Interpretation of synchrotron radiation circular dichroism spectra of anionic, cationic, and zwitterionic dialanine forms

Water-Mediated Electronic Structure of Oligopeptides Probed by Their UV Circular Dichroism, Absorption Spectra, and Time-Dependent DFT Calculations

We investigate the UV absorption spectra of a series of cationic GxG peptides (where x denotes a guest residue) in aqueous solution and find that only a subset of these spectra show a strong dependence with temperature. To explore whether or not this observation reflects conformational dependencies, we carry out time-dependent density functional calculations for the polyproline II (pPII) and β-strand conformations in implicit and explicit water. We find that the calculated CD spectra for pPII can qualitatively account for the experimental spectra irrespective of the water model. The β-strand UV-CD spectra, however, require the explicit consideration of water. Contrary to conventional wisdom, we find that both the NV₁ and NV₂ band are the envelopes of contributions from multiple transitions that involve more than just the HOMOs and LUMOs of the peptide groups. A natural transition orbital analysis reveals that some of the transitions have a charge-transfer character. The overall manifold of transitions depends on the peptide's backbone conformation, peptide hydration, and side chain of the guest residue. Our results reveal that peptide groups, side chains, and hydration shells must be considered as an entity for a physically valid characterization of UV absorbance and circular dichroism.

A new interpretation of the structure and solvent dependence of the far UV circular dichroism spectrum of short oligopeptides

UV circular dichroism (UVCD) spectroscopy is a prominent tool for exploring secondary structures of polypeptides and proteins. In the unfolded state of these biomolecules, most of the individual residues primarily sample a conformation called polyproline II. Its CD spectrum contains a negatively biased positive couplet with a pronounced negative maximum below and a weak positive maximum above 200 nm. It is traditionally rationalized in terms of an excitonic coupling mechanism augmented by polarization effects. In this work, we carry out new time-dependent density functional theory calculations on the cationic tripeptide GAG in implicit and explicit water to determine the transitions that give rise to the observed CD signals of polyproline II and β-strand conformations. Our results reveal a plethora of electronic transitions that are governed by configurational interactions between multiple molecular orbital transitions of comparable energy. We also show that reproducing the CD spectra of polyproline II and β-strand conformations requires the explicit consideration of water molecules. The structure dependence of delocalized occupied orbitals contributes to the experimentally-observed invalidation of Flory's isolated pair hypothesis.

Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview

Circular dichroism spectroscopy is widely used for analyzing the structures of chiral molecules, including biomolecules. Vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy using synchrotron radiation can extend the short-wavelength limit into the vacuum-ultraviolet region (down to ~160 nm) to provide detailed and new information about the structures of biomolecules in combination with theoretical analysis and bioinformatics. The VUVCD spectra of saccharides can detect the high-energy transitions of chromophores such as hydroxy and acetal groups, disclosing the contributions of inter- or intramolecular hydrogen bonds to the equilibrium configuration of monosaccharides in aqueous solution. The roles of hydration in the fluctuation of the dihedral angles of carboxyl and amino groups of amino acids can be clarified by comparing the observed VUVCD spectra with those calculated theoretically. The VUVCD spectra of proteins markedly improves the accuracy of predicting the contents and number of segments of the secondary structures, and their amino acid sequences when combined with bioinformatics, for not only native but also nonnative and membrane-bound proteins. The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in comparative analyses of synthetic poly-nucleotides composed of selected bases. This review surveys these recent applications of synchrotron-radiation VUVCD spectroscopy in structural biology, covering saccharides, amino acids, proteins, and nucleic acids.

Exploring the boundaries of direct detection and characterization of labile isomers - a case study of copper(ii)-dipeptide systems

The investigation of the linkage isomers of biologically essential and kinetically labile metal complexes in aqueous solutions poses a challenge, as these microspecies cannot be separately studied. Therefore, derivatives are commonly used to initially determine the stability or spectral characteristics of at least one of the isomers. Here we directly detect the isomers, describe the metal ion coordination sphere, speciation and thermodynamic parameters by a synergistic application of temperature dependent EPR and CD spectroscopic measurements in copper(ii)-dipeptide systems including His-Gly and His-Ala ligands. The ΔH = (-23 ± 4) kJ mol^-1 value of the standard enthalpy change corresponding to the peptide-type to histamine-type isomerisation equilibrium of the [CuL]⁺ complex was corroborated by several techniques. The preferential coordination of the side-chains was observed at lower temperatures, whereas, metal-binding of the backbone atoms became favourable upon increasing temperature. This study exemplifies the necessity of using temperature dependent multiple methodologies for a reliable description of similar systems for upstream applications.

Identifying dominant conformations of N-acetyl-L-cysteine methyl ester and N-acetyl-L-cysteine in water: VCD signatures of the amide I and the C=O stretching bands

Infrared (IR) and vibrational circular dichroism (VCD) spectra of N-Acetyl-L-Cysteine Methyl Ester (NALCME) and N-Acetyl-L-Cysteine (NALC) in D2O under different pHs were measured. We focus on the VCD signatures of the amide I and the C=O stretching spectral signatures of the neutral NALCME and NALC species and the related ones of the deprotonated NALC species in the region of 1800-1500 cm(-1). A sign inversion is observed for the amide I VCD band going from the neutral NALCME and NALC to the deprotonated NALC species. Density functional theory (DFT) calculations were carried out to search for the possible conformations of these three species and to simulate their IR and VCD spectra at the B3LYP/aug-cc-pVTZ level in the gas phase and with the polarization continuum model of water solvent. The most stable conformations found for neutral NALCME and NALC exhibit drastically difference VCD patterns, whereas those of deprotonated NALC show similar patterns. We establish an empirical structural-spectral relationship where the aforementioned VCD signatures can be used as spectral markers to identify dominant conformations of these two amino acid derivatives under different pHs. It is recognized that the dominant conformers identified using the VCD spectral markers differ from those based on the relative DFT energies for neutral NALCME and NALC. The influence of solvent on both the conformational geometries and their relative stabilities is discussed. The aforementioned discrepancy can be attributed to the explicit solute-solvent hydrogen-bonding interactions which are not accounted for in the calculations. The empirical structural-spectral relationship identified can potentially be applied to large, related amino acids and polypeptides in water.

Reconciliation of chemical, enzymatic, spectroscopic and computational data to assign the absolute configuration of the DNA base lesion spiroiminodihydantoin

The diastereomeric spiroiminodihydantoin-2'-deoxyribonucleoside (dSp) lesions resulting from 2'-deoxyguanosine (dG) or 8-oxo-7,8-dihydro-2'-deoxyguanosine (dOG) oxidation have generated much attention due to their highly mutagenic nature. Their propeller-like shape leads these molecules to display mutational profiles in vivo that are stereochemically dependent. However, there exist conflicting absolute configuration assignments arising from electronic circular dichroism (ECD) and NOESY-NMR experiments; thus, providing definitive assignments of the 3D structure of these molecules is of great interest. In the present body of work, we present data inconsistent with the reported ECD assignments for the dSp diastereomers in the nucleoside context, in which the first eluting isomer from a Hypercarb HPLC column was assigned to be the S configuration, and the second was assigned the R configuration. The following experiments were conducted: (1) determination of the diastereomer ratio of dSp products upon one-electron oxidation of dG in chiral hybrid or propeller G-quadruplexes that expose the re or si face to solvent, respectively; (2) absolute configuration analysis using vibrational circular dichroism (VCD) spectroscopy; (3) reinterpretation of the ECD experimental spectra using time-dependent density functional theory (TDDFT) with the inclusion of 12 explicit H-bonding waters around the Sp free bases; and (4) reevaluation of calculated specific rotations for the Sp enantiomers using the hydration model in the TDDFT calculations. These new insights provide a fresh look at the absolute configuration assignments of the dSp diastereomers in which the first eluting from a Hypercarb-HPLC column is (-)-(R)-dSp and the second is (+)-(S)-dSp. These assignments now provide the basis for understanding the biological significance of the stereochemical dependence of enzymes that process this form of DNA damage.

Vacuum-ultraviolet electronic circular dichroism study of methyl α-D-glucopyranoside in aqueous solution by time-dependent density functional theory

The vacuum-ultraviolet (VUV) electronic circular dichroism (ECD) spectrum of methyl α-D-glucopyranoside (methyl α-D-Glc) was measured down to 163 nm in aqueous solution using a synchrotron-radiation VUV-ECD spectrophotometer. The spectrum exhibited two characteristic ECD peaks around 170 nm, which depend on the trans (T) and gauche (G) configurations of the hydroxymethyl group at C-5. To elucidate the influences of the T and G configurations on the spectrum, the ECD spectra of three rotamers (α-GT, α-GG, and α-TG) of methyl α-D-Glc were calculated using time-dependent density functional theory (TDDFT) combined with molecular dynamics simulation. A linear combination of the ECD spectra of these three rotamers, which differ markedly from each other, produced a methyl α-D-Glc spectrum similar to that observed experimentally. The spectrum was assignable to the n-σ* transitions of the ring oxygen and methoxy oxygen with minor contributions from the hydroxyl oxygen. The differences in α-GT, α-GG, and α-TG spectra were attributed to fluctuations of the configurations of the hydroxymethyl group at C-5 and the hydroxyl group at C-4, which strongly affected the orientations of intramolecular hydrogen bonds around the ring oxygen. These findings demonstrate that combining VUV-ECD and TDDFT is useful for structural characterization of saccharides in aqueous solution.

Ferric complexes of 3-hydroxy-4-pyridinones characterized by density functional theory and Raman and UV-vis spectroscopies

Deferiprone and other 3-hydroxy-4-pyridinones are used in metal chelation therapy of iron overload. To investigate the structure and stability of these compounds in the natural aqueous environment, ferric complexes of deferiprone and amino acid maltol conjugates were synthesized and studied by computational and optical spectroscopic methods. The complexation caused characteristic intensity changes, a 300× overall enhancement of the Raman spectrum, and minor changes in UV-vis absorption. The spectra were interpreted on the basis of density functional theory (DFT) calculations. The CAM-B3LYP and ωB97XD functionals with CPCM solvent model were found to be the most suitable for simulations of the UV-vis spectra, whereas B3LYP, B3LYPD, B3PW91, M05-2X, M06, LC-BLYP, ωB97XD, and CAM-B3LYP functionals were all useful for simulation of the Raman scattering. Characteristic Raman band frequencies for 3-hydroxy-4-pyridinones were assigned to molecular vibrations. The computed conformer energies consistently suggest the presence of another isomer of the deferiprone-ferric complex in solution, in addition to that found previously by X-ray crystallography. However, the UV-vis and Raman spectra of the two species are similar and could not be resolved. In comparison to UV-vis, the Raman spectra and their combination with calculations appear more promising for future studies of iron sequestrating drugs and artificial metalloproteins as they are more sensitive to structural details.

Experimental and theoretical studies of vacuum-ultraviolet electronic circular dichroism of hydroxy acids in aqueous solution

The electronic circular dichroism (ECD) spectra of three L-hydroxy acids (L-lactic acid, (+)-(S)-2-hydroxy-3-methylbutyric acid, and (-)-(S)-2-hydroxyisocaproic acid) were measured down to 160 nm in aqueous solution using a vacuum-ultraviolet ECD spectrophotometer. To assign the two positive peaks around 210 and 175 nm and the one negative peak around 190 nm in the observed spectra, the ECD spectrum of L-lactic acid was calculated using time-dependent density functional theory (DFT) for the optimized structures by DFT and a continuum model. The observed ECD spectrum was successfully reproduced as the average spectrum for four optimized structures with seven water molecules that localized around the COO(-) and OH groups of L-lactic acid. The positive peak around 210 nm and the negative peak around 185 nm in the calculated spectrum were attributable to the nπ* transition of the carboxyl group, with the latter peak also being influenced by the ππ* transition of the carboxyl group; however, the positive peak around 165 nm involved unassignable higher energy transitions. The comparison of the calculated ECD spectra for L-lactic acid and L-alanine revealed that the network with loose hydrogen bonding around the COO(-) and OH groups is responsible for the flexible conformation of hydroxy acids and complicated side-chain dependence of ECD spectra relative to amino acids.

Structure of the alanine hydration shell as probed by NMR chemical shifts and indirect spin-spin coupling

The structure of the alanine hydration shell was modeled by Carr-Parinello molecular dynamics (CPMD) to explain subtle differences in NMR chemical shifts and indirect spin-spin coupling constants of the neutral (zwitterionic), cationic, and anionic forms of this amino acid. In comparison with classical molecular dynamics (MD), the quantum mechanical CPMD approach revealed a more structured solvent and significant differences in the radial and angular distributions of the water molecules around the solute. In particular, the solvent was predicted to be organized around the uncharged COOH and NH(2) residues to a similar degree as that for the charged ones. This was not the case with MD. For snapshot CPMD configurations, the NMR parameters were computed by density functional theory (DFT) and averaged. Obtained values were significantly closer to experimental parameters known for (15)N and (13)C isotopically labeled alanine than those calculated by the conventional implicit dielectric solvent model. The NMR results also quantitatively reflect a superiority of the CPMD over the MD explicit solvent treatment. A further improvement of the computed spin-spin coupling constants could be achieved by taking into account vibrational averaging beyond the harmonic approximation. Differently positioned water molecules in the clusters cause an unexpectedly large scattering of the NMR parameters. About 10-15 dynamics snapshots were required for a satisfactory convergence of the shifts and couplings. The NMR chemical shift was found to be much more sensitive to the molecular hydration than the coupling. The results thus indicate a large potential of the NMR spectroscopy and quantum simulations to probe not only the structure of molecules but also their interactions with the environment.

Theoretical study of the effective Chemical Shielding Anisotropy (CSA) in peptide backbone, rating the impact of CSAs on the cross-correlated relaxations in L-alanyl-L-alanine

The dependence of the effective chemical shielding anisotropy (effective CSA, Deltasigma(eff)) on the phi and psi peptide backbone torsion angles was calculated in the l-alanyl-l-alanine (LALA) peptide using the DFT method. The effects of backbone conformation, molecular charge including the cation, zwitterion, and anion forms of the LALA peptide, and the scaling taking into account the length of the dipolar vector were calculated for the effective CSAs in order to assess their structural behaviors and to predict their magnitudes which can be probed for the beta-sheet and alpha-helix backbone conformations via measurement of the cross-correlated relaxation rates (CCR rates). Twenty different CSA-DD cross-correlation mechanisms involving the amide nitrogen and carbonyl carbon chemical shielding tensors and the C(alpha)H(alpha) (alpha-carbon group), NH(N) (amide group), C(alpha)H(N), NH(alpha), C'H(alpha), and C'H(N) (alpha = alpha1, alpha2) dipolar vectors were investigated. The X-C(alpha)H(alpha) (X = N, C'; alpha = alpha1, alpha2) cross-correlations, which had already been studied experimentally, exhibited overall best performance of the calculated effective CSAs in the LALA molecule; they spanned the largest range of values upon variation of the psi and phi torsions and depended dominantly on only one of the two backbone torsion angles. The X-NH(N) (X = N, C') cross-correlations, which had been also probed experimentally, depended on both backbone torsions, which makes their structural assignment more difficult. The N-NH(alpha2) and N-C'H(alpha1) cross-correlations were found to be promising for the determination of various backbone conformations due to the large calculated range of the scaled effective CSA values and due to their predominant dependence on the psi and phi torsions, respectively. The 20 calculated dependencies of effective CSAs on the two backbone torsion angles can facilitate the structural interpretation of CCR rates.

When is a molecule properly solvated by a continuum model or in a cluster ansatz? A first-principles simulation of alanine hydration

In order to test the validity of the cluster ansatz approach as well as of the continuum model approach and to learn about the solvation shell, we carried out first-principles molecular dynamics simulations of the alanine hydration. Our calculations contained one alanine molecule dissolved in 60 water molecules. Dipole moments of individual molecules were derived by means of maximally localized Wannier functions. We observed an average dipole moment of about 16.0 D for alanine and of about 3.3 D for water. In particular, the average water dipole moment in proximity of alanine's COO(-) group decayed continously with increasing distance, while, surprisingly, close to the CH3 and NH3+ group, the dipole moment first rose before its value dropped. In a cluster ansatz approach, we considered snapshots of alanine surrounded by different water molecule shells. The dipole moments from the cluster approaches utilizing both maximally localized Wannier functions as well as natural population analysis served to approximate the dipole moments of the total trajectory. Sufficient convergence of the cluster ansatz approach is found for either of the two solvent shells around the polar groups and one solvent shell around the apolar groups or two solvent shells around the polar groups surrounded by a dieletric continuum.