Probing solution conformations of l-DOPA: Integration of experiment and simulation via vibrational optical activity.

l-DOPA plays a critical role as a precursor to dopamine and is a standard treatment for Parkinson's disease. Recent research has highlighted the potential therapeutic advantages of deuterated l-DOPA analogs having a longer biological half-life. For their spectroscopic characterization, the in-detail characterization of l-DOPA itself is necessary. This article presents a thorough examination of the vibrational spectra of l-DOPA, with a particular emphasis on chirally sensitive VOA techniques. We successfully obtained high-quality Raman and ROA spectra of l-DOPA in its cationic form, under low pH conditions, and at a high concentration of 100 mg/ml. These spectra cover a broad spectral range, allowing for precise comparisons with theoretical simulations. We also obtained IR and VCD spectra, but they faced limitations due to the narrow accessible spectral region. Exploration of l-DOPA's conformational landscape revealed its intrinsic flexibility, with multiple coexisting conformations. To characterize these conformations, we employed two methods: one involved potential energy surface scans with implicit solvation, and the other utilized molecular dynamics simulations with explicit solvation. Comparing ROA spectra from different conformer groups and applying spectral decomposition proved crucial in determining the correct conformer ratios. The use of explicit solvation significantly improved the quality of the final simulated spectral profiles. The accurate determination of conformer ratios, rather than solely relying on the number of averaged spectra, played a crucial role in simulation accuracy. In conclusion, our study offers valuable insights into the structure and conformational behavior of l-DOPA and represents a valuable resource for subsequent spectroscopic studies of its deuterated analogs.

Effects of sulfation and the environment on the structure of chondroitin sulfate studied via Raman optical activity.

Glycosaminoglycans are linear carbohydrate polymers with essential roles in many biological processes. Chondroitin sulfate (CS) is one of them, omnipresent in living organisms as an important structural component of cartilage. It provides much of its resistance to compression. Despite its biological importance, little is still known about the relation of the CS structure to chemical composition and interaction with the environment. We therefore measured Raman and Raman optical activity (ROA) spectra of five CS samples of different biological origin and variously sulfated CS building blocks (GlcA, GalNAc, and basic disaccharide units) in a wide frequency range between 200 cm-1 and 1800 cm-1 and analyzed them with respect to specific structure marker bands. We show that ROA spectroscopy is sensitive to the conformational stability and rigidity of pyranose rings of saccharides, the orientation of sugar hydroxyl groups and the secondary structure of the CS's backbone. The CS secondary structure has been found to be quite stable, with a minor variation as a reaction to physicochemical parameters (concentration, pH, temperature, and the presence of cations). Larger changes were observed under chemical changes (sulfation) of the CS chain. ROA spectroscopy thus exhibited useful potential to study the structure of similar biopolymers.

Absolute Configuration Determination of a Taxol Precursor Based on Raman Optical Activity Spectra.

Enantiomeric purity of drugs is essential for their biological activity. In the present study, we investigate the performance of Raman optical activity (ROA) spectroscopy in distinguishing four possible stereoisomers of the synthetic precursor used for the production of taxol from baccatin III. Taxol is one of the best-selling medicaments used in the treatment of ovarian, lung, and breast cancers and Kaposi's sarcoma. In a low yield, it may be isolated from the bark of the Pacific yew tree (Taxus brevifolia); however, its industrial production is largely dependent on the precursor. It is shown that for reliable comparison of the experimental and computed Raman and ROA intensities a large number of conformers had to be averaged, to properly account for molecular flexibility in solution. In addition, if combined with the density functional theory computations, ROA spectra provide convenient and economic means of absolute configuration determination.

Influence of ligand binding on structure and thermostability of human α1-acid glycoprotein.

Ligand binding of neutral progesterone, basic propranolol, and acidic warfarin to human α1-acid glycoprotein (AGP) was investigated by Raman spectroscopy. The binding itself is characterized by a uniform conformational shift in which a tryptophan residue is involved. Slight differences corresponding to different contacts of the individual ligands inside the ß-barrel are described. Results are compared with in silico ligand docking into the available crystal structure of deglycosylated AGP using quantum/molecular mechanics. Calculated binding energies are -18.2, -14.5, and -11.5 kcal/mol for warfarin, propranolol, and progesterone, respectively. These calculations are consistent with Raman difference spectroscopy; nevertheless, minor discrepancies in the precise positions of the ligands point to structural differences between deglycosylated and native AGP. Thermal dynamics of AGP with/without bounded warfarin was followed by Raman spectroscopy in a temperature range of 10-95 °C and analyzed by principal component analysis. With increasing temperature, a slight decrease of α-helical content is observed that coincides with an increase in ß-sheet content. Above 45 °C, also ß-strands tend to unfold, and the observed decrease in ß-sheet coincides with an increase of ß-turns accompanied by a conformational shift of the nearby disulfide bridge from high-energy trans-gauche-trans to more relaxed gauche-gauche-trans. This major rearrangement in the vicinity of the bridge is not only characterized by unfolding of the ß-sheet but also by subsequent ligand release. Hereby, ligand binding alters the protein dynamics, and the more rigid protein-ligand complex shows an improved thermal stability, a finding that contributes to the reported chaperone-like function of AGP.

Electronic circular dichroism of the chiral rigid tricyclic dilactam with nonplanar tertiary amide groups.

Electronic circular dichroism (ECD) of the spirocyclic dilactam 5,8-diazatricyclo[6,3,0,0(1,5)]undecane-4,9-dione has been measured in the extended wavelength range (170-260 nm) utilizing far-UV CD instrumentation including synchrotron radiation light source. The data of this model of two nonplanar tertiary amide groups interacting within the rigid chiral environment provided new information particularly about the shorter wavelength π-π* transition region below 190 nm. The interpretation using TDDFT calculations confirmed that effects of amide nonplanarity follow our previous observations on monolactams as far as amide n-π* transitions are concerned. ECD band in the n-π* transition region of the nonplanar diamide exhibits an identical bathochromic shift and its sign remains tied to the sense of nonplanar deformation in the same way. As far as n-π* transitions are concerned amide nonplanarity acts as a local phenomenon independently reflecting sum properties of single amide groups. On the other hand, CD bands associated with π-π* transitions (found between ∼170 to 210 nm) form an exciton-like couplet with the sign pattern determined by mutual orientation of the associated electric transition moments. This sign pattern follows predictions pertaining to a coupled oscillator. The influence of amide nonplanarity on π-π* transitions is only minor and concentrates into the shorter wavelength lobe of the π-π* couplet. The detailed analysis of experimental ECD with the aid of TDDFT calculations shows that there is only little interaction between effects of inherent chirality caused by nonplanarity of amide groups and amide-amide coupling. Consequently these two effects can be studied nearly independently using ECD. In addition, the calculations indicate that participation of other type of transitions (n-σ*, π-σ* or Rydberg type transitions) is only minor and is concentrated below 180 nm.

Protonation effect of tyrosine in a segment of the SRF transcription factor: a combined optical spectroscopy, molecular dynamics, and density functional theory calculation study.

The high sensitivity to pH of a short segment (an octamer) of serum response factor (SRF), an important member of the MADS box family of transcription factors, was investigated by Raman scattering, infrared and circular dichroism spectroscopies. Molecular dynamics (MD) and density functional theory (DFT) calculations enabled interpretation of spectral changes in close detail. Although there was a negligible difference between spectra in acidic and neutral environments, the spectrum in basic pH was substantially different. The major changes were attributed to the deprotonation of tyrosine. The secondary structure of the SRF octamer fragment was estimated experimentally as well as predicted theoretically by MD. All techniques proved that it exists in a dynamical equilibrium among several conformations mostly close to ß turn, unordered conformations, and extended structure, in contrast to the stable secondary structure it possesses as a part of SRF. Generally, this approach represents a useful tool for the study of various short oligopeptides.

Nonplanar tertiary amides in rigid chiral tricyclic dilactams. Peptide group distortions and vibrational optical activity.

We investigate amide nonplanarity in vibrational optical activity (VOA) spectra of tricyclic spirodilactams 5,8-diazatricyclo[6,3,0,0(1,5)]undecan-4,9-dione (I) and its 6,6',7,7'-tetradeuterio derivative (II). These rigid molecules constrain amide groups to nonplanar geometries with twisted pyramidal arrangements of bonds to amide nitrogen atoms. We have collected a full range vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectra including signals of C-H and C-D stretching vibrations. We report normal-mode analysis and a comparison of calculated to experimental VCD and ROA. The data provide band-to-band assignment and offer a possibility to evaluate roles of constrained nonplanar tertiary amide groups and rigid chiral skeletons. Nonplanarity shows as single-signed VCD and ROA amide I signals, prevailing the couplets expected to arise from the amide-amide interaction. Amide-amide coupling dominates amide II (mainly C'-N stretching, modified in tertiary amides by the absence of a N-H bond) transitions (strong couplet in VCD, no significant ROA) probably due to the close proximity of amide nitrogen atoms. At lower wavenumbers, ROA spectra exhibit another likely manifestation of amide nonplanarity, showing signals of amide V (δ(oop)(N-C) at ~570 cm(-1)) and amide VI (δ(oop)(C'═O) at ~700 cm(-1) and ~650 cm(-1)) vibrations.

CH Stretching Region: Computational Modeling of Vibrational Optical Activity.

Most organic compounds provide vibrational spectra within the CH stretching region, yet the signal is difficult to interpret because of multiple difficulties in experiment and modeling. To better understand various factors involved, the ability of several harmonic and anharmonic computational approaches to describe these vibrations was explored for α-pinene, fenchone, and camphor as test compounds. Raman, Raman optical activity (ROA), infrared absorption (IR), and vibrational circular dichroism (VCD) spectra were measured and compared to quantum chemical computations. Surprisingly, the harmonic vibrational approach reasonably well reproduced the measured spectral patterns, including the vibrational optical activity (VOA). The CH stretching, however, appeared to be more sensitive to the basis set and solvent variations than lower-frequency vibrations. For a higher accuracy in frequencies and spectral shapes, anharmonic corrections were necessary. Accurate harmonic and anharmonic force fields were obtained with the mPW2PLYP double-hybrid functional. A limited vibrational configuration interaction (LVCI) where the CH stretching motion was decoupled from other vibrations provided the best simulated spectra. A balanced harmonic oscillator basis set had to be used, containing also states indirectly interacting with fundamental vibrations. A simpler second-order perturbational approach (PT2) appeared less useful. The modeling provided unprecedented agreement with experimental vibrational frequencies; spectral shapes were reproduced less faithfully. The possibility of ab initio interpretation of the CH spectral region for relatively large molecules further broadens the application span of vibrational spectroscopy.

Electronic and vibrational optical activity of several peptides related to neurohypophyseal hormones: disulfide group conformation.

Electronic and vibrational optical activity of the set of neurohypophyseal hormones and their analogs was investigated to clarify the S-S bond solution conformation. The selected compounds include oxytocin (I), lysine vasopressin (II), arginine vasopressin (III), and their analogs (IV-IX), differing widely in their pharmacological properties. We have extended the already known electronic circular dichroism data by new information provided by vibrational circular dichroism (VCD) and Raman optical activity (ROA). The use of VCD brought additional details on three-dimensional structure of the chain reversal in the ring moiety and on its left handedness. Furthermore, Raman scattering and ROA allowed us to deduce the sense of the disulfide bond torsion.

Tracking of the polyproline folding by density functional computations and Raman optical activity spectra.

Polyprolines offer many opportunities to study factors influencing peptide and protein folding and structure. Longer chains can adopt two well-defined forms (PPI and PPII), but shorter peptides are quite flexible. To understand in detail the dependence of the secondary structure on the length and the interplay between the side chain and main chain conformation, zwitterionic (Pro)(N) models (with N = 2, 3, 4, 6, 9, 12 and longer inhomogeneous chains) were studied by a combination of the Raman and Raman optical activity (ROA) spectroscopy with the density functional theory (DFT). Potential surfaces were systematically explored for the shorter oligoprolines, and Boltzmann conformational ratios were obtained both for the main chain and the proline ring puckering. The predictions were verified by comparison of the experimental and simulated ROA spectra. The conformer ratios extracted from a decomposition of the experimental ROA into scaled computed spectra well reproduced Boltzmann populations calculated from relative energies. For example, an "A" puckering of the proline ring was found prevalent, relatively independent of the length, whereas the cis-amide backbone form adopted by shorter peptides rapidly disappeared for N > 4. The results are consistent with previous NMR and vibrational circular dichroism (VCD) data. Delocalized exciton vibrations along the peptide chain often enhance the ROA signal, and can thus be used to indicate a longer regular peptide structure. The ROA technique appeared to be very sensitive to the ring puckering; less distinct spectral features were produced by changes in the main chain geometry.

Disulfide chromophore and its optical activity.

The compounds I-IV derived from α-D-cyclodextrin moiety by bridging and/or interconnecting with various patterns of disulfide bonds were chosen as models for the spectroscopic study of conformation of the disulfide bridge. The energy gap between the disulfide and cyclodextrin's electronic transitions allows us to investigate absorption and electronic circular dichroism spectra without disturbing spectral overlaps with amides or aromatic amino acids in peptides or proteins. Raman optical activity (ROA) spectra were measured and the bands due to S-S and C-S stretching motion identified. Comparison with the quantum mechanical calculations of simple models indicates that sense of disulfide twist follows sign of the measured S-S ROA band.

Side chain and flexibility contributions to the Raman optical activity spectra of a model cyclic hexapeptide.

A model peptide, cyclo-(Phe-d-Pro-Gly-Arg-Gly-Asp), with a distinct folded structure containing short beta-hairpin and beta-sheet patterns was studied by Raman and Raman optical activity (ROA) spectroscopies. Unlike for previously analyzed vibrational circular dichroism of the same compound (Chirality 2008, 20, 1104), the Raman spectrum is dominated by side chain contributions and is more sensitive to their geometry fluctuations. The spectra and molecular motion were analyzed with the aid of the density functional theory simulations combined with molecular dynamics (MD). The side chain geometry fluctuations were found to significantly contribute to the broadening of the spectral bands, while dynamics of the backbone is rather restricted. According to our MD results, the side chains do not move freely but largely oscillate around preferred conformations. Averaging of computed spectra for many structures derived from the MD trajectories provided better spectral profiles than did a fixed geometry. The Raman and ROA scattering is dominated by the more polarizable phenylalanine and proline groups, as could be verified both by the computations and by comparison to experiments with a model Phe-d-Pro dipeptide. Computational analyses suggest that the ROA spectrum mostly senses local side chain conformation, whereas a vibrational coupling between different side chains contributes less. The coupling is mostly mediated by the peptide backbone and is restricted to specific vibrational region. The ROA spectroscopic technique thus provides important local structural information that needs, however, to be extracted by multiscale (QM/MM) simulation techniques.

A Fourier Transform Method for Generation of Anharmonic Vibrational Molecular Spectra.

Accurate computations of vibrational energies and vibrational spectra of molecules require inclusion of the anharmonic forces. In standard computational protocols, this leads to a large vibrational Hamiltonian matrix that needs to be diagonalized. Spectral intensities are calculated for individual transitions separately. In this work, an alternate direct generation of the spectral curves is proposed, based on a temporal propagation of a trial vibrational wave function followed by the Fourier transformation (FT). The method was applied to model water dimer and fenchone molecules. Arbitrary resolutions could be achieved by longer-time propagations, although a smaller integration time step (∼0.02 fs) was needed for accurate peak frequencies than previously found for similar time-dependent applications within the harmonic approximation. Acceptably accurate relative vibrational spectra intensities were obtained when many random vectors used in the propagations were averaged. For a model fenchone Hamiltonian, simulated Raman and Raman optical activity (ROA) spectral shapes compared well with those obtained by the classical approach. The algorithm is amendable to parallelization. The lack of the lengthy and computer-memory-demanding diagonalization thus makes the FT procedure especially convenient for spectral simulations of larger molecules.

L-alanyl-L-alanine conformational changes induced by pH as monitored by the Raman optical activity spectra.

Fine effects of the hydration, charge, and conformational structural changes in L-alanyl-L-alanine (Ala-Ala) dipeptide were studied with the aid of Raman and Raman optical activity (ROA) spectra. The spectra were recorded experimentally and analyzed by means of density functional computations. A (15)N and (13)C isotopically labeled analogue was synthesized and used to verify the vibrational mode assignment. Calculated shifts in vibrational frequencies for isotopically labeled molecule agreed well with the experiment. The assignment made it possible to scale computed vibrational frequencies and extract better structural information from the intensities. Solvent modeling with clusters obtained from molecular dynamics led to a qualitatively correct inhomogeneous broadening of Raman spectral lines but did not bring a convincing improvement of ROA signal when compared to a standard dielectric solvent correction. In comparison with the zwitterionic form, charged anionic and cationic dipeptides provided spectral variations that indicated different conformational behavior. Only minor backbone conformational change occurs in the cation, whereas the results indicate the presence of more anion conformers differing in the rotation of the NH(2) group and the backbone psi-angle. These findings are in agreement with previous electronic circular dichroism (ECD) and NMR studies. The results confirm the large potential of the ROA technique for the determination of final details in molecular structure and conformation.

Interpretation of Raman and Raman optical activity spectra of a flexible sugar derivative, the gluconic acid anion.

Raman scattering and its polarized extension, Raman optical activity (ROA), are commonly used for monitoring of molecular conformational equilibria in solutions. This is complicated for saccharides due to extensive motions of the hydroxyl groups and other molecular parts. Standard interpretation procedures involving ab initio spectral simulations for a limited set of conformers are not adequate. In this study, a more general approach is proposed for the gluconic acid anion taken as a model compound, where quantum simulations of the spectra are directly coupled with molecular dynamics (MD) techniques. Such a multiscale approach reveals how the structural information is encoded in the broadened spectral lines. The spectra were simulated for solvent-solute clusters generated by MD. Conformational averaging was enabled by a limited library of conformers for which the spectral parameters could be calculated ab initio and moved on the MD geometries by Cartesian coordinate tensor transfer techniques. The B3LYP/CPCM/6-31+G** approximation was used as a default for computation of the source force fields and polarizability derivatives. The spectra thus obtained relatively faithfully reproduced most of the experimental features. The Amber and polarizable Amoeba MD force fields produced similar results; application of the latter, however, was limited by the long time necessary to achieve a converged conformational equilibrium. Both MD simulation and spectral averaging suggest that the hydroxyl groups as well as the backbone C-C bonds rotate relatively freely, with some restrictions in the vicinity of the carboxyl group. In spite of the averaging, spectral response of characteristic vibrational normal mode families, such as CH and OH bending, can clearly be identified in the spectra. The simulations thus confirm the experimental fact that flexible saccharides exhibit significant vibrational activity that reveals precious information about molecular structure and dynamics encoded in the Raman and ROA spectral shapes.

Comparison of quantitative conformer analyses by nuclear magnetic resonance and Raman optical activity spectra for model dipeptides.

Interpretation of the Raman optical activity (ROA) of peptides is difficult because of molecular flexibility and interaction with the solvent. Typically, simulations and experiments are compared in terms of a qualitative agreement between the spectra. However, on a series of the Pro-Gly, Gly-Pro, Pro-Ala, and Ala-Pro dipeptides more precise conformer ratios could be obtained with the aid of the density functional computations and numerical decomposition of the spectral shapes. All observed transitions were assigned, and the computed transition frequencies were scaled accordingly. Then the populations predicted by the optical spectroscopy agreed within a few percent with an analysis of the spin-spin coupling constants based on the Karplus equations, which was confirmed also by a comparison of calculated and experimental NMR couplings. The results are supported by molecular dynamics simulations and related to the previous conformational studies of similar molecules.

Conformational properties of the Pro-Gly motif in the D-Ala-l-Pro-Gly-D-Ala model peptide explored by a statistical analysis of the NMR, Raman, and Raman optical activity spectra.

The Pro-Gly sequence in designed peptides and proteins is often used to mimic natural beta-hairpin turns. Shorter peptides containing this moiety, however, adopt multiple conformations, and their propensity to form the turn is not obvious. In this study, conformational flexibility of Pro-Gly was investigated with the aid of NMR, Raman scattering, and Raman optical activity (ROA). The spectra of a model tetrapeptide NH3+-D-Ala-L-Pro-Gly-D-Ala-CO2- were analyzed on the basis of statistical methods and density functional computations. Other peptide derivatives were adopted as supporting theoretical and experimental models. The results suggest that the loop conformation of the Pro-Gly core is not inherently stable in vacuum. On the other hand, in aqueous environment the propensity to form the beta-hairpin loops is an intrinsic property of the Pro-Gly sequence. It was observed also in a shorter Ac-D-Pro-Gly-NH-Me dipeptide. The attached alanine residues in the tetrapeptide stabilize the structure only partially. Thus an inclusion of the solvent in the calculations is important for correct description of peptide folding in the aqueous environment. The agreement of the optical spectra with the experiment was determined from overlaps between simulated and measured spectral curves. The comparison of the computed NMR, Raman, and ROA was hampered by experimental noise and limited accuracy of the computations. However, the statistical analysis of the spectroscopic data provided conformer distribution consistent with the computation of the relative energies. The combination of the NMR and Raman techniques with the quantum computations appeared very beneficial for the investigation of Pro-Gly conformational behavior, and can be recommended for future peptide folding studies.

Anharmonic effects in IR, Raman, and Raman optical activity spectra of alanine and proline zwitterions.

The difference spectroscopy of the Raman optical activity (ROA) provides extended information about molecular structure. However, interpretation of the spectra is based on complex and often inaccurate simulations. Previously, the authors attempted to make the calculations more robust by including the solvent and exploring the role of molecular flexibility for alanine and proline zwitterions. In the current study, they analyze the IR, Raman, and ROA spectra of these molecules with the emphasis on the force field modeling. Vibrational harmonic frequencies obtained with 25 ab initio methods are compared to experimental band positions. The role of anharmonic terms in the potential and intensity tensors is also systematically explored using the vibrational self-consistent field, vibrational configuration interaction (VCI), and degeneracy-corrected perturbation calculations. The harmonic approach appeared satisfactory for most of the lower-wavelength (200-1800 cm(-1)) vibrations. Modern generalized gradient approximation and hybrid density functionals, such as the common B3LYP method, provided a very good statistical agreement with the experiment. Although the inclusion of the anharmonic corrections still did not lead to complete agreement between the simulations and the experiment, occasional enhancements were achieved across the entire region of wave numbers. Not only the transitional frequencies of the C-H stretching modes were significantly improved but also Raman and ROA spectral profiles including N-H and C-H lower-frequency bending modes were more realistic after application of the VCI correction. A limited Boltzmann averaging for the lowest-frequency modes that could not be included directly in the anharmonic calculus provided a realistic inhomogeneous band broadening. The anharmonic parts of the intensity tensors (second dipole and polarizability derivatives) were found less important for the entire spectral profiles than the force field anharmonicities (third and fourth energy derivatives), except for a few weak combination bands which were dominated by the anharmonic tensor contributions.

Structure of the dimeric N-glycosylated form of fungal beta-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies.

BACKGROUND: Fungal beta-N-acetylhexosaminidases catalyze the hydrolysis of chitobiose into its constituent monosaccharides. These enzymes are physiologically important during the life cycle of the fungus for the formation of septa, germ tubes and fruit-bodies. Crystal structures are known for two monomeric bacterial enzymes and the dimeric human lysosomal beta-N-acetylhexosaminidase. The fungal beta-N-acetylhexosaminidases are robust enzymes commonly used in chemoenzymatic syntheses of oligosaccharides. The enzyme from Aspergillus oryzae was purified and its sequence was determined. RESULTS: The complete primary structure of the fungal beta-N-acetylhexosaminidase from Aspergillus oryzae CCF1066 was used to construct molecular models of the catalytic subunit of the enzyme, the enzyme dimer, and the N-glycosylated dimer. Experimental data were obtained from infrared and Raman spectroscopy, and biochemical studies of the native and deglycosylated enzyme, and are in good agreement with the models. Enzyme deglycosylated under native conditions displays identical kinetic parameters but is significantly less stable in acidic conditions, consistent with model predictions. The molecular model of the deglycosylated enzyme was solvated and a molecular dynamics simulation was run over 20 ns. The molecular model is able to bind the natural substrate - chitobiose with a stable value of binding energy during the molecular dynamics simulation. CONCLUSION: Whereas the intracellular bacterial beta-N-acetylhexosaminidases are monomeric, the extracellular secreted enzymes of fungi and humans occur as dimers. Dimerization of the fungal beta-N-acetylhexosaminidase appears to be a reversible process that is strictly pH dependent. Oligosaccharide moieties may also participate in the dimerization process that might represent a unique feature of the exclusively extracellular enzymes. Deglycosylation had only limited effect on enzyme activity, but it significantly affected enzyme stability in acidic conditions. Dimerization and N-glycosylation are the enzyme's strategy for catalytic subunit stabilization. The disulfide bridge that connects Cys448 with Cys483 stabilizes a hinge region in a flexible loop close to the active site, which is an exclusive feature of the fungal enzymes, neither present in bacterial nor mammalian structures. This loop may play the role of a substrate binding site lid, anchored by a disulphide bridge that prevents the substrate binding site from being influenced by the flexible motion of the loop.

Proline zwitterion dynamics in solution, glass, and crystalline state.

Raman and Raman optical activity spectra of L- and D-proline zwitterionic (PROZW) forms were recorded for H(2)O and D(2)O solutions in a wide frequency range and analyzed with respect to the motion of the proline ring and rotation of the carbonyl group. The solution spectra were additionally compared to Raman scattering of glass and crystalline powder proline. Solution and glass spectral band broadenings are similar and reveal information about the extent of internal molecular motion. Two distinct but equally populated flexible forms were found in the glass and the solution. The equal population is consistent with NMR data, temperature, and concentration dependencies. The molecular flexibility is reduced significantly in the crystal, however, where only one conformer is present. Consequently, the crystal bands are narrow and exhibit minor frequency shifts. The spectra were interpreted with the aid of density functional theory computations involving both continuum and explicit solvent. A two-dimensional potential energy surface pertaining to the five-member ring puckering coordinates was constructed and used for dynamical averaging of spectral properties. Comparison of the computed and experimental bandwidths suggests that the puckering is strongly correlated with the carbonyl rotation. An averaging over these two motions produces similar results. The interpretation of the Raman experiments with the aid of the simulation techniques also indicates that the environment modulates properties of the hydrophobic part of the molecule indirectly by interacting with the ionic group. Such behavior may be important for the reactivity and biological activity of proline-containing peptides and proteins.