Conformational analyses of peptides and proteins by vibrational Raman optical activity

Recent developments of vibrational Raman optical activity (ROA) spectroscopy enabled the detailed analyses of the backbone and side chain conformations of peptides and proteins in solution phases. ROA can be used as a powerful analytical technique for determining not only the structures of conformers, but also their populations even for systems in fast conformational equilibria where NMR spectroscopy is difficult to be applied. ROA enabled the monitoring of the secondary structures of denatured or unfolded proteins, such as an amyloid fibril and its prefibril intermediates.     

Polarised Raman and infrared spectral analysis of L-alanine oxalate (C5H9NO6)--a non-linear optical single crystal

L-alanine oxalate (C5H9NO6), a promising material for effective frequency conversion, was grown by standard slow evaporation technique. Solubility studies were carried out at different temperatures. Unambiguous assignments of fundamental modes of various molecular groups were made from the recorded infrared and polarised Raman spectra. The non-linear optical property has been confirmed from the optical transmission and fluorescence spectra.     

Resonance Raman optical activity and surface enhanced resonance Raman optical activity analysis of cytochrome c

High-resolution resonance Raman (RR) and resonance Raman optical activity (ROA) spectra of cytochrome c were obtained in order to perform full assignment of spectral features of the resonance ROA spectrum. The resonance ROA spectrum of cytochrome c revealed a distinct spectral signature pattern due to resonance enhanced skeletal porphyrin vibrations, more pronounced than any contribution from the protein backbone. Combining the intrinsic resonance properties of cytochrome c with the surface plasmon enhancement achieved with colloidal silver particles, the surface enhanced resonance Raman scattering (SERRS) and surface enhanced resonance ROA (SERROA) spectra of the protein were successfully obtained at concentrations as low as 1 microM. The assignments of spectral features were based on the information obtained from the RR and resonance ROA spectra. Excellent agreement between RR and SERRS spectra is reported, while some disparities were observed between the resonance ROA and SERROA spectra. These differences can be ascribed to perturbations of the physical properties of the protein upon adhesion to the surface of the silver colloids.     

A combined theoretical and experimental study of the structure and vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra of the L-histidine zwitterion

A combined theoretical and experimental study of the vibrational absorption (VA)/IR, vibrational circular dichroism (VCD), Raman and Raman optical activity (ROA) spectra of l-histidine in aqueous solution has been undertaken to answer the questions (i) what are the species present and (ii) which conformers of the species are present under various experimental conditions. The VA spectra of l-histidine have been measured in aqueous solution and the spectral bands which can be used to identify both species (cation, zwitterion, anion) and conformer of the species have been identified and subsequently used to identify the species (zwitterion) and conformer (gauche minus minus, gauche minus plus for the side chain dihedral angles) present in solution at pH 7.6. The VCD spectral intensities have been used subsequently in combination with further theoretical studies to confirm the conclusions that have been arrived at by only analyzing the VA/IR spectra. Finally a comparison of measured Raman and ROA spectra of l-histidine with Raman and ROA spectral simulations for the conformers and species derived from the combined VA/IR and VCD experimental and theoretical work is presented as a validation of the conclusions arrived at from VA/IR and VCD spectroscopy. The combination of VA/IR and VCD with Raman and ROA is clearly superior and both sets of experiments should be performed.     

Conformational flexibility of longifolene

The flexibility of the bicyclo[2.2.1]heptane-based tricyclic bridged system in longifolene is analysed based on x-ray structural data. In this context, the molecular structure of three differently substituted longifolenes has been analysed. The highly substituentdependent conformation provides scope for the synthesis of a variety of commercially oriented products. NCL Communication Number 3459     

Conformational flexibility of DNA

Pulsed Electron-Electron Double Resonance (PELDOR) on double-stranded DNA (ds-DNA) was used to investigate the conformational flexibility of helical DNA. Stretching, twisting, and bending flexibility of ds-DNA was determined by incorporation of two rigid nitroxide spin labels into a series of 20 base pair (bp) DNA duplexes. Orientation-selective PELDOR experiments performed at both X-band (9 GHz/0.3 T) and G-band (180 GHz/6.4 T) with spin label distances in the range of 2-4 nm allowed us to differentiate between different simple models of DNA dynamics existing in the literature. All of our experimental results are in full agreement with a dynamic model for ds-DNA molecules, where stretching of the molecule leads to a slightly reduced radius of the helix induced by a cooperative twist-stretch coupling.     

Conformational flexibility and aromaticity of azanaphthalenes

Conformational flexibility of naphthalene and its different mono-and diaza analogues has been studied by MP2/6-31G(d, p) quantum chemical computations. It is shown that all molecules possess a considerable conformational flexibility. The out-of-plane deformation energy of both a bicyclic π-system on the whole and separate rings directly depends on the degree of aromaticity of the conjugated system. Effects of the amount and arrangement of nitrogen atoms on conformational features and aromaticity of the molecules considered were analyzed.     

Conformational flexibility of six-membered dihydrocycles

The conformational flexibility of six-membered 1,4- and 1,2-dihydrocycles caused by a flattened shape of the minimum on the potential energy surface is discussed. The effect of the conformational flexibility of the rings on the physicochemical characteristics of compounds is considered. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2095–2105, December, 1997.     

EPR, optical, infrared and Raman spectral studies of Actinolite mineral

Electron paramagnetic resonance (EPR), optical, infrared and Raman spectral studies have been performed on a natural Actinolite mineral. The room temperature EPR spectrum reveals the presence of Mn(2+) and Fe(3+) ions giving rise to two resonance signals at g = 2.0 and 4.3, respectively. The resonance signal at g = 2.0 exhibits a six line hyperfine structure characteristic of Mn(2+) ions. EPR spectra have been studied at different temperatures from 123 to 433 K. The number of spins (N) participating in the resonance at g = 2.0 has been calculated at different temperatures. A linear relationship is observed between log N and 1/T in accordance with Boltzmann law and the activation energy was calculated. The paramagnetic susceptibility (chi) has been calculated at different temperatures and is found to be increasing with decreasing temperature as expected from Curie's law. From the graph of 1/chi versus T, the Curie constant and Curie temperature have been evaluated. The optical absorption spectrum exhibits bands characteristic of Fe(2+) and Fe(3+) ions. The crystal field parameter Dq and the Racah parameters B and C have been evaluated from the optical absorption spectrum. The infrared spectral studies reveal the formation of Fe(3+)--OH complexes due to the presence of higher amount of iron in this mineral. The Raman spectrum exhibits bands characteristic of Si--O--Si stretching and Mg?OH translation modes.     

Anti-stokes magnetic Raman optical activity and time reversal

Time-reversal arguments are used to relate the sign of the magnetic Raman optical activity in corresponding Stokes and anti-Stokes bands in the two distinct cases of a system with an odd and an even number of electrons. Observations on IrCl^2?₆ are reported which confirm some of the predictions.     

Raman optical activity of tartaric acid and related molecules

The Raman optical activity spectra of (2R, 3R) (+)- and (2S,3S) (?)-tartaric acid, (2R, 3R) (+)-dimethyl tartrate, (2R,3R) (?)-2,3-butanediol and (2S, 3S) (+)-dibenzoyl tartaric acid are presented. A large couplet at about 500cm^?1 in the first three molecules, which probably originates in deformations of a chiral structural unit, might serve as an indicator of conformation and absolute configuration.     

Coupled-cluster calculations of vibrational Raman optical activity spectra

We present the first calculations of Raman optical activity spectra at the coupled-cluster level of theory. Calculations are presented for (S)-methyloxirane and compared to recent experimental gas-phase measurements as well as the results obtained at the Hartree-Fock and density functional level of theory using the popular B3LYP functional. For the experimentally relevant frequency region of 400-1600 cm(-1), the Hartree-Fock, B3LYP and coupled-cluster spectra are very similar when the same force field is used, and the results also agree well with experiment. For high-frequency vibrational modes, differences in the ROA difference parameters are observed and are analyzed. The new coupled-cluster ROA code will allow for critical benchmarking of the accuracy of modern exchange-correlation functionals in the calculation of ROA spectra.     

Conformational flexibility and structure of creatine kinase.

The structural flexibility of creatine kinase has been investigated with the covalent hydrophobic probe 2-[4'-(2"-iodoacetamido) phenyl] aminonaphthalene-6-sulfonic acid (IAANS) which reacts at vastly different rates with the two subunits to give a protein conjugate with fluorescence characteristic of reaction with a site in a hydrophobic cleft. Binding of purine nucleotides greatly enhances the probe fluorescence while pyrimidine nucleotides quench the fluorescence. Small anions bind to nucleotide-free creatine kinase near the location of the transferable phosphoryl group and quench both the IAANS fluorescence of modified creatine kinase and the tryptophan fluorescence of native creatine kinase. Chloride and nitrate non-competitively inhibit MgADP binding both with and without creatine. Fluorescence energy transfer demonstrates that the active sites of creatine kinase are well separated and become further apart after the nucleotide-induced conformational change.     

Conformational flexibility of the twelve-membered siloxane ring

Conclusions The conformational analysis of the molecules of twelve-membered cis- and trans-2,8-dihydroxycyclohexasiloxanes showed that intramolecular dehydration with the formation of a bicyclic system is possible for the cis isomer with the approach of the OH groups on account of the large conformational flexibility of the ring. For the trans isomer this approach is only possible with cleavage of the bonds in the ring at the intermediate stages.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1871–1874, August, 1984.     

Conformational flexibility of 1,4-dihydroazine carbonyl derivatives

Summary The molecular geometry of 4-oxo derivatives of 1,4-dihydropyridine, 1,4-dihydropyrimidine, 1,4-dihydropyridazine, and 1,4-dihydro-1,3,5-triazine has been calculated by the semi-empirical quantum-chemical AM1 method. It could be shown that the dihydrocycle in these compounds is not conformationally rigid. Changing the angle between the endocyclic double bond planes ±15° causes less than 1 kcal/mol increase of energy.

---

Konformative Flexibilität von 1,4-Dihydroazin-carbonyl-Derivaten (Kurze Mitt.)

Zusammenfassung Die molekulare Geometrie von 4-Oxo-Derivaten von 1,4-Dihydropyridin, 1,4-Dihydropyrimidin, 1,4-Dihydropyridazin und 1,4-Dihydro-1,3,5-triazin wurde mittels der semiempirischen quantenchemischen AM1-Methode berechnet. Es konnte gezeigt werden, daß der zweifach hydrierte Ring in diesen Verbindungen nicht starr ist. Eine Änderung des Winkels zwischen den Ebenen der endocyclischen Doppelbindungen um ±15° bewirkt eine Energieerhöhung von weniger als 1 kcal/mol.

     

Surface enhanced Raman optical activity (SEROA)

Raman optical activity (ROA) directly monitors the stereochemistry of chiral molecules and is now an incisive probe of biomolecular structure. ROA spectra contain a wealth of information on tertiary folding, secondary structure and even the orientation of individual residues in proteins and nucleic acids. Extension of ROA to an even wider range of samples could be facilitated by coupling its structural sensitivity to the low-concentration sensitivity provided by plasmon resonance enhancement. This leads to the new technique of surface enhanced ROA, or SEROA, which is complementary to both SERS and ROA. In this tutorial review, we present a survey of theoretical and experimental work undertaken to develop SEROA and discuss these efforts in the context of the ROA technique, and, based on the authors' work, outline possible future directions of research for this novel chiroptical spectroscopy.