Antimicrobial Peptides (AMPs)

Antimicrobial peptides (AMPs) are extensive group of molecules that produced by variety tissues of invertebrate, plants, and animal species which play an important role in their immunity response. AMPs have different classifications such as; biosynthetic machines, biological sources, biological functions, molecular properties, covalent bonding patterns, three dimensional structures, and molecular targets.These molecules have multidimensional properties including antimicrobial activity, antiviral activity, antifungal activity, anti-parasite activity, biofilm control, antitumor activity, mitogens activity and linking innate to adaptive immunity that making them promising agents for therapeutic drugs. In spite of this advantage of AMPs, their clinical developments have some limitation for commercial development. But some of AMPs are under clinical trials for the therapeutic purpose such as diabetic foot ulcers, different bacterial infections and tissue damage. In this review, we emphasized on the source, structure, multidimensional properties, limitation and therapeutic applications of various antimicrobial peptides

Investigation the UV Effect on Uranium Bioleaching Process in Acidithiobacillus sp FJ2 ‎and its Possible Consequences on the CoxB Gene Sequence ‎

Introduction: The increasing use of uranium as a suitable source of energy in various industries has led to the depletion of high-grade uranium mines in different countries. Today, the uranium bioleaching process has been used in different countries for easy and cheap access to uranium. In this process, microorganisms are used to extract uranium from low-grade mines. Materials and methods: The Acidithiobacillus sp. FJ2 bacterium was exposed to UV radiation. Then, the uranium bioleaching process was conducted in the presence of bacteria exposed to UV and non-exposed bacteria. In followings, this gene was amplified by PCR technique after DNA extraction from bacterial species and coxB gene primer design. Subsequent to gene sequencing and editing with bioedit software, the final sequence of the coxB gene was determined from both bacterial species. Later than, the sequences were examined and compared to prove the presence or absence of the mutation in the radiation sample. Results: The amount of uranium extraction in the presence of bacteria exposed to UV reached to 100% on the second day at the 5% pulp density, whereas the 96.36% extraction yield was obtained on the thirteenth day in pulp density of 50%. This amount was recorded in an unexposed bacterium, in the third and thirteenth days at 5& 50% pulp densities, respectively. The coxB gene sequence was identical in both bacterial specimens. Discussion and conclusion: In this study, UV irradiation to Acidithiobacillus sp. FJ2 increased the rate of uranium bioleaching in the pulp density of 5%, whereas uranium extraction yield was sustained in the 50% pulp density. These effects were independent to the coxB gene

Molecular Insight into Human Lysozyme and Its Ability to Form Amyloid Fibrils in High Concentrations of Sodium Dodecyl Sulfate: A View from Molecular Dynamics Simulations.

Changes in the tertiary structure of proteins and the resultant fibrillary aggregation could result in fatal heredity diseases, such as lysozyme systemic amyloidosis. Human lysozyme is a globular protein with antimicrobial properties with tendencies to fibrillate and hence is known as a fibril-forming protein. Therefore, its behavior under different ambient conditions is of great importance. In this study, we conducted two 500000 ps molecular dynamics (MD) simulations of human lysozyme in sodium dodecyl sulfate (SDS) at two ambient temperatures. To achieve comparative results, we also performed two 500000 ps human lysozyme MD simulations in pure water as controls. The aim of this study was to provide further molecular insight into all interactions in the lysozyme-SDS complexes and to provide a perspective on the ability of human lysozyme to form amyloid fibrils in the presence of SDS surfactant molecules. SDS, which is an anionic detergent, contains a hydrophobic tail with 12 carbon atoms and a negatively charged head group. The SDS surfactant is known to be a stabilizer for helical structures above the critical micelle concentration (CMC) [1]. During the 500000 ps MD simulations, the helical structures were maintained by the SDS surfactant above its CMC at 300 K, while at 370 K, human lysozyme lost most of its helices and gained β-sheets. Therefore, we suggest that future studies investigate the β-amyloid formation of human lysozyme at SDS concentrations above the CMC and at high temperatures

The contribution energy per residue in the total binding free energies 2.

<p>(a), (b), and (c) represent the polar, non-polar, and total contributions of free energy of per residue, respectively to the binding free energy at 370 K. Left, hydrophilic residues; right hydrophobic residues of human lysozyme. The critical residues for the formation of the human lysozyme-SDS complex (residues with ΔG_b < -10 Kj/mol (< -2.4 Kcal/mol)) are labeled and shown with blue bars. The contribution of free energy for Lys-1 in a and c is not shown because of its high values ΔG_pb < 201.05 Kj/mol and ΔG_b < 72.17 Kj/mol.</p

Orientation of SDS surfactants around human lysozyme.

<p>(a) and (b) show the first and the last frames of the trajectory in two ambient conditions (aqueous SDS solution at 300 K (upper) and 370 K (lower)).</p

The structures of human lysozyme and sodium dodecyl sulfate.

<p>(a) The native structure of human lysozyme represented as a new cartoon model. The α- helix structures are shown with the letter H and C6-C128, C30-C116, C65-C81, and C77-C95 represent disulfide bounds in the human lysozyme structure. (b) The structure of an SDS surfactant molecule with its polar head group (in red and green) and hydrophobic tail (in cyan and yellow) is shown as a ball and stick model.</p

Summary of MD simulations with details ^a.

<p>Summary of MD simulations with details <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165213#t001fn001" target="_blank">^a</a>.</p

The Cα RMSD and the radius of gyration of human lysozyme.

<p>(a) and (b) represent the time evolution of the Cα RMSD and the radius of gyration of human lysozyme in pure liquid water and aqueous SDS solution at 300 K and 370 K, respectively. (c) represents the RMSF of Cα atoms as a function of residue number.</p

The critical residues for the absorption of SDS on lysozyme, based on their total binding free energy contributions (residues with ΔG < -10 Kj/mol (< -2.4 Kcal/mol)) ^a.

<p>The critical residues for the absorption of SDS on lysozyme, based on their total binding free energy contributions (residues with ΔG < -10 Kj/mol (< -2.4 Kcal/mol)) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165213#t003fn001" target="_blank">^a</a>.</p