Vibrational circular dichroism studies of the A-to-B conformational transition in DNA.

The vibrational circular dichroism (VCD) spectra of several natural DNAs as well as tRNA, poly(dG-dC).poly(dG-dC), and poly(dA-dT).poly(dA-dT) are reported for the base deformation modes in the IR region from 1700 to 1550 cm-1 for the polymers in D2O as well as in high alcohol dehydrating conditions. Spectra of both the B- and A-forms were identified. The A-form DNA VCD, not previously reported, has characteristics that can be found in the VCD spectra of RNAs as would be expected from the similarity of their structures. The VCD is sequence-dependent. Under the dehydrating conditions studied, poly(dA-dT)poly(dA-dT),poly(dA).poly(dT), and a high-A-T fraction natural DNA had a different bandshape from the other DNAs, which was similar to that of poly(rA).poly(rU). Poly(dG-dC).poly-(dG-dC) did not form an A-form in high-alcohol conditions but instead had a VCD spectrum much like that of its high-salt-induced Z-form. Qualitative differences seen experimentally between A- and B-form DNA VCD were suggested by the differences in the coupled oscillator VCD calculated for the two forms.     

High-field NMR studies of 3beta-tetrahydropyranyloxy steroids

Comprehensive NMR studies were carried out on 3beta-hydroxy-pregnene and cholestene analogs, each containing a tetrahydropyranyl ether group at the 3-position. Two-dimensional NMR experiments (COSY, TOCSY, HSQC, and HSQC-TOCSY) permitted the complete assignments of both the (1)H and (13)C resonances of these derivatives in deuterated benzene or chloroform. The aromatic solvent-induced NMR signal shifts (ASIS) were also investigated.     

Fluorescence and circular dichroism studies on binding and conformational aspects of an anti-leukemic drug with DNA

In the present study, we have explored the mode of binding of an anti-leukemic drug, imatinib (IMT) mesylate with DNA and resulting conformational changes in DNA double helix. UV–Vis absorption, fluorescence and circular dichroism spectroscopic techniques were employed to study these interactions. Spectroscopic results revealed that the intercalation was the primary mode of interaction between IMT and DNA. The binding constant value of 6.62 × 10³ M^?1 indicated the moderate interaction between IMT and DNA. Melting temperature of DNA increased from 75 to 80 °C upon interaction with IMT.     

Protein conformational relaxation following photodissociation of CO from carbonmonoxymyoglobin: picosecond circular dichroism and absorption studies

Picosecond time-resolved polarization spectroscopy is used to study relaxation dynamics in myoglobin following photoelimination of CO from carbonmonoxymyoglobin. Evolution of the transient circular dichroism signal of the N band of myoglobin (probed at 355 nm) to that characteristic of equilibrium myoglobin requires approximately 300 ps. This time scale is significantly longer than that corresponding to the photoinitiated bond cleavage. Transient linear dichroism of the Soret band and picosecond time-resolved magnetic circular dichroism measurements of the Q band demonstrate that the circular dichroism kinetics do not result from either time-dependent changes in the orientation of the transition moments of the heme ring or the doming of the heme that accompanies the out-of-plane motion of the iron. Finally, transient absorption data of the near-IR optical transition of photogenerated myoglobin suggest that the circular dichroism data are not a measure of the tilting of the proximal histidine. The circular dichroism data are discussed in terms of a relaxation in the tertiary structure of the protein following dissociation.     

Study of the conformational properties of C-terminal fragments of histones H1, H5, and beta-endorphin by circular dichroism]

Circular dichroism technique has been used for investigating the conformation of histone H1 and H5 C-terminal fragments and beta-endorphin. It has been shown that in aqueous solution these polypeptides adopt preferably the left-handed helical conformation of the poly-L-proline II type. The linear temperature dependence of the CD value during solution heating was found to be broken in the temperature interval between 50 and 55 degrees C. It was supposed to occur due to the conformation destruction.     

Conformational features of bradykinin. A circular dichroism study of the aromatic side-chains

The circular dichroism (CD) of the peptide hormone bradykinin and its analogues, [Phe(H4)5]-bradykinin, [Phe(H4)8]bradykinin, [Phe(H4)5,8]bradykinin, [TyrOMe5]bradykinin, [TyrOMe8]bradykinin and [TyrOMe5.8]bradykinin, is described. The comparison of the CD spectra of these analogues with each other, recorded under a variety of conditions (pH, solvent, temperature), allows the monitoring of the behaviour of the aromatic side-chains (phenylalanine, tyrosine) and an estimation of their respective spectral contributions in both spectral regions (320-250 nm, 250-190 nm) with good precision. Conformational non-equivalence of the residues Phe-5 and Phe-8 together with some overall conformational features of bradykinin are thus established.     

Synthesis and conformational studies of ribooligonucleotides which contain an alternating C-G sequence and show unusual circular dichroism spectra

The poly [r(C-G)] duplex shows an unusually large negative CD band in the long wavelength region. In order to elucidate this phenomenon, r(C-G-C-G) and r(C-G-C-G-C-G) were synthesized by a phosphotriester method and their properties were examined by UV, CD, 1H and 31P NMR spectroscopy. These ribooligomers form self-duplexes at low temperature, the CD spectra of which show negative bands at around 290 nm and positive bands at around 265 nm. The results of 1H nuclear Overhauser effect experiments, 1H chemical shift-temperature profiles of base protons, and the sharp singlet observed for all H1' protons are consistent with a normal A-RNA structure but not with a Z-DNA like structure. The CD-temperature profiles and 31P NMR spectra support this conclusion. These results indicate that RNA duplexes with an alternating C-G sequence can give an unusually large negative CD band in the long wavelength region despite their right-handed helical structure.     

Synthesis, conformational and pharmacological studies on dermorphin N-terminal tetrapeptide analogues

Summary Dermorphin structure-activity relationships toward μ and δ opioid receptors were investigated using a series of synthetic peptides, in which the aromatic residues at positions 1 or/and 3 of the N-terminal tetrapeptide analogue H-Tyr-d-Arg-Phe-β-Ala-NH₂ were replaced by unnatural or constrained amino acids.     

Fluorescence-detected circular dichroism studies of serum albumins

Multidimensional fluorescence-detected circular dichroism (FDCD) is used to investigate the binding of bilirubin to four mammalian serum albumins. It is shown that the complexes formed with the albumins have distinctly different FDCD spectra. The effect of the pH-dependent transition from basic to acidic conditions on the complexes is examined. The binding of warfarin to albumin is also presented to demonstrate the general analytical utility of the multidimensional FDCD measurement for biochemical analysis.     

Bicelle membranes and their use for hydrophobic peptide studies by circular dichroism and solid state NMR

Mixtures of dicaproyl- (DC), dimyristoyl- (DM) and 1-tetradecanoyl-2-biphenylbutanoyl-(TBB) phosphatidylcholine (PC) in water produce bicelle membranes that are oriented by magnetic fields. DMPC/DCPC systems orient such that their membrane plane is parallel to the magnetic field, whereas for TBBPC/DCPC, the plane is perpendicular to the field. Partial temperature-composition-hydration diagrams are established using solid-state 31P-NMR. DMPC/DCPC bicelles exist on a large range of composition but on a narrow temperature domain (25-45 degrees C). At converse, TBBPC/DCPC form bicelles on a narrow compositional range but over a large temperature span (10-70 degrees C). The TBBPC/DCPC bicelles are shown to be a very powerful potential tool to study the orientation of hydrophobic helices in membranes using wide line 15N-NMR. The DMPC/DCPC system that undergoes a micelle-to-bicelle transition on going from 10 degrees C to 40 degrees C may be used with circular dichroism to study the state of association of hydrophobic helices within the membrane. Results suggest that the transmembrane fragment of the neu/erbB-2 receptor is monomeric in micellar medium and dimeric/multimeric in bicelle membranes.     

Assessment of configurational and conformational properties of naringenin by vibrational circular dichroism

The electronic circular dichroism (ECD) and vibrational circular dichroism (VCD) spectra of both enantiomers of naringenin (4',5,7-trihydroxyflavanone) in acetonitrile solution have been measured. The enantiomers were obtained by chiral HPLC separation of the racemic sample. DFT calculations have been performed for relevant conformers and subsequent evaluations of VCD spectra are compared with VCD experiments: safe assignment of the absolute configuration is provided, based in particular on the VCD data. The relevance of the rotational conformers of the hydroxyl groups and of the mobility of phenol moiety is studied: based on this, we provide a first interpretation of the observed intense and broad couplet at 1325/1350 cm(-1). Four conformers contribute to this pattern with different sign and amplitude as shown by DFT calculations. Time dependent DFT calculations have been performed and compared with ECD experimental data, under the same assumption of conformational properties and mobilities investigated by VCD.     

Fluorescence,circular dichroism,NMR, and docking studies of the interaction of the alkaloid malbrancheamide with calmodulin

A new malbrancheamide analogue, isomalbrancheamide B (3), along with three known compounds, malbrancheamide (1), isomalbrancheamide (2), and premalbrancheamide (4), were isolated in higher yields from the alkaloid fraction of the fungus Malbranchea aurantiaca. The interaction of the alkaloids 1–4 with calmodulin (CaM) was analyzed using different enzymatic, fluorescence, spectroscopic, nuclear magnetic resonance (NMR), and molecular modelling techniques. On the basis of the enzymatic and fluorescence experiments, malbrancheamides 1–3 are classical CaM inhibitors. Compound 4, however, did not quench the extrinsic fluorescence of the CaM biosensor indicating that it could be a functional inhibitor. Circular dichroism, NMR, and molecular modelling studies revealed that 1 binds to CaM in the same hydrophobic pocket than the chlorpromazine and trifluoperazine, two classical CaM inhibitors. Thus, malbrancheamide and related monochlorinated analogues are compounds with a high potential for the development of new therapeutic agents, involving CaM as their molecular target.     

Synthesis, conformational and pharmacological studies on dermorphin N-terminal tetrapeptide analogues

Dermorphin structure–activity relationships toward and opioid receptors were investigated using a series of synthetic peptides, in which the aromatic residues at positions 1 or/and 3 of the N-terminal tetrapeptide analogue H-Tyr-d-Arg-Phe--Ala-NH₂ were replaced by unnatural or constrained amino acids.     

Protein and peptide secondary structure and conformational determination with vibrational circular dichroism

Vibrational circular dichroism (VCD) provides alternative views of protein and peptide conformation with advantages over electronic (UV) CD (ECD) or IR spectroscopy. VCD is sensitive to short-range order, allowing it to discriminate beta-sheet and various helices as well as disordered structure. Quantitative secondary structure analyses use protein VCD bandshapes, but are best combined with ECD and IR for balance. Much recent work has focused on empirical and theoretical VCD analyses of peptides, with detailed prediction of helix, sheet and hairpin spectra and site-specific application of isotopic substitution for structure and folding.     

Conformational features of bradykinin. A circular dichroism study of some peptide fragments and structural analogues of bradykinin.

The vasoactive hormone bradykinin, its N-and C-terminal fragments and some structural analogues were studied by Circular Dichroism. Conformational features of the peptide can be detected by comparative analysis of the various CD spectra recorded as a function of aqueous pH, solvent and temperature. It is shown that the two biologically essential arginine residues (Arg1 and Arg9) are important for the specific folded bradykinin conformation. Differences between bradykinin, its fragments and analogues become clearly established in conformational terms, and are discussed in relation to the biological activity of these peptides.     

Fourier transform vibrational circular dichroism as a decisive tool for conformational studies of peptides containing tyrosyl residues

Previous UV-circular dichroism (UV-CD) and NMR studies showed that Ac-AAAAAAAEAAKA-NH(2) has an alpha-helical structure in 50% (v/v) aqueous trifluoroethanol. Replacement of Ala(1) to Ala(6) with Tyr results in spectra that show an apparent loss of helicity in the same solvent. This apparent loss of helicity could be attributed to the coupling of the tyrosyl side chain chromophore with the backbone amide. However, such electronic coupling does not affect the vibrational CD (VCD) spectra. The VCD spectra of the peptides with tyrosyl residues were identical to that of the peptide containing no Tyr, which shows the same alpha-helical structure. Because it is now clear that Tyr replacement does not change the backbone conformation of peptides, UV-CD measurements should be complemented by VCD to determine the secondary structure when electronic effects can disturb the UV-CD spectrum of the inherent structure.