGpG) (10(-5) M) have been reacted with cis-[Pt(NH3)2(H2O)2](NO3)2 (1 Pt/dinucleotide) in water at pH 5.5 and 37 degrees C. In each case a single product is formed. The three complexes have been characterized by proton nuclear magnetic resonance (1H NMR) and circular dichroism (CD) analyses. They are N(7)-N(7) chelates of the metal with an anti-anti configuration of the bases. They present a conformational change upon deprotonation of guanine N(1)H whose pKa is ca. 8.7 (D2O). Their CD spectra, compared to those of the free dinucleotides, exhibit an increase of ellipticity in the 275-nm region, which can be qualitatively related to the characteristic increase reported for platinated DNA and poly(dG) . poly(dC). These results are in favor of the hypothesis of intrastrand cross-linking of adjacent guanines, by the cis-PtII(NH3)2 moiety, after a local denaturation of DNA.

Raman spectral evidence for a mu-oxo bridge in the binuclear iron center of ribonucleotide reductase.

Abstract: The Raman spectrum of the B2 subunit of Escherichia coli ribonucleotide reductase shows a peak at 496 cm-1 that appears to be in resonance with the 370-nm electronic transition of the binuclear iron center in both the native and radical-free forms of the protein. Exposure of the protein to H218O causes the peak to shift to 481 cm-1, indicating that the vibrational mode is due to an Fe-O moiety in which the oxygen can exchange with solvent. The rate of oxygen exchange (kobsd = 8.3 x 10-4 s-1) is consistent with a mu-oxo-bridged structure. Protonation of the oxygen is unlikely since the Fe-O vibration fails to shift to lower frequency in D2O. Instead, there is a gradual increase in the vibrational frequency with time to a maximum value of 502 cm-1 after 3 h in 70% with time to a maximum value of 602 cm-1 after 3 h in 70% D2O. Apparently, the deuteration of successive protein functional groups causes a slight alteration in the structure of the binuclear iron center. The resonance Raman characteristics of the Fe-O-Fe group in protein B2 are similar to those previously reported for the mu-oxo-bridged binuclear iron center in hemerythrin. A further similarity between the two proteins is the high degree of alpha-helical content. Circular dichroism measurements place this value at approximately 60% for the B2 subunit of ribonucleotide reductase.

Conformational transitions of poly(dA-dC).poly(dG-dT) induced by high salt or in ethanolic solution

Abstract: Poly(dA-dC).poly(dG-dT) was studied by circular dichroism in the presence of high CsCl concentrations and in ethanolic solutions. This alternating purine-pyrimidine duplex may undergo two conformational transitions from a B-type to a novel structure and subsequently into an A-form. Cs+ ions or increasing ethanol concentrations induced a change of the B-type CD spectrum and an inversion of the long wavelength CD band. Lowering the temperature below 0 C or addition of small amounts of Ca++ ions were particularly potent in producing a large negative CD band. A modified B-type structure or a conversion into a left-handed Z-form is considered for this conformational transition.