Immunogenic decapeptide in melanoma immunotherapy.

Melanoma is a cancer associated with melanocytes of epidermis. There has been a consistent increase in the number of melanoma patients because of the depletion of the ozone layer which makes it of paramount importance to explore the immunogenic potential of various peptides in melanoma therapy. In the current study, a mutated decapeptide (ELAGIGILTV) epitope ID 12941 was taken from the melanoma antigen recognized by T-cells. This epitope displayed relatively better affinity for histocompatibility leukocyte antigen influencing the proliferation of cytotoxic T-cells. Immunogenicity of the oligopeptide can be further intensified by its simultaneous binding to the programmed death receptor of the T lymphocytes. We have used the molecular dynamics (MD) simulation approach to reveal the dynamics of the decapeptide and its consequences to immunogenic effects. The dynamics have ensembled various conformations of the peptide which have been clustered in their representative conformers. During the dynamics, the peptide was found to fold to its conformation with a minimum free energy. Moreover, multiple analysis of the MD trajectory has provided many physiochemical features involved in the biological activity to improve the immunogenicity of this antigenic peptide. The manuscript concludes by proposing this decapeptide as a potential vaccine for the melanoma cancer.

Brevibacillus borstelensis and Streptomyces albogriseolus have roles to play in degradation of herbicide, sulfosulfuron.

Use of herbicides, in particular sulfosulfuron, at more than recommended doses has raised major concerns about the health hazards for animals and humans. In the present study, isolation of sulfosulfuron-degrading Brevibacillus borstelensis and Streptomyces albogriseolus from the field soils in the northwestern region of India was carried out where the use of sulfosulfuron is predominant, and further assessed for their potential to degrade sulfosulfuron individually and together in a consortium form under lab conditions. Concentration of sulfosulfuron was reduced from 10 to 7.72 µg/ml in 12 h to 5.13 µg/ml in 20 h by B. borstelensis and the metabolites detected by LCMS-MS were aminopyrimidine and a rearranged amine in 12 and 20 h of growth. Similarly, S. albogriseolus reduced the concentration of sulfosulfuron from 10 to 6.74 µg/ml in 12 h to 6.62 µg/ml in 20 h with aminopyrimidine and a rearranged amine as metabolites. B. borstelensis and S. albogriseolus together also reduced the concentration of sulfosulfuron from 10 µg/ml in initial hour to 8.34 µg/ml in 12 h to 6.66 µg/ml in 20 h. Hence, B. borstelensis and S. albogriseolus provide a safer, inexpensive and effective way to bio-remediate the harmful and toxic sulfosulfuron from the environment if further explored at a larger field scale in near future.

Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations.

In this study, interactions of selected monosaccharides with the Pseudomonas aeruginosa Lectin II (PA-IIL) are analyzed in detail. An interesting feature of the PA-IIL binding is that the monosaccharide is interacting via two calcium ions and the binding is unusually strong for protein-saccharide interaction. We have used Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) and normal mode analysis to calculate the free energy of binding. The impact of intramolecular hydrogen bond network for the lectin/monosaccharide interaction is also analyzed.

Importance of oligomerisation on Pseudomonas aeruginosaLectin-II binding affinity. In silico and in vitro mutagenesis.

The effect of terminal GLY114* deletion on the binding affinity of the PA-IIL lectin toward L: -fucose was investigated. Both experimental (isothermal titration calorimetry) and computational (molecular dynamics simulations) methods have shown that the deletion mutation decreases the L-fucose affinity. It implies that the PA-IIL saccharide binding affinity is influenced by the dimerization of the lectin. A detailed analysis of computational data confirms the key role of electrostatic interactions in the PA-IIL/saccharide binding.

Molecular dynamics study of Pseudomonas aeruginosa lectin-II complexed with monosaccharides.

We present the results of a series of 10-ns molecular dynamics simulations on Pseudomonas aeruginosa lectin-II (PA-IIL) and its complexes with four different monosaccharides. We compare the saccharide-free, saccharide-occupied, and saccharide- and ion-free forms of the lectin. The results are coupled with analysis of the water density map and calcium coordination. The water density pattern around the binding site in the free lectin molecular dynamics was fitted with that in the X-ray and with the hydroxyl groups of the monosaccharide within the lectin/monosaccharide complexes and the best ligand was predicted based on the best fit. Interestingly, the water density pattern around the binding site in the uncomplexed lectin exactly fitted the O2, O3, and O4 hydroxyl groups of the fucose complex with the lectin. This observation could lead to a hypothesis that the replacement of these three water molecules from the binding site by the monosaccharide decreases the entropy of the complex and increases the entropy of the water molecules, which favors the binding. It suggests that the high density peaks of the solvent around the binding site in the free protein could be the tool to predict hydroxyl group orientation of the sugar in the protein/sugar complexes. The high affinity of PA-IIL binding site is also attributed to the presence of two calcium ions, each of them making five to six coordinations with the protein part and two coordinations with either water or the monosaccharide. When the calcium ions are removed from the simulated system, they are replaced by sodium ions from the solvent. These observations rationalize the high binding affinity of PA-IIL towards fucose.