Quantitative Determination of Ala-Ala Conformer Ratios in Solution by Decomposition of Raman Optical Activity Spectra

Phosphorylation site of L-alanyl-L-glutamine identified by Raman optical activity spectroscopy

Phosphorylated peptides are instrumental in studying protein phosphorylation events. In the present study, Raman optical activity (ROA) is employed to elucidate the structure of a dipeptide, L-alanyl-L-glutamine (L-Ala-L-Gln) and its two differently alkylated N-phosphorylated derivatives. Theoretical simulations were conducted to aid the interpretation of peptide conformation variations upon phosphorylation, and of the measured Raman and ROA spectra. Induced circularly polarized luminescence (CPL) was also recorded in solution, in the presence of a simple europium aqua ion. As the spectra are peptide specific, this type of stereochemical analysis is expected to aid identification of the phosphorylation sites also in other peptides and possibly proteins.

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.

Monitoring Conformation and Protonation States of Glutathione by Raman Optical Activity and Molecular Dynamics

Glutathione (GSH) is a common antioxidant and its biological activity depends on the conformation and protonation state. We used molecular dynamics, Raman and Raman optical activity (ROA) spectroscopies to investigate GSH structural changes in a broad pH range. Factor analysis of the spectra provided protonation constants (2.05, 3.45, 8.62, 9.41) in good agreement with previously published values. Following the analysis, spectra of differently protonated forms were obtained by extrapolation. The complete deprotonation of the thiol group above pH 11 was clearly visible in the spectra; however, many spectral features did not change much with pH. Experimental spectra at various pH values were decomposed into the simulated ones, which allowed us to study the conformer populations and quality of molecular dynamics (MD). According to this combined ROA/MD analysis conformation of the GSH backbone is affected by the pH changes only in a limited way. The combination of ROA with the computations thus has the potential to improve the MD force field and obtain more accurate populations of the conformer species. The methodology can be used for any molecule, but for a more detailed insight better computational techniques are needed in the future.

Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution

Nucleotide conformational flexibility affects their biological functions. Although the spectroscopy of Raman optical activity (ROA) is well suited to structural analyses in aqueous solutions, the link between the spectral shape and the nucleotide geometry is not fully understood. We recorded the Raman and ROA spectra of model nucleotides (rAMP, rGMP, rCMP, and dTMP) and interpreted them on the basis of molecular dynamics (MD) combined with density functional theory (DFT). The relation between the sugar puckering, base conformation and spectral intensities is discussed. Hydrogen bonds between the sugar's C3' hydroxyl and the phosphate groups were found to be important for the sugar puckering. The simulated spectra correlated well with the experimental data and provided an understanding of the dependence of the spectral shapes on conformational dynamics. Most of the strongest spectral bands could be assigned to vibrational molecular motions. Decomposition of the experimental spectra into calculated subspectra based on arbitrary maps of free energies provided experimental conformer populations, which could be used to verify and improve the MD predictions. The analyses indicate some flaws of common MD force fields, such as being unable to describe the fine conformer distribution. Also the accuracy of conformer populations obtained from the spectroscopic data depends on the simulations, improvement of which is desirable for gaining a more detailed insight in the future. Improvement of the spectroscopic and computational methodology for nucleotides also provides opportunities for its application to larger nucleic acids.

Constructing Potential Energy Surface with Correlated Theory for Dipeptides Using Molecular Tailoring Approach

We demonstrate a cost-effective alternative employing the fragment-based molecular tailoring approach (MTA) for building the potential energy surface (PES) for two dipeptides viz. alanine-alanine and alanine-proline employing correlated theory, with augmented Dunning basis sets. About 1369 geometries are generated for each test dipeptide by systematically varying the dihedral angles Φ ${{\rm{\Phi }}}$ and Ψ ${{{\Psi }}}$ . These conformational geometries are partially optimized by relaxing all the other Z-matrix parameters, fixing the values of Φ ${{\rm{\Phi }}}$ and Ψ ${{{\Psi }}}$ . The MP2 level PES is constructed from the MTA-energies of chemically intact geometries using minimal hardware. The fidelity of MP2/aug-cc-pVDZ level PES is brought out by comparing it with its full calculation counterpart. Further, we bring out the power of the method by reporting the MTA-based CCSD/aug-cc-pVDZ level PES for these two dipeptides containing 498 and 562 basis functions respectively.

A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides

Cyclic peptides are a promising class of compounds for next-generation antibiotics as they may provide new ways of limiting antibiotic resistance development. Although their cyclic structure will introduce some rigidity, their conformational space is large and they usually have multiple chiral centers that give rise to a wide range of possible stereoisomers. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) are used to assign stereochemistry and discriminate enantiomers of chiral molecules, often in combination with electronic structure methods. The reliable determination of the absolute configuration of cyclic peptides will require robust computational methods than can identify all significant conformers and their relative population and reliably assign their stereochemistry from their chiroptical spectra by comparison with ab initio calculated spectra. We here present a computational protocol for the accurate calculation of the VCD spectra of a series of flexible cyclic oligopeptides. The protocol builds on the Conformer-Rotamer Ensemble Sampling Tool (CREST) developed by Grimme and co-workers ( Phys. Chem. Chem. Phys. 2020, 22, 7169-7192 and J. Chem. Theory. Comput. 2019, 15, 2847-2862) in combination with postoptimizations using B3LYP and moderately sized basis sets. Our recommended computational protocol for the computation of VCD spectra of cyclic oligopeptides consists of three steps: (1) conformational sampling with CREST and tight-binding density functional theory (xTB); (2) energy ranking based on single-point energy calculations as well as geometry optimization and VCD calculations of conformers that are within 2.5 kcal/mol of the most stable conformer using B3LYP/6-31+G*/CPCM; and (3) VCD spectra generation based on Boltzmann weighting with Gibbs free energies. Our protocol provides a feasible basis for generating VCD spectra also for larger cyclic peptides of biological/pharmaceutical interest and can thus be used to investigate promising compounds for next-generation antibiotics.

Paving the way to conformationally unravel complex glycopeptide antibiotics by means of Raman optical activity

It is crucial for fundamental physical chemistry techniques to find their application in tackling real-world challenges. Hitherto, Raman optical activity (ROA) spectroscopy is one of the examples where a promising future within the pharmaceutical sector is foreseen, but has not yet been established. Namely, the technique is believed to be able to contribute in investigating the conformational behaviour of drug candidates. We, herein, strive towards the alignment of the ROA analysis outcome and the pharmaceutical expectations by proposing a fresh strategy that ensures a more complete, reliable, and transferable ROA study. The strategy consists of the treatment of the conformational space by means of a principal component analysis (PCA) and a clustering algorithm, succeeded by a thorough ROA spectral analysis and a novel way of estimating the contributions of the different chemical fragments to the total ROA spectral intensities. Here, vancomycin, an antibiotic glycopeptide, has been treated; it is the first antibiotic glycopeptide studied by means of ROA and is a challenging compound in ROA terms. By applying our approach we discover that ROA is capable of independently identifying the correct conformation of vancomycin in aqueous solution. In addition, we have a clear idea of what ROA can and cannot tell us regarding glycopeptides. Finally, the glycopeptide class turns out to be a spectroscopically curious case, as its spectral responses are unlike the typical ROA spectral responses of peptides and carbohydrates. This preludes future ROA studies of this intriguing molecular class.

Raman optical activity tackles the complex conformational space of glycopeptide antibiotics.

Mapping Conformational Space of All 8000 Tripeptides by Quantum Chemical Methods: What Strain Is Affordable within Folded Protein Chains?

To gain more insight into the physicochemical aspects of a protein structure from the first principles, conformational space of all 8000 "capped" tripeptides (i.e., N-Ac-X₁X₂X₃-NH-CH₃, where X_i is one of the 20 natural amino acids) was investigated computationally. An enormous dataset (denoted P-CONF_1.6M and containing close to 1 600 000 conformers in total) has been obtained by employing a composite protocol combining density functional theory, semiempirical quantum mechanics (SQM), and state-of-the-art solvation methods with 1000 K molecular dynamics (MD) used to generate initial structures (200 snapshots for each tripeptide). This allowed us to present the first rigorous QM-based glimpse at the vast conformational space spanned by small protein fragments. The same computational procedure was repeated for tripeptide fragments taken from the SCOPe database of three-dimensional protein folds, by restraining them to their geometry in a protein. Such complementary data allowed us to compare the distribution of conformational strain energies of unrestrained tripeptidic fragments "in solvent" with those in existing protein chains. Besides providing a rigorous (ab initio) proof of a few well-known concepts and hypotheses concerning protein structures, such as the distribution of (φ, ψ) angles in Ramachandran plots, we have made several observations that came as a certain surprise: (1) distribution of conformational energies does not significantly differ between the "unbiased/unrestrained" conformers obtained from MD sampling in solvent and the biased conformers, i.e., those of a given tripeptide obtained from protein structures; (2) conformational (strain) energy window up to ∼20 to 25 kcal·mol^-1 is readily available to tripeptide fragments within the context of a protein chain; (3) overpopulation in certain regions of Ramachandran plot was observed for the unbiased conformers. Last but not least, the massive dataset of accurate (DFT-D3//COSMO-RS) conformational (free) energies of ∼1.6 M peptide conformers, P-CONF_1.6M, obtained throughout this work may serve as excellent dataset for calibrating and benchmarking of popular force fields.

Pressure dependence of vibrational optical activity of model biomolecules. A computational study

Change of molecular properties with pressure is an attracting means to regulate molecular reactivity or biological activity. However, the effect is usually small and so far explored rather scarcely. To obtain a deeper insight and estimate the sensitivity of vibrational optical activity spectra to pressure-induced conformational changes, we investigate small model molecules. The Ala-Ala dipeptide, isomaltose disaccharide and adenine-uracil dinucleotide were chosen to represent three different biomolecular classes. The pressure effects were modeled by molecular dynamics and density functional theory simulations. The dinucleotide was found to be the most sensitive to the pressure, whereas for the disaccharide the smallest changes are predicted. Pressure-induced relative intensity changes in vibrational circular dichroism and Raman optical activity spectra are predicted to be 2-3-times larger than for non-polarized IR and Raman techniques.

Tracking Conformational Changes in Phosvitin throughout a Crowding-Agent-Based Titration

The sensitivity of Raman optical activity (ROA) towards small conformational changes is explored by tracking the structural changes in an intrinsically disordered protein-phosvitin-induced by different concentrations of crowding agent. It is shown that ROA is capable of tracking small conformational changes involving β-sheet and α-helical secondary structural properties of the protein. Furthermore, it is indicated that the influences of the crowding agents employed, Ficoll 70 and dextran 70, on the structural properties of phosvitin differ significantly, with the structural changes induced by the presence of Ficoll 70 being more pronounced and already being visible at a lower concentration. The data also suggest that some spectral changes do not arise from a change in the secondary structure of the protein, but are related to differences in interaction between the phosphorylated residues of the protein and the sugar-based crowding agent.

Theoretical and experimental adsorption studies of sulfamethoxazole and ketoprofen on synthesized ionic liquids modified CNTs

The adsorption of sulfamethoxazole (SMZ) and ketoprofen (KET) using carbon nanotubes (CNTs) and CNTs modified with ionic liquids (ILs) was investigated. Two ionic liquids (1-benzyl, 3-hexyl imidazolium, IL1 and 1-benzyl, 3-decahexyl imidazolium, IL2) were synthesized, and characterized by nuclear magnetic resonance (¹H and ¹³C NMR) and high resolution-mass spectrometry (HR-MS). CNTs and modified CNTs were characterized using FT-IR, X-ray diffraction (XRD), surface area and porosity analysis, thermal gravimetric analysis (TGA), Zeta potential, Raman and scanning electron microscopy (SEM). Kinetics, isotherm and computational studies were carried out to determine the efficiency and adsorption mechanism of SMZ and KET on modified CNTs. A density functional theory (DFT) method was applied to shed more light on the interactions between the pharmaceutical compounds and the adsorbents at the molecular level. The effects of adsorbent dosage, concentration, solution pH, energetics and contact time of SMZ and KET on the adsorption process were investigated. The adsorption of SMZ and KET on CNTs and modified CNTs were pH dependent, and adsorption was best described by pseudo-second-order kinetics and the Freundlich adsorption isotherm. Ionic liquid modified CNTs showed improved adsorption capacities compared to the unmodified ones for both SMZ and KET, which is in line with the computational results showing performance order; CNT+KET/SMZ < CNT-ILs+SMZ < CNT-ILs+KET.