Observed CD Spectra Research Articles

Combination of a New Chiroptical Probe and Theoretical Calculations for Chirality Detection of Primary Amines

A method to determine absolute configurations of primary amines by combined use of a chiroptical probe 1 and theoretical calculations is reported. Probe 1 is linked to chiral primary amines yielding 1-amine conjugates, which exhibited exciton coupled circular dichroism in the m-quaterphenyl chromophores. The ratios between the P and M conformers of the 1-amine conjugates, which are calculated with DFT, were correlated highly with the sign and amplitude of the observed CD spectra.

Designed Coiled Coils Promote Folding of a Recombinant Bacterial Collagen

Collagen triple helices fold slowly and inefficiently, often requiring adjacent globular domains to assist this process. In the Streptococcus pyogenes collagen-like protein Scl2, a V domain predicted to be largely α-helical, occurs N-terminal to the collagen triple helix (CL). Here, we replace this natural trimerization domain with a de novo designed, hyperstable, parallel, three-stranded, α-helical coiled coil (CC), either at the N terminus (CC-CL) or the C terminus (CL-CC) of the collagen domain. CD spectra of the constructs are consistent with additivity of independently and fully folded CC and CL domains, and the proteins retain their distinctive thermal stabilities, CL at ∼37 °C and CC at >90 °C. Heating the hybrid proteins to 50 °C unfolds CL, leaving CC intact, and upon cooling, the rate of CL refolding is somewhat faster for CL-CC than for CC-CL. A construct with coiled coils on both ends, CC-CL-CC, retains the ∼37 °C thermal stability for CL but shows less triple helix at low temperature and less denaturation at 50 °C. Most strikingly however, in CC-CL-CC, the CL refolds slower than in either CC-CL or CL-CC by almost two orders of magnitude. We propose that a single CC promotes folding of the CL domain via nucleation and in-register growth from one end, whereas initiation and growth from both ends in CC-CL-CC results in mismatched registers that frustrate folding. Bioinformatics analysis of natural collagens lends support to this because, where present, there is generally only one coiled-coil domain close to the triple helix, and it is nearly always N-terminal to the collagen repeat.

A significant role for high‐energy transitions in the ultraviolet circular dichroism spectra of polypeptides and proteins

The nπ* and ππ* transitions of polypeptides mix significantly with very high energy transitions in the poly(Pro)II conformation, as evidenced by the strongly nonconservative CD spectrum in the 170-250 nm region. Because of this, the exciton model, the standard quantum mechanical model for predicting absorption and CD spectra of polypeptides, gives poor results for the poly(Pro) II (P(II)) conformation, although it works well for the α-helix, β-sheet, and β-turns. The exciton theory has been extended to include the effects of mixing of discrete peptide transitions near 200 nm with the large number of uncharacterized transitions in the deep ultraviolet. These latter transitions dominate the polarizability, and their mixing with the discrete transitions can be described via bond and lone-pair polarizability tensors, derivable by ab initio methods. This extended exciton method gives a good description of the CD spectrum of (Ala)(n) oligomers in the P(II) conformation. For this conformation, the polarizability contributions lead to a strong negative band near 200 nm that dominates the calculated and observed CD spectrum. The model does not give a good description of the CD of (Pro)(n) oligomers, probably because of conformational heterogeneity or nonadditive contributions of the Pro side chains. The model improves the calculated CD spectra of α-helical (Ala)(n) oligomers. Although the high-energy transitions make only a small net contribution to the CD of the α-helix in the 200 nm region, they enhance the negative exciton band at ∼205 nm and largely cancel the negative exciton band near 175 nm, substantially improving agreement with experiment.

Role of Environmental Factors on the Structure and Spectroscopic Response of 5′‐DNA–Porphyrin Conjugates Caused by Changes in the Porphyrin–Porphyrin Interactions

We have explored the utility, strength, and limitation of through-space exciton-coupled circular dichroism in determination of the secondary structure of optically active chromophoric nanoarrays using the example of end-capped porphyrin- and metalloporphyrin-oligodeoxynucleotide conjugates. We put special emphasis on the explanation of the origin and significance of the distinctive multiple bands in the CD spectra (trisignate and tetrasignate CD bands). Such CD profiles are often observed in chiral aggregates or multichromophoric arrays but have never before been studied in detail. We found that variation of temperature and ionic strength has a profound effect on the geometry of the porphyrin-DNA conjugates and thus the nature of electronic interactions. At lower temperatures and in the absence of NaCl all three 5'-DNA-porphyrin conjugates display negative bisignate CD exciton couplets of variable intensity in the Soret region resulting from through-space interaction between the electric transition dipole moments of the two end-capped porphyrins. As the temperature is raised these exciton couplets are transformed into single positive bands originating from the porphyrin-single-strand DNA interactions. At higher ionic strengths and low temperatures, multisignate CD bands are observed in the porphyrin Soret region. These CD signature bands originate from a combination of intermolecular, end-to-end porphyrin-porphyrin stacking between duplexes and porphyrin-DNA interactions. The intermolecular aggregation was confirmed by fluorescence and absorption spectroscopy and resonance light scattering. DeVoe theoretical CD calculations, in conjunction with molecular dynamics simulations and Monte Carlo conformational searches, were used to mimic the observed bisignate exciton-coupled CD spectra as well as multiple CD bands. Calculations correctly predicted the sign and shape of the experimentally observed CD spectra. These studies reveal that the exciton-coupled circular dichroism is a very useful technique for the determination of the structure of optically active arrays.

CD spectra of d-f heterobimetallic helicates with segmental di-imine ligands.

We have investigated the CD spectra of a series of enantiomerically pure heterobimetallic helicates, Lambda,Lambda-[LnCr(1)(3)](6+) (Ln = Eu, Gd, Tb), which contain segmental di-imine ligands. For the mononuclear precursor of these helicates, Lambda-[Cr(1)(3)](3+), a positive exciton couplet was observed around 330 nm, as expected for a tris(di-imine) complex with this absolute configuration. The titration of Ln(III) ions into a solution of this complex leads to the formation of Lambda,Lambda-[LnCr(1)(3)](6+). During this process, the CD signal was observed to invert to give a signal which was negative at lower energies. We investigated the observed changes in the CD spectra using a ZINDO-based computational method which we have previously developed. We were able to show that the exciton coupling of the chromophores coordinated to the Cr and Ln ions give rise to CD signals of opposite phase, despite having the same nominal absolute configuration. Exciton coupling between chromophores located on different metal centers ("internuclear" exciton coupling) is also predicted to have a significant impact on the observed spectrum. We were able to "deconstruct" the observed CD spectra into a set of competing exciton coupling effects and show that the sign of these spectra does not correlate with the absolute configuration of the individual metal centers.

Trans‐diaryl epoxides: Asymmetric synthesis, ring‐opening, and absolute configuration

Anthryl-phenyl, phenanthryl-phenyl, and naphthyl-phenyl trans-epoxides (1, 2, and 3, respectively) having enantiomeric purities of 95%, 99%, and 96% were synthesized from a diastereo and enantiopure sulfonium salt derived from Eliel's oxathiane. The determination of their (1R,2R) absolute configurations was achieved by application of the CD exciton chirality method using a Zn-porphyrin tweezer on the corresponding alcohols obtained after opening of these epoxides with LiAlH(4). The R-configuration at C2 of these epoxides, (-)-1, (+)-2, and (-)-3, is consistent with our previous results concerning asymmetric synthesis of monoaryl epoxides, cyclopropanes, and aziridines. The (1S,2R)-configuration of the cis isomer (when present) was also confirmed. Moreover, the agreement between the negative exciton chirality for conjugates of (S)-configuration predicted by molecular modeling and the observed CD spectra helps to clarify the relative steric size of phenyl and CH(2)-aryl (phenanthryl or anthryl), which is critical when the tweezer method is applied for absolute configurational assignment (phenyl = medium group; anthacenyl CH(2) and phenanthryl CH(2) = large group).

Creation of double silica nanotubes by using crown-appended cholesterol nanotubes.

New crown-appended cholesterol-based organogelators 1-3, which have one or two cholesterol skeletons as a chiral aggregate-forming site, two amino groups as an acidic proton binding site, and one crown moiety as a cation binding site, were synthesized, and the gelation ability was evaluated in organic solvents. These gelators could gelatinize several organic solvents under 1.0 wt %, indicating that 1-3 act as a versatile gelator of various organic solvents. We observed CD spectra of the acetic acid or propionic acid gels of 1-3 to characterize the aggregation mode in the organogel system. In the CD spectrum of the acetic acid gel 1, the positive sign for the first Cotton effect indicates that the dipole moments of azobenzene chromophores tend to orient into the clockwise direction. On the other hand, propionic acid gels 2 and 3, bearing only one cholesterol, moiety exhibit a negative sign for the first Cotton effect, strongly suggesting that the dipole moments of the azobenzene chromophores orient into the anticlockwise direction. The TEM images of the 1+acetic acid gel resulted in the helical ribbon and tubular structures. Sol-gel polycondensation of tetraethoxysilane (TEOS) was carried out with 1-3 as templates in the gel phase. The silica obtained from the 1+acetic acid gel showed the helical ribbon with 200-1700 nm width and the tubular structure of the silica with constant about 560 nm outer diameter. As far as can be recognized, all the helicity possesses a right-handed helical motif. Since the exciton coupling band of the organogel also shows P (right-handed) helicity, we consider that a microscopic helicity is reflected by a macroscopic helicity. On the other hand, the tubular structure of the silica obtained from the organogels 2 and 3 is somewhat different from that prepared from the organogel 1. The careful examination of SEM and TEM pictures revealed that the tube wall of the silica features a roll-paper-like multilayer structure. Thus, this paper demonstrates successful and rare examples for precise transcription of gel superstructures into inorganic silica materials.

Calcium and domain interactions contribute to the thermostability of domains of the multimodular cellobiohydrolase, CbhA, a subunit of the Clostridium thermocellum cellulosome.

Each of three internal domains of multi-modular cellobiohydrolase CbhA from Clostridium thermocellum, X1(1), X1(2) (previously designated as fibronectin type 3-like modules, Fn3(1) and Fn3(2)) and family 3 carbohydrate-binding module (CBM3) binds 1 mol of Ca(2+). Structures and thermal stabilities of X1(1), X1(2), CBM3, X1(1)X1(2), and X1(1)X1(2)-CBM3 containing Ca(2+) (holo-proteins) and without Ca(2+) (apo-proteins) have been studied using CD spectroscopy. All domains are beta-proteins with irregular far-UV CD spectra due to the aromatic side chain contributions. The positive signal at 294 nm in the near-UV CD spectrum of X1(1) lacking a tryptophan residue might be attributed to the presence of aromatic clusters. Thermal denaturation of all proteins is reversible and results in the total loss of tertiary structure and preservation of significant amount of ordered secondary structure. Removal of Ca(2+) destabilizes polypeptides in a different way and to a different extent. It decreases the melting temperature ( T (m)) (by 20 degrees C) and co-operativity of thermal transition of X1(1), increases the number of transitions and lowers the co-operativity of unfolding of CBM3, and slightly decreases T (m)s (2.4-4.2 degrees C) of X1(2), X1(1)X1(2), and X1(1)X1(2)-CBM3. Transitions of X1(1)X1(2) and X1(1)X1(2)-CBM3 follow a two-state model regardless of the presence of Ca(2+). X1(1) is strongly stabilized in the apo-X1(1)X1(2) and apo-X1(1)X1(2)-CBM3 as they display T (m)s similar to those of individual and combined holo-modules. Observed CD spectra of X1(1)X1(2) and X1(1)X1(2)-CBM3 differ from those calculated as the simple weighted sum of individual modules. These differences are more prominent in spectra of apo-proteins. The results indicate the presence of inter-domain interactions in CbhA. Holo-modules, i.e. containing Ca(2+), behave essentially independently, but in the absence of Ca(2+) domain interactions are more important for the conformation of the polypeptides.

Contrasting chiroptical properties of sparteine lactams and thiolactams

The CD spectra of several mono- and dilactams and thiolactams of sparteine were measured with the purpose of clarifying spectra–structure relations. It is shown that the Cotton effects of lactams are predominantly of the opposite sign to those of the corresponding thiolactams. In bichromophoric molecules 7– 9 the observed CD spectra are dominated by exciton type interactions.

Human Soluble Guanylate Cyclase: Functional Expression, Purification and Structural Characterization

Soluble guanylate cyclase is an enzyme that catalyzes formation of cGMP from GTP and is a member of the nucleotide cyclase family of enzymes. sGC is a receptor for endogenous and exogenous nitric oxide and is activated several-fold upon its binding, constituting a core enzyme in the nitric oxide signal transduction pathway. cGMP generated by sGC is an important second messenger that regulates activity of several enzymes triggering such important physiologic reactions as vasodilation, smooth muscle relaxation and platelet aggregation. We report here the functional expression of the human isoform of soluble guanylate cyclase in HighFive insect cells using a baculovirus expression system. Highly active recombinant protein was obtained without heme reconstitution or supplementation of the cell growth medium and the level of protein expression was found to be heavily affected by the composition of the growth medium. We have successfully purified highly active sGC (sp act up to 940 nmol/min/mg) from adherent cultures using a three-column, 1-day procedure. The UV-Vis spectrum of the isolated protein shows a Soret band at 431 nm, consistent with a histidine-ligated, 5-coordinate heme as previously reported. Far UV CD spectroscopy, intrinsic tryptophan fluorescence, fluorescence of the hydrophobic dye bis-ANS, size-exclusion chromatography, and small angle X-ray scattering (SAXS) were used to characterize the structural properties of the purified sGC. We used two hierarchical neural network methods to predict the secondary structure of sGC and found it to be consistent with the observed CD spectrum of sGC.

Globular Protein Ultraviolet Circular Dichroic Spectra. Calculation from Crystal Structures via the Dipole Interaction Model

The dipole interaction model is used to calculate ultraviolet circular dichroic spectra of 16 globular proteins with various amounts of helix, sheet, and disordered regions. Structures for the calculations are based on crystal coordinates taken from the Brookhaven Protein Data Bank. Calculations for “reassembled fragment” models of the proteins reproduce the main features of observed solution CD spectra in the region of the amide π−π* transition near 200 nm. The predicted spectra for helix and sheet regions show considerable variation in magnitudes and wavelengths of the CD peaks, and a still wider variation is predicted for the disordered regions. A comparison of reassembled-molecule spectra with weighted averages of the spectra of the component fragments shows that deviations from additivity of the component spectra are generally small. The implications of these findings for attempts to resolve observed CD spectra in terms of a small number of components are discussed.

Determination of Absolute Configurations of N-Formyl-3,3‘,4,4‘-tetrahydrospiro[naphthalene-1(2H),2‘(1‘H)-pyridine] (2) and N-Formyl-3‘,4‘-dihydrospiro[indan-1,2‘(1‘H)-pyridine] (3) by Analysis of Circular Dichroism Spectra. A Case of Two Compounds with Similar Configuration But Nearly Mirror Image CD Spectra

N-Formyl-3,3‘,4,4‘-tetrahydrospiro[naphthalene-1(2H),2‘(1‘H)-pyridine] (2) and N-Formyl-3‘,4‘-dihydrospiro[indan-1,2‘(1‘H)-pyridine] (3) were resolved into enantiomers, compound 3 partly and compound 2 completely, by chromatography on triacetylcellulose. The CD spectra were recorded and compared with theoretical spectra calculated by a semiempirical method, using geometries from empirical force-field calculations. In the observed CD spectra, the carbonyl n → π* transitions did not give rise to visible bands, but their signs and energies were found by analysis of CD spectra in solvents of different polarity. The theoretical spectra of 2 and 3 showed complete agreement with the observed spectra in sign and qualitatively in intensity, for the five transitions observed between 190 and 280 nm, which permitted a safe assignment of the absolute configurations. The enantiomers of 2 and 3 with the aryl rings located on the same side of the tetrahydropyridine ring showed CD spectra, which were nearly mirror images,...

Comparison of calculated and observed CD spectra of liquid crystalline dispersions formed from double-stranded DNA and from DNA complexes with coloured compounds

Abstract The CD spectra of dispersions of DNA, in the form of cholesteric liquid crystalline droplets, in an aqueous continuum have been studied. Calculated curves have been fitted to experimental spectra. The amplitude and the sign of the intense absorption band of the purine and pyrimidine bases vary with the droplet size, the pitch and the twist sense of the cholesteric phase. The CD spectra of dispersions of the complex formed by DNA and a coloured intercalating antibiotic have been similarly studied. A general satisfactory level of fitting between observed and calculated CD spectra was found.

Chiroptical methods in conformational analysis

AbstractCD spectra of flexible organic molecules in solution are normally very sensitive to conformation. In a system composed of two or more chromophores joined by one or more single bonds and with one fixed or strongly preferred conformation, it is often possible to reproduce the CD spectrum by semiempirical calculations based on interactions between the electronic transitions in the respective chromophores. In a system containing two or more conformations of appreciable weight, the observed CD spectrum is the superposition of those of the individual conformations and has to be analyzed in terms of the individual calculated spectra and the relative energies of the respective conformations. The effect of temperature variation on conformational equilibria and on the composite CD spectra will be discussed and exemplified. © 1995 Wiley‐Liss, Inc.

CD spectrum of bacteriorhodopsin: Best evidence against exciton model

We summarize the predictions of the exciton model that was originally proposed to explain the observed biphasic band shape of its CD spectrum in the visible region of bacteriorhodopsin (bR). It is shown that to reconcile these predictions with the observed results on the linear dichroism, the retinal isomerization time and, the retinal-retinal distance, the biphasic nature of the observed CD spectrum of bR becomes itself an evidence against the exciton model because of the uncertainty principle.Reduced bR (RbR), which retains its hexagonal structure, shows a monophasic CD spectrum with relatively small rotational strength as compared to bR. This is shown to disagree with predictions made by the exciton model. The results could best be explained in terms of retinal-protein heterogeneity leading to two or more types of bR in which their retinals suffer opposite sense of intramolecular rotational distortion along their retinal long axis. Such a retinal-protein heterogeneity disappears in reduced bR which is known to have a planar (nondistorted) retinal conjugated system, resulting in a monophasic CD with reduced rotational strength, as observed.

Absorption and circular dichroism spectra of dimeric systems. Extended dimer model

An extended dimer model is formulated. It differs from the simple dimer model in allowing for mixing of monomer electronic states by intermolecular interaction. The exact and approximate mathematical treatments of the model are discussed in detail. The model is applied to studies of absorption and circular dichroism spectra of dimers. It is shown that the transfer of intensity and rotatory power due to interstate mixing leads to readily observable changes in the vibronic structure of the corresponding spectra. The model is used to reinterpret the observed CD spectra of two different 1,1′-bianthryls.

Physical probes of polysaccharide conformation and interactions

In the solid state most polysaccharides adopt regular chain geometry corresponding to fixed values of the angles between adjacent residues. Such ordered conformations may persist in solution or as the fundamental structural unit in polysaccharide gels or biological tissue. Physical techniques may be used (1) to detect conformational order in solution, (2) to characterise chain geometry and packing, often by reference to known solid-state conformations, and (3) to monitor order-disorder transitions. Characterisation of solution conformation is often facilitated by the use of structurally regular short chain segments, which show the same conformational behaviour as the intact polymer, but are capable of participating in only one ordered intermolecular junction zone. Nmr relaxation behaviour, measured either directly from the exponential decay of magnetisation, or indirectly from high resolution linewidth, provides a convenient index of conformational rigidity. Polysaccharides show two conformation-sensitive circular dichroism (cd) bands in the vacuum uv at about 150 and 170 nm. These are inaccessible to commercial cd instruments, but may be monitored indirectly by optical rotation, which shows a simple quantitative correlation with the linkage geometry between adjacent sugars in the polymer chain. Accessible pendant chromophores, in particular carboxy groups, also show conformation-sensitive cd behaviour and provide a direct probe of specific cation chelation. The masking effect of such chromophores on the optical activity of the polymer backbone may be eliminated by Kronig-Kramers transform of their observed cd spectra. Order-disorder transitions are conveniently monitored by discontinuities in optical rotation behaviour, intensity of discernible high resolution nmr resonances, differential scanning calorimetry, solution viscosity and, for segments, by light scattering. Transition kinetics show the number of chains involved in the fundamental ordered structure, a source of frequent difficulty in solid-state x-ray analysis. Further association of ordered structures may be probed by competitive inhibition studies with short chain segments or, where appropriate, by the stoichiometry of cation chelation.

Polypeptide models of collagen. II. Solution properties of (Pro-Gly-Phe)n.

AbstractThe conformation of (Pro‐Gly‐Phe)n in trifluoroethanol was investigated using CD, nmr and ir techniques. After making appropriate correction for the contribution of the phenylalanine chromophore to the observed CD spectra of the polytripeptide at several temperatures, it is found that (Pro‐Gly‐Phe)n can exist in a partially triple‐helical conformation in this solvent a t low temperatures. The nmr and ir data support this conclusion. In conjunction with recent theoretical sutdies, our data offer an explanation for the preferential occurrence of the Phe residue in position 2 of the tripeptide sequence Gly‐R2‐R3, in collagen.

Near-UV circular dichroism of trypsin inhibitor of adzuki beans attributable to disulfide groups.

The trypsin inhibitor of adzuki (Phaseolus angularis) beans shows a CD spectrum with a negative extremum at 280 nm and a positive shoulder around 245 nm. Since the inhibitor lacks tryptophan and tyrosine, the observed CD spectrum can be attributed to the six disulfide groups in the molecule. The CD features completely disappeared on reduction of the disulfide groups, and converged into a single negative extremum at 270 nm when the groups were modified to form mixed disulfides with glutathione. These observations of the CD properties of the inhibitor strongly suggest the presence of disulfide groups constrained with respect to their dihedral angles.

Infrared circular dichroism associated with the C-H strecthing vibration of tartaric acid

The infrared circular dichroism associated with the C-H stretching vibration of tartaric acid- d 4 [-CH(OD)COOD] 2, has been measured. The observed CD spectra are most readily attributable to the chirality of the separate -CH(OD)COOD groups, rather than to a coupling between the groups.