Infrared and Raman spectroscopy and DFT calculations of DL amino acids: Valine and lysine hydrochloride

Structural, spectroscopic, molecular docking, ADME, molecular dynamics studies of Val-Trp dipeptide

Hypertension is a significant risk factor for various diseases, especially heart, brain, and kidney diseases. It is known that many peptides have the property of lowering blood pressure and determine as ACE inhibitors. The purpose of this study is to obtain information about the molecular structure of Val-Trp (L-valyl-L-tryptophan), which is one of the antihypertensive peptides, by molecular mechanical, quantum mechanical, and spectroscopic methods (FT-IR and Raman). Also, it is aimed to investigate the interactions of Val-Trp dipeptide with receptors related to hypertension and to determine the pharmacokinetic profile due to the potential of the peptide to be a drug candidate. The peptide structure was optimized by DFT/B3LYP/6-311++G(d,p) basis set, then vibrational wavenumbers, molecular electrostatic potential (MEP), HOMO-LUMO (highest occupied molecular orbital- lowest unoccupied molecular orbital), NBO (natural bond orbital) analyzes were performed. The assignment of fundamental theoretical vibration wavenumbers was carried out with potential energy distribution analysis (PED). After the structural analyzes of the peptide were performed, the interactions of the peptide with Angiotensin-converting enzyme (ACE), Angiotensin II Receptor Type 1 (AT1R) and Renin were investigated by molecular docking study. Then, the molecular dynamic (MD) simulation of the peptide-ACE complex with the best binding affinity in the molecular docking studies was carried out for 50 ns. ADME (absorption, distribution, metabolism, and excretion) analysis of Val-Trp dipeptide was performed. In support of the studies carried out, enlightening information about the feasibility of the antihypertensive drug of Val-Trp dipeptide with the help of the ADME profile was presented to the literature.Communicated by Ramaswamy H. Sarma.

Structural, spectroscopic, in silico, in vitro and DNA binding evaluations of tyrosyl-lysyl-threonine

The main objective of the present study is to investigate the molecular structure and DNA binding interaction of the tyrosyl-lysyl-threonine (YKT) tripeptide, which has anticancer, antioxidant and analgesic properties, using various in silico (MD, QM, molecular docking), spectroscopic (UV, FT-IR, FTIR-ATR, Raman, gel electrophoresis) and in vitro (MCF-7 and HeLa cancer cell lines and BEAS-2B cell line) methods. The optimized geometry, vibrational wavenumbers, molecular electrostatic potential (MEP), natural bond orbital (NBO) and HOMO-LUMO (highest occupied molecular orbital- lowest unoccupied molecular orbital) calculations were carried out with Density Functional Theory (DFT) using B3LYP/6-311++G(d,p) basis set to indicate conformational, vibrational and intramolecular charge transfer characteristics. The assignment of all fundamental theoretical vibration wavenumbers was performed using potential energy distribution analysis (PED). DNA is a significant pharmacological target of drugs in several diseases such as cancer. For this reason, molecular docking calculation was used to elucidate the binding and interaction between YKT tripeptide and DNA at the atomic level. Also, the dynamic behaviors of YKT and DNA was examined using MD simulations. Besides, the interaction of YKT with DNA was experimentally examined by UV titration method and agarose gel electrophoresis method. Experimental results showed that YKT was intercalatively and electrostatically bound to CT-DNA (Calf thymus DNA) and cleavage pBR322 DNA in the presence of H₂O₂. The pharmacokinetic profile of YKT was also obtained. Cytotoxic effect of YKT was evaluated on MCF-7, HeLa and BEAS-2B cell lines. Hence, these studies about YKT tripeptide may pave the way for the development of various cancer drugs. Communicated by Ramaswamy H. Sarma.

Theoretical and experimental study of the infrared and Raman spectra of L-lysine acetylation

Acetylation is a common and extremely important protein modification in biology, referring to the covalent attachment of an acetyl group to the amino group. There are two forms of protein acetylation, which are lysine Nε-acetylation and N-terminal Nα-acetylation, respectively. Protein lysine Nε-acetylation is a globally important post-translational modification which plays a critical regulatory role in almost all aspects of cell metabolism. In addition, whether lysine on the N-terminal of protein can undergo Nα-acetylation is still a controversial viewpoint. Carrying out further molecular study of the role of acetylation is also the one of challenges. In order to investigate the protein acetylation more effectively, it is thus necessary to have a thorough and comprehensive understanding of lysine acetylation. In this work, both Raman and infrared (IR) spectra of L-lysine Nε-Ace-Lys, Nα-Ace-Lys, and NαNε-Ace-Lys were explored through both experimental experiment and theoretical computation based on density function theory (DFT). Vibration assignments and geometry structures of three acetylated lysines were therefore obtained for the first time in this work. The IR or Raman spectra of four molecules are very different from each other, which can be easily distinguished from the characteristic bands at 1500-1700 cm^-1 and 3200-3400 cm^-1 regions. Therefore, this work may provide the guide for probing the protein acetylation by Raman and IR spectroscopy.

Development of a Hybrid Biomimetic Enamel-Biocomposite Interface and a Study of Its Molecular Features Using Synchrotron Submicron ATR-FTIR Microspectroscopy and Multivariate Analysis Techniques

Using a biomimetic strategy and bioinspired materials, our work proposed a new technological approach to create a hybrid transitional layer between enamel and dental biocomposite. For this purpose, an amino acid booster conditioner based on a set of polar amino acids (lysine, arginine, hyaluronic acid), calcium alkali, and a modified adhesive based on BisGMA and nanocrystalline carbonate-substituted hydroxyapatite are used during dental enamel restoration. The molecular properties of the hybrid interface formed using the proposed strategy were understood using methods of multivariate statistical analysis of spectral information collected using the technique of synchrotron infrared microspectroscopy. The results obtained indicate the possibility of forming a bonding that mimics the properties of natural tissue with controlled molecular properties in the hybrid layer. The diffusion of the amino acid booster conditioner component, the calcium alkali, and the modified adhesive with nanocrystalline carbonate-substituted hydroxyapatite in the hybrid interface region creates a structure that should stabilize the reconstituted crystalline enamel layer. The developed technology can form the basis for an individualized, personalized approach to dental enamel restorations.

Human Angiotensin I-Converting Enzyme Produced by Different Cells: Classification of the SERS Spectra with Linear Discriminant Analysis

Angiotensin I-converting enzyme (ACE) is a peptidase widely presented in human tissues and biological fluids. ACE is a glycoprotein containing 17 potential N-glycosylation sites which can be glycosylated in different ways due to post-translational modification of the protein in different cells. For the first time, surface-enhanced Raman scattering (SERS) spectra of human ACE from lungs, mainly produced by endothelial cells, ACE from heart, produced by endothelial heart cells and miofibroblasts, and ACE from seminal fluid, produced by epithelial cells, have been compared with full assignment. The ability to separate ACEs’ SERS spectra was demonstrated using the linear discriminant analysis (LDA) method with high accuracy. The intervals in the spectra with maximum contributions of the spectral features were determined and their contribution to the spectrum of each separate ACE was evaluated. Near 25 spectral features forming three intervals were enough for successful separation of the spectra of different ACEs. However, more spectral information could be obtained from analysis of 50 spectral features. Band assignment showed that several features did not correlate with band assignments to amino acids or peptides, which indicated the carbohydrate contribution to the final spectra. Analysis of SERS spectra could be beneficial for the detection of tissue-specific ACEs.

Investigation of the Effect of Nanocrystalline Calcium Carbonate-Substituted Hydroxyapatite and L-Lysine and L-Arginine Surface Interactions on the Molecular Properties of Dental Biomimetic Composites

Differences in the surface interactions of non-stoichiometric nanocrystalline B-type carbonate-substituted hydroxyapatite (n-cHAp) with the amino acids L-Lysine hydrochloride (L-LysHCl) and L-Arginine hydrochloride (L-ArgHCl) in acidic and alkaline media were determined using structural and spectroscopic analysis methods. The obtained data confirm that hydroxyapatite synthesized using our technique, which was used to develop the n-cHAp/L-LysHCl and n-cHAp/L-ArgHCl composites, is nanocrystalline. Studies of molecular composition of the samples by Fourier transform infrared spectroscopy under the change in the charge state of L-Lysine in environments with different alkalinity are consistent with the results of X-ray diffraction analysis, as evidenced by the redistribution of the modes' intensities in the spectra that is correlated with the side chains, i.e., amide and carboxyl groups, of the amino acid. During the formation of a biomimetic composite containing L-Lysine hydrochloride and n-cHAp, the interaction occurred through bonding of the L-Lysine side chain and the hydroxyl groups of hydroxyapatite, which created an anionic form of L-Lysine at pH ≤ 5. In contrast, in biocomposites based on L-Arginine and n-cHAp, the interaction only slightly depends on pH value, and it proceeds by molecular orientation mechanisms. The X-ray diffraction and infrared spectroscopy results confirm that changes in the molecular composition of n-cHAp/L-ArgHCl biomimetic composites are caused by the electrostatic interaction between the L-ArgHCl molecule and the carbonate-substituted calcium hydroxyapatite. In this case, the bond formation was detected by Fourier transform infrared (FTIR) spectroscopy; the vibrational modes attributed to the main carbon chain and the guanidine group of L-Arginine are shifted during the interaction. The discovered interaction mechanisms between nanocrystalline carbonate-substituted hydroxyapatite that has physicochemical properties characteristic of the apatite in human dental enamel and specific amino acids are important for selecting the formation conditions of biomimetic composites and their integration with the natural dental tissue.

Differential Surface Capping Effects on the Applications of Simple Amino-Acid-Capped ZnS:Mn Nanoparticles

Water-dispersible ZnS:Mn nanoparticles (NPs) were prepared by capping their surface with simple structured amino acids: l-alanine (Ala), l-glycine (Gly), and l-valine (Val) molecules, which have very similar structures except for the terminal organic functional groups. The detailed characterization works for the prepared colloidal NPs were performed using various spectroscopic methods. In particular, the NPs commonly showed UV/visible absorption peaks around 325 nm and PL emission peaks around 590 nm, corresponding to the wavelength of orange color light. In this study, these amino-acid-capped NPs were applied as optical photosensors in the detection of specific divalent transition metal cations in the same conditions. Consequently, all three NPs showed exclusive fluorescence quenching effects upon the addition of Cu (II) metal ions, whereas their quenching efficiencies were quite different to each other. These experimental results indicated that the Gly-ZnS:Mn NPs (k = 4.09 × 10⁵ M⁻¹) can be the most effective optical photosensor for the detection of Cu²⁺ ions in water among the three NPs in the same conditions. This study showed that the steric effect of the capping ligand can be one of the key factors affecting the sensor activities of the ZnS:Mn NPs.

High pressure Raman scattering of DL‑isoleucine crystals and DFT calculations

DL‑isoleucine single crystals were grown by the slow evaporation method at ambient temperature. Their vibrational properties were studied at ambient temperature as a function of pressure by Raman scattering. At ambient conditions the mode assignment was done in terms of the Potential Energy Distribution (PED) through density functional theory calculations. Both nitrogen and neon were used as pressure transmitting media. The pressure-dependent investigation shows modifications in the Raman spectra recorded between 30 and 3200 cm^-1 that were interpreted as phase transitions undergone by the crystal between 1.3 and 1.9 GPa and between 3.6 and 5.1 GPa. Finally, stress was simulated on the unit cell of the crystal from ambient up to 5.0 GPa.

Methionine-mediated synthesis of magnetic nanoparticles and functionalization with gold quantum dots for theranostic applications

Biocompatible superparamagnetic iron oxide nanoparticles (NPs) through smart chemical functionalization of their surface with fluorescent species, therapeutic proteins, antibiotics, and aptamers offer remarkable potential for diagnosis and therapy of disease sites at their initial stage of growth. Such NPs can be obtained by the creation of proper linkers between magnetic NP and fluorescent or drug probes. One of these linkers is gold, because it is chemically stable, nontoxic and capable to link various biomolecules. In this study, we present a way for a simple and reliable decoration the surface of magnetic NPs with gold quantum dots (QDs) containing more than 13.5% of Au+. Emphasis is put on the synthesis of magnetic NPs by co-precipitation using the amino acid methionine as NP growth-stabilizing agent capable to later reduce and attach gold species. The surface of these NPs can be further conjugated with targeting and chemotherapy agents, such as cancer stem cell-related antibodies and the anticancer drug doxorubicin, for early detection and improved treatment. In order to verify our findings, high-resolution transmission electron microscopy (HRTEM), atomic force microscopy (AFM), FTIR spectroscopy, inductively coupled plasma mass spectroscopy (ICP-MS), and X-ray photoelectron spectroscopy (XPS) of as-formed CoFe2O4 NPs before and after decoration with gold QDs were applied.