Showing papers on "Circular dichroism published in 1979"

Interaction of DNA with a porphyrin ligand: evidence for intercalation

Abstract: The porphyrin photosensitizer, meso-Tetra (4-N-methylpyridyl) porphine tetraperchlorate binds to calf thymus DNA by intercalation and by external electrostatic association. This was concluded from the results of measruements involving Scatchard analysis, viscometry, thermal denaturation, and circular dichroism.

Effect of acid pH on the absorption spectra and photoreactions of bacteriorhodopsin.

Abstract: Purple membranes (PM) from Halobacterium halobium were incorporated into 7.5% polyacrylamide gels to prevent aggregation which occurs in suspensions at low pH. At pH 7.0, the circular dichroism (CD) spectra and visible absorption spectra of light- and dark-adapted bacteriorhodopsin (bR558, respectively) and the flash photolysis cycle of bR568 in gels were essentially the same as those in PM suspensions. Titration of the gels with hydrochloric acid showed the transition to a form absorbing at 605 nm (bR605 acid) with pK = 2.9 and to a second form absorbing at 565 nm (bR565 acid) with pK = 0.5. Isosbestic points were seen for each transition in both light- and dark-adapted gels. In addition, a third isosbestic point was evident between pH 3.5 and 7. Visible CD spectra of bR568, bR605 acid, and bR565 acid all showed the bilobed pattern typical of bR568 in suspensions of PM. Flash kinetic spectrophotometry (with 40-microseconds time resolution) of bR605 acid and bR565 acid showed transient absorbance changes with at least one transiently blue-shifted form for each and an early red-shifted intermediate for bR565 acid. Chromophore extraction from membrane suspensions yielded all-trans-retinal for bR565 acid and a mixture of 13-cis and trans isomers for bR605 acid.

Circular dichroism and DNA secondary structure

Abstract: The change in average rotation of the DNA helix has been determined for the transfer from 0.05 M NaCl to 3.0 M CsCl, 6.2 M LiCl and 5.4 M NH4Cl. This work, combined with data at lower salt from other laboratories, allows us to relate the intensity of the CD of DNA at 275 nm directly to the change in the number of base pairs per turn. The change in secondary structure for the transfer of DNA from 0.05 M NaCl (where it is presumably in the B-form) to high salt (where the characteristic CD has been interpreted as corresponding to C-form geometry) is found to be -0.22 (+/- 0.02) base pairs per turn. In the case of mononucleosomes, where the CD indicates the "C-form", the change in secondary structure (including temperature effects) would add -0.31 (+/- 0.03) turns about the histone core to the -1.25 turns estimated from work on SV40 chromatin. Accurate winding angles and molar extinction coefficients were determined for ethidium.

Nonionic nucleic acid analogs. Synthesis and characterization of dideoxyribonucleoside methylphosphonates

Abstract: A series of dideoxyribonucleoside methylphosphonate analogues, dNpN and dNpNp, which contain a nonionic 3'--5' methylphosphonyl internucleoside linkage were prepared. The two diastereoisomers, designated isomers 1 and 2, of each dimer differ in configuration of the methylphosphonate group and were separated by column chromatography. The diastereoisomers of each dimer have different conformations in solution as shown by ultraviolet hypochromicity data and their circular dichroism spectra. For example, dApA isomer 1 is more highly stacked than isomer 2, although both isomers are less stacked than the dinucleoside monophosphate, dApA. The circular dichroism spectrum of isomer 1 is very similar to that of dApA, while the CD spectrum of isomer 2 shows a loss of molecular ellipticity, [theta], at 270 nm and a greatly diminished [theta] at 250 nm. These results suggest that the stacked bases of dApA isomer 1 tend to orient in an oblique manner, while those in isomer 2 tend to orient in a parallel manner. This interpretation is verified by the 1H NMR study of these dimers (L. S. Kan, D. M. Cheng, P. S. Miller, J. Yano, and P. O. P. Ts'o, unpublished experiments). Both diastereoisomers of dAaA form 2U:1A and 2T:1A complexes with poly(U) and poly(dT), respectively. The higher Tm (Tm of poly(U)--isomer 1, 15.4 degrees C; Tm of poly(U)--isomer 2, 19.8 degrees C; Tm of poly(dT)--isomer 1, 18.7 degrees C; Tm of poly(dT)--isomer 2, 18.4 degrees C) values of these complexes vs. those of the corresponding dApA--polynucleotide complexes (Tm of poly(U)--dApA, 7.0 degrees C; Tm of poly(dT)--DApA, 9.2 degrees C) result from decreased charge repulsion between the nonionic dimer backbone and the negatively charged polymer backbone. The difference in conformations between dApA isomer 1 and dApA isomer 2 is reflected in the Tm of the isomer 1-poly(U) complex which is 4.4 degrees C lower than that of the isomer 2-poly(U) complex. Since these nonionic oligonucleotide analogues are taken up by cells in culture, they show promise as molecular probes for the function and structure of nucleic acids inside living cells.

The interpretation of near-ultraviolet circular dichroism.

Abstract: Publisher Summary Circular dichroism (CD) is an absorptive phenomenon. It is defined as the difference between the absorbances of left and right circularly polarized light. This chapter describes a scheme for calculating the CD spectrum of proteins of known three-dimensional structure. Rotating about covalent bonds to modify the conformation with recalculation of the spectrum for the new three-dimensional structure gives the dependence of the optical activity upon conformation. The protein Hamiltonian constructed in the chapter has as its basis set the wave functions of the separate, individual chromophores that are present in the macromolecule. In the wave functions, isolated chromophoric states are mixed with one another, expressing the fact that the electrons of each chromophore may perturb those of all others. To formulate the Hamiltonian that yields these interactions, the chapter establishes a naming and ordering convention for the states of the macromolecule. It also examines interpretive work on the side chains of tyrosine, tryptophan, and the disulfide. These are the major contributors to the near-UV CD of proteins. Phenylalanine and histidine are omitted partly because their contributions are generally much weaker and partly because the state of our understanding of them is less advanced. For each chromophore model, compounds are examined followed by protein studies where available.

Conformation and circular dichroism of DNA

Abstract: CD spectra of calf thymus, C. perfringens, E. coli, and M. luteus DNA have been measured in the vacuum-uv region to about 168 nm for the A-, B-, and C-forms. The positive band at about 187 nm and the negative band at about 170 nm found for each type and form of DNA are sensitive to the source of the DNA and the base–base interactions of the double-stranded helix. The A-form spectra confirm that these bands are indeed sensitive to secondary structure. In the near-uv, the CD of B-form DNA is well analyzed as a linear combination of 27% A-form and 78% C-form. However, an analysis of the extended spectrum demonstrates that the near-uv analysis is not correct. The extended analysis shows that the base–base interactions are similar for B- and C-forms in solution, which implies that these two forms have nearly the same number of base pairs per turn. Various types of CD difference spectra are also discussed.

Induced Circular Dichroism of β-Cyclodextrin Complexes with Substituted Benzenes

Abstract: The induced circular dichroism (ICD) of β-Cyclodextrin(β-CDx)-substituted benzene complexes was investigated. We observed the ICD on the absorption bands of achiral substituted benzene molecules, which is considered to be induced by the dissymmetric field of the chiral β-CDx host molecule. The electronic transitions which are polarized along the long axis of the substituted benzenes showed positive ICD, while the sings of the ICD of short-axis polarized transitions are negative. The rotational strengths of these inclusion complexes were calculated by the Kirkwood-Tinoco expression. From the comparison between the experimental and calculated results, it is concluded that these β-CDx complexes favor the axial inclusion in which the long axis of the substituted benzenes is parallel to the axis of the β-CDx cavity.

Micellar Solubilization of Proteins in Aprotic Solvents and their Spectroscopic Characterisation

Abstract: The quaternary ammonium salt methyl-trioctylammonium chloride enables the transfer of α-chymotrypsin, trypsin, pepsin and glucagone from water to cyclohexane. Reversed micelles, whose polar core solubilizes both protein and water, are probably formed in the apolar phase. The influence of various parameters on the phase transfer (concentration, pH, solvent, temperature, etc.) has been investigated. Absorption, fluorescence and circular dichroism studies of the biopolymers in the cyclohexane system have been carried out. For trypsin and chymotrypsin, the CD. signal in the 200 nm region is very similar in water and in cyclohexane, which suggests that the polypeptide folding is not substantially different in the two phases. The fluorescence quantum yield is always much larger in the cyclohexane phase than in water. The longer wavelength region of the UV. absorption spectrum is slightly red-shifted relative to water, and a band at 225 nm, probably arising from the aromatic chromophore, is apparent in the organic phase. Reasons for these spectral perturbations are discussed. The enzymes transferred from water into cyclohexane phases can be continuously retransferred into a second water phase. The possible relevance of this ‘double transfer’ as a model for the vectorial transport of biopolymers or a separation technique is discussed.

Characterization of pepsin fragments of basement membrane collagen obtained from a mouse tumor.

Abstract: Basement membrane collagen was purified from an acetic acid extract of a mouse tumor and subjected to pepsin treatment. At initial stages disulfide-linked molecules, consisting of peptide chains with an apparent molecular weight of 140000, were formed which were some 15 - 20 smaller than the chains in the original protein. In a second stage further fragmentation occurred producing at least five peptides ranging in molecular weight from 27000 to 72000. Each of these peptides was isolated and characterised by amino acid composition, cyanogen bromide cleavage, circular dichroism and antigenic activity. The data indicate that the major portion of the initial pepsin-resistant fragment is degraded forming two triple-helical segments, the disulfide-linked fragment P3 and the cysteine-free fragment P1 containing chains with molecular weights of 72000 and 55000 respectively. The other fragments (P2, P3B and P3C) were recovered at lower yields and may originate from a second, genetically distinct type of basement membrane collagen. This interpretation is supported by partial amino acid sequence analysis of the two non-disulfide-linked fragments (Pl, P2). These sequences show that P1 and P2 are different and start with a non-helical sequence followed by the helical triplet structure Gly-X-Y. Studies on pepsin fragments of the insoluble tumor collagen demonstrated a pattern similar to that obtained with the soluble form except for the occurrence of disulfide-linked a-chain-like material. These chains also have an amino acid composition characteristic for basement membrane collagen. Taken together, the findings suggest that the tumor produces several related collagens. Pepsin digestion is a convenient method to solubilize and characterize interstitial collagens, since the enzyme removes short, non-helical cross-linking sequences from the ends of the molecule but leaves the large, triple-helical body of the molecule intact [l, 21. Kefalides [3] has reported that basement membrane collagen has a structure similar to other collagens and consists of three ul(1V) chains after pepsin treatment. Others have not found abundent amounts of u-chainlike material in pepsin digests of basement membranes but rather collagenous polypeptides both larger and smaller than x chains [4 - lo]. Circular dichroism studies [7,11] and electron microscopy [7,12,13] have, however, shown that basement membrane collagen possesses a typical triple-helical structure which is as long as or even extends beyond the triple helix of interstitial collagens. The marked heterogeneity of fragments from the basement membrane collagen after

Purification and Characterization of 3,4-Dihydroxyphenylalanine Decarboxylase from Pig Kidney

Abstract: A procedure for 3,4-dihydroxyphenylalanine decarboxylase from pig kkdney purification is described in detail. The preparation has no detectable impurity on electrophoresis and on ultracentrifugation and authors. However two significant differences are observed: a different stimulation of activity by added pyridoxal 5'-phosphate and a nearly complete decarboxylation of L-3,4-dihydroxyphenylalanine in absence of added coenzyme. Absorption, fluorescence and circular dichroism properties of the coenzyme-apoenzyme interaction are also described. The results are consistent with the existence of at least four coenzyme-apoenzyme complexes, three of them active.

Chirale 2,2′‐Polyoxaalkano‐9,9′‐spirobifluorene

Abstract: Chiral 2,2′-polyoxaalkano-9,9′-spirobifluorenes From 2,2′-diacetyl-9,9′-spirobifluorene (2), twelve chiral polyethers have been prepared as potential ion- and enantiomer-selective ionophores. The absolute configuration of the polyethers 15–17, 19–22, and 25 has been determined by chemical correlation with vespirenes [11] [29], by circular dichroism, and by X-ray analysis. The circular dichroism of 15–17, 19 and 21 depends on the size of the macrocycle and indicates that the fluorene chromophores of 19 and 21 with 13- and 16-membered rings respectively deviate considerably from orthogonality.

The Molecular Basis of Optical Activity: Optical Rotatory Dispersion and Circular Dichroism

Abstract: Demonstrates how the phenomena of optical activity are treated by spectroscopists and theoreticians. Bridges the gap between chiroptical observations and underlying physical laws. Emphasizes the treatment of optical activity as absorptive processes in which the radiation-molecule interaction results in a transition which carries the molecule from one quantum state to another.

Plant proanthocyanidins. Part 6. Chiroptical studies. Part 95. Circular dichroism of procyanidins

Abstract: Circular dichroism spectra of 26 procyanidins and their derivatives have been measured. All exhibit a strong positive or negative couplet at 200–220 nm and this has been correlated with the absolute stereochemistry at C-4 on the interflavan linkage.

Fluorescence studies of native and modified neurophysins. Effects of peptides and pH.

Abstract: The effect of neurophysin-hormone interaction on the environment of the single tyrosine of bovine neurophysin (Tyr-49) and on that of the tyrosine of oxytocin and vasopressin was studied by fluorescence; tyrosine-free peptides were used to determine effects on Tyr-49, and acetylated neurophysin was used to determine effects on the hormone tyrosine Binding increases the fluorescence intensity of Tyr-49 by 130% while the fluorescence of the hormone tyrosine is almost completely quenched Correlation of these results with those obtained on binding oxytocin or vasopressin to native neurophysin indicates that in the hormone complexes less than half of the fluorescence of Tyr-49 is lost by Forster energy transfer to the quenched hormone tyrosine These results support spin-label studies in indicating that the distance between Tyr-49 and the tyrosine of hormone bound to the strong hormone binding site is greater than 5 A In the absence of peptides, the fluorescence of Tyr-49 increases by 40% on lowering the pH from 62 to 2 Titration of the acid fluorescence transition in bovine neurophysins-I and -II, and in bovine neurophysin-II treated with carboxypeptidase B to remove the Arg-Arg-Val sequence at the carboxyl terminus, indicates that this transition is due to titration of a side-chain carboxyl with an intrinsic pK of 46 The effects of guanidine, glycerol, and disulfide cleavage on the magnitude of the acid transition indicate that the conformational information necessary for the transition resides within the amino acid sequence adjacent to Tyr-49 Accordingly, the fluorescence acid transition is attributed to decreased quenching by Glu-46 or Glu-47 upon protonation Glycerol is shown to perturb the glutamate-tyrosine interaction in the absence of general conformational effects Comparison of the fluorescence low-pH transition with that of the low-pH circular dichroism transition of nitrated neurophysins suggests that the fluorescence and CD transitions reflect related, but not necessarily identical, phenomena In an appendix, evidence is presented which suggests that the products of carboxy-peptidase digestion of bovine neurophysin-II are the same as two minor bovine neurophysin components, one of which is neurophysin-C