Charge calculations in molecular mechanics. Part 8. Partial atomic charges from classical calculations

The adenine-modified edible chitosan films containing choline chloride and citric acid mixture

A series of biopolymeric chitosan-based (Ch) films were prepared with choline chloride and citric acid plasticizer (deep eutectic solvent, DES). An effect of adenine (A, vitamin B4) addition on the functional properties of these films was evaluated. Several physicochemical and mechanical properties were tested: Fourier-transformed infrared spectra proved DES's plasticizing and crosslinking effect, while scanning electron microscopy and atomic force microscopy techniques confirmed the possible phase separation after adenine addition. These changes affected the mechanical characteristics and the water vapor and oxygen permeability. The prepared materials are not water soluble because the CA acts as a crosslinker. The adenine addition on antioxidative and antimicrobial properties was also checked. It was found that Ch-DES materials with A exhibit improved antioxidative properties (55.8-66.1% of H2O2 scavenging activity) in contrast to the pristine chitosan-DES material (51.1% of H2O2 scavenging activity), while the material is still non-mutagenic (lack of growth of Salmonella typhimurium) and possesses antimicrobial features (no E. coli observed for all the tested films and inhibition zones noted for S. aureus). The mentioned properties, reduced oxygen transmission (1.6-2.1 g m-2 h-1), and mechanical characteristics within the range of typical food packaging plastics proved the potential of Ch-DES-A films in the packaging sector. Moreover, the antioxidative properties, usage of substrates being allowed as food additives, and the presence of adenine create the advantage of the Ch-DES-A materials as edible coatings, being also a source of Vitamin B4.

Computation of nitroxide-nitroxide distances in spin-labeled DNA duplexes

Nanometer distances in nucleic acids can be measured by EPR using two 1-oxyl-2,2,5,5-tetramethylpyrroline radicals, with each label attached via a methylene group to a phosphorothioate-substituted backbone position as one of two phosphorothioate diastereomers (R(P) and S(P)). Correlating the internitroxide distance to the geometry of the parent molecule requires computational analysis of the label conformers. Here, we report sixteen 4-ns MD simulations on a DNA duplex d(CTACTGCTTTAG) .d(CTAAAGCAGTAG) with label pairs at C7/C19, T5/A17, and T2/T14, respectively. For each labeled duplex, four simulations were performed with S(P)/S(P), R(P)/R(P), S(P)/R(P), and R(P)/S(P) labels, with initial all trans label conformations. Another set of four simulations was performed for the 7/19-labeled duplex using a different label starting conformation. The average internitroxide distance r(MD) was within 0.2 A for the two sets of simulations for the 7/19-labeled duplex, indicating sufficient sampling of conformational space. For all three labeled duplexes studied, r(MD) agreed with experimental values, as well as with average distances obtained from an efficient conformer search algorithm (NASNOX). The simulations also showed that the labels have conformational preferences determined by the linker chemistry and label-DNA interactions. These results establish computational algorithms that allow use of the 1-oxyl-2,2,5,5-tetramethylpyrroline label for mapping global structures of nucleic acids.

The use of molecular electrostatic potentials as hydrogen-bonding-donor parameters for QSAR studies

Hydrogen bonding is an important interaction, which controls solubility, partitioning and transport of drugs and is an important force in drug-receptor interactions. Unfortunately it is difficult to quantify, and so inclusion of hydrogen bonding descriptors into quantitative structure-activity relationships (QSARs) is often restricted to indicator variables. The prime objective of this work was to devise readily accessible hydrogen bonding descriptors by means of theoretical chemistry to use in QSAR studies. Because of the dominantly electrostatic nature of this bond, molecular-electrostatic potential was considered and the highest electrostatic potential on the solvent accessible surface (ESP+) was used as the hydrogen-bonding-donor ability of the molecule. The ability of this descriptor to predict the measured hydrogen bonding parameter of sigmalphaH2 was compared with that of the empirically derived atomic charges. The efficiency of ESP+ in a QSAR was also examined. The results suggested that ESP+ was superior to the atomic charge descriptor and that the use of this parameter as the hydrogen bonding parameter in QSAR studies was successful.

The effect of structural QSAR parameters on skin penetration

The permeability coefficients (log kp) of solutes through stratum corneum have been previously related to the octanol-water partition coefficients (log Poct) and solvatochromic parameters. In this study, permeation coefficient data are related to the theoretical chemistry-derived structural parameters and also molecular connectivity and molecular shape indices. The results show that these parameters are comparable with the solvatochromic parameters in correlation with log kp. Log Poct can be corrected by the theoretical parameters to explain permeation coefficients and the equilibrium distribution of compounds between the stratum corneum and water (log Km). Diffusion estimated from the expression log(D/h)=log kp-log Km, where D is the diffusion coefficient and h is the path length for diffusion was also analyzed successfully by the structural parameters.

Effects of glycosylation on fragments of tumour associated human epithelial mucin MUC1

The glycodecapeptide AcPAPGS(alpha GalNAc)T(alpha GalNAc)APPA and the C-terminal glycohexapeptide AcS(alpha GalNAc)T(alpha GalNAc)APPA have been synthesized by applying the N-terminal Fmoc group in combination with the heptyl ester cleavable by lipase-catalyzed hydrolysis at pH 7. The solution conformation of these MUC1-related synthetic glycopeptides and the control, non-glycosylated decapeptide AcPAPGSTAPPA have been investigated using NMR spectroscopy. The structural studies indicate that the glycohexapeptide has a folded structure in solution. For this molecule, unrestrained molecular dynamics has been used to confirm the presence of the observed solution through-space connections. The results indicate that the non-globular nature of MUC1 is due to both protein core sequence and the effect of carbohydrate.

Correlation functions as a tool for protein modeling and structure analysis

Proteins present unique folding structures whose conformations are determined primarily by their amino acid sequences. At present, there is no algorithm that would correlate the sequences with the structures determined by X-ray analysis or NMR. Comparative modeling of a new protein sequence based on the known structure of a functionally related protein promises to yield model structures that may provide relevant properties of the protein. To analyze the quality of a model structure, a set of correlation functions was derived from calculations on a subset of proteins from the structure database. Twenty-three highly resolved protein structures with resolutions of at least 1.7 A from various protein families were used as the primary database. The purpose of this initial work was to find highly sensitive functions (including statistical error limits for the parameters) that describe properties of "real" proteins. Each correlation described is characterized by the correlation coefficient, the parameters for linear or nonlinear regression (coefficients of the equation), standard deviation and variance, and the confidence limits describing the statistical probability for values to occur within these limits, e.g., the natural variability of the property under examination. In addition, a method was developed for creating reasonably misfolded proteins. The ability of a correlation function to discriminate between the native structure and the misfolded conformations is expressed by the reliability index, which indicates the sensitivity of a correlation function. The term correlation functions thus summarizes a variety of efforts to find a mathematical description for the properties of protein structures, for their correlation, and for their significance.

Structural and computational investigations of the conformation of antigenic peptide fragments of human polymorphic epithelial mucin

Human polymorphic epithelial mucins (PEM) are complex glycoproteins that are associated with breast and ovarian carcinomas. The PEM core protein consists of variable numbers of a tandem repeat sequence which contains a short antigenic hydrophilic region (Pro1-Asp-Thr-Arg-Pro-Ala-Pro7). High-field n.m.r. studies undertaken on antigenic 20- and 11-amino acid fragments of the PEM core protein in dimethyl sulphoxide have identified a type-I beta-turn to be present in the region Pro1-Asp-Thr-Arg4. This region includes and overlaps the identified type-I (Asp2-Thr-Arg4) and type-II (Arg4-Pro-Ala6) epitopes of anti-PEM monoclonal antibodies. The studies indicate that the beta-turn is stabilized by the presence of a salt-bridge interaction between Asp-2 and Arg-4. In order to probe the conformations accessible to the PEM peptides a computational study was undertaken independently on the peptide Pro-Asp-Thr-Arg-Pro using a modified Metropolis Monte Carlo algorithm. This study identified the n.m.r.-observed salt-bridge type-I beta-turn as the major low-energy conformer. These results suggest that this structural motif may be involved in the immune recognition of PEM.