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

Chlamydia trachomatis Serovar Distribution in Patients with Follicular Conjunctivitis in Iran

Objectives:Chlamydia trachomatis infects the urogenital tract and eyes. Anatomical tropism is correlated with serovars which are characterized according to the variation in the major outer membrane proteins encoded by the ompA gene. The aim of the present study was to determine the distribution of C. trachomatis serovars among patients with follicular conjunctivitis in Iran.Materials and Methods:A total of 68 conjunctival specimens from symptomatic adults were studied for the presence of C. trachomatis using polymerase chain reaction (PCR) analysis. Serovars were determined by Omp1 PCR-RFLP analysis.Results:C. trachomatis was detected in 38 (55.9%) of patients with follicular conjunctivitis, with higher C. trachomatis prevalence in the younger age groups. Twenty-six (38.2%) of these patients had a history of urinary tract infection. Four distinct serovars were identified in the conjunctiva samples using molecular genotyping. The most prevalent was serovar E, followed by G, I, and F.Conclusion:Our serovar distribution indicated that chlamydial follicular conjunctivitis usually has a genital source. Genital serovars may cause eye diseases, especially in sexually active adults. On the other hand, conjunctivitis might be the only sign of sexually transmitted infection. Therefore, genotyping C. trachomatis in ocular and genital specimens could be beneficial for acquiring more detailed epidemiological information about the etiology of the disease and monitoring treatment success

Effects of sorbitol and glycerol on the structure, dynamics, and stability of Mycobacterium tuberculosis pyrazinamidase

Objective/background: Mycobacterium tuberculosis pyrazinamidase (PZase) is known an enzyme that is involved in degradation of pyrazinamide to ammonia and pyrazinoic acid. Pyrazinamide is an important first-line drug used in the short-course treatment of tuberculosis. Previous investigations have indicated that the pyrazinamide (PZA)-resistant M. tuberculosis strains are caused by point mutations in the PZase enzyme which is the activator of the prodrug PZA. Although the general fold of PZase was determined, the structural and functional properties of the enzyme in solution were not understood very well. In this study, the PZase enzyme was overexpressed and purified. In addition, two polyols, namely sorbitol and glycerol, were chosen to study their effects on the structure, dynamics, and stability of the enzyme. To gain a deeper insight, molecular dynamics simulation and spectroscopic methods, such as fluorescence spectroscopy and circular dichroism (CD), were used. Methods: The genes were cloned in Escherichia coli BL21 (DE3), harboring the recombinant pET-28a (+) plasmid, overexpressed and purified by Ni-NTA Sepharose. The far UV–visible CD spectra were measured by a Jasco-810 spectropolarimeter. The intrinsic fluorescence spectra were measured on a Cary Varian Eclipse spectrofluorometer. For molecular dynamics (MD) simulations, we have applied GROMACS4.6.5. Results: The results showed that glycerol and sorbitol increased the enzyme activity up to 130% and 110%, respectively, at 37°C. The stability of PZase was decreased and the half-life was 20 min. Glycerol and sorbitol increased the PZase half-life to 99 min and 23 min, respectively. The far UV CD measurements of PZase indicated that the CD spectra in glycerol and sorbitol give rise to an increase in the content of α-helix and β-sheets elements. The average enzyme root mean square deviation (RMSD) in sorbitol solution was about 0.416nm, a value that is higher than the enzyme RMSD in the pure water (0.316). In dictionary of protein secondary structure (DSSP) results, we observed that the secondary structures of the protein are partially increased as compared to the native state in water. The experimental and simulation data clearly indicated that the polyols increased the PZase stabilization in the order: glycerol>sorbitol. Conclusion: It can be concluded that the native conformation of the enzyme was stabilized in the sorbitol and glycerol and tend to exclude from the PZase surface, forcing the enzyme to keep it in the compactly folded conformation. The glycerol molecules stabilized PZase by decreasing the loops flexibility and then compacting the enzyme structure. It appears that more stability of PZase in glycerol solution correlates with its amphiphilic orientation, which decreases the unfavorable interactions of hydrophobic regions

Insight to the molecular mechanisms of the osmolyte effects on Mycobacterium tuberculosis pyrazinamidase stability using experimental studies, molecular dynamics simulations, and free energy calculation

Background: In this study, we have experimentally investigated the effects of different osmolytes including sucrose, sorbitol, urea, and guanidinium chloride (GdmCl) on the stability and structure of the Mycobacterium tuberculosis pyrazinamidase (PZase). PZase converts pyrazinamide to its active form. Methods: In addition, in order to gain molecular insight into the interactions between osmolytes and PZase, we have conducted 1000-ns molecular dynamics simulations. Results: The results indicated that sucrose and sorbitol increase the stability and compactness of the enzyme, whereas in the presence of urea and GdmCl, PZase loses its stability and compactness. Furthermore, the activity of PZase in the presence of sucrose was more than the other solutions. The energetic analyses imply that the electrostatic and van der Waals interactions are the major factors in the osmolyte–PZase interactions. Sorbitol and sucrose, as protective osmolytes, protect the protein structure by utilizing the van der Waals interaction from denaturation. In addition, urea molecules affect the structure of the protein using the hydrogen bonds and van der Waals interactions. Conclusion: The results show that the most important factor in the denaturing effect of GdmCl is the strong interactions of positively charged guanidinium ions with the aspartate and glutamate residues

The electrostatic interactions (kJ/mol) between pardaxin charged residues and the membrane models.

<p>The electrostatic interactions (kJ/mol) between pardaxin charged residues and the membrane models.</p

Mass density analyses.

<p>Density distribution of the membrane components along the membrane normal direction for (A) DMPC, (B) DPPC, (C) POPC, (D) POPG, (E) POPG/POPE (3:1), (F) POPG/POPE (1:3) simulation systems.</p

Order analyses.

<p><b>(A)</b> Ordering of the hydrophobic tails in the pure lipid bilayer (orange) and pardaxin-membrane complex (violet) for (A) DMPC, (B) DPPC, (C) POPC, (D) POPG, (E) POPG/POPE (3:1), (F) POPG/POPE (1:3) bilayers.</p

The average thickness of the membrane models and mean square displacement (MSD) of the lipid molecules.

<p><b>(A), (B), (C), (D), (E), and (F)</b> Represents the average thickness of all membrane models over the last 150 ns of the MD simulations for DMPC, DPPC, POPC, POPG, POPG/POPE (3:1), and POPG/POPE (1:3) bilayers. The average structure of pardaxin during the last 150 ns of MD simulations is shown as cartoon model for each system. <b>(G)</b> Demonstrates MSD of the pure lipid bilayers (filled line) and pardaxin-membrane complex (dashed lines).</p

Represents van der Waals interactions between all residues of pardaxin and the membrane models.

<p>Pardaxin is shown as a cartoon model (upper) and (I), (II), (III), (IV), (V), and (VI) indicate the van der Waals interactions between each pardaxin residue and the lipid bilayers (bar plots) for DMPC, DPPC, POPC, POPG, POPG/POPE (3:1), and POPG/POPE (1:3) systems. (A), (B), and (C) indicate the amino terminal, amphipathic helix, and carboxy terminal regions of pardaxin, respectively. Hydrophobic and hydrophilic residues of pardaxin are colored as teal and cyan in the cartoon model. Each hydrophobic residue side chain of the amphipathic helix is shown in (B) section. The label numbers represent the van der Waals interaction values.</p

Insight into the interactions, residue snorkeling, and membrane disordering potency of a single antimicrobial peptide into different lipid bilayers - Fig 2

<p><b>Represents the torsion angles of pardaxin residues in the (A) DMPC, (B) DPPC, and (C) POPC</b>. Red dashed lines in the left and right columns show -60 and -45 values, respectively.</p