Elucidating the molecular interaction of Zebrafish (Danio rerio) peptidoglycan recognition protein 2 with diaminopimelic acid and lysine type peptidoglycans using in silico approaches

Abstract

Peptidoglycan recognition proteins (PGRPs) belong to the family of pattern recognition receptor, represent the major constituent of innate immunity. Although PGRPs are structurally conserved through evolution, their involvement in innate immunity is different in vertebrates and invertebrates. They are highly specific towards recognition of ligands and can hydrolyze bacterial peptidoglycans (PGNs). Zebrafish PGRPs (zPGRPs) have both peptidoglycans lytic amidase activity and broad-spectrum bactericidal activity, but far less is known about how these receptors recognize these microbial ligands. Such studies are hindered due to lack of structural and functional configuration of zPGRPs. Therefore, in this study, we predicted the three-dimensional structure of zPGRP2 through theoretical modeling, investigated the conformational and dynamic properties through molecular dynamics simulations. Molecular docking study revealed the microbial ligands, that is, muramyl pentapeptide–DAP , muramyl pentapeptide–LYS, muramyl tripeptide–DAP, muramyl tripeptide–Lys, muramyl tetrapeptide–DAP, muramyl tetrapeptide–LYS and tracheal cytotoxin interacts with the conserved amino acids of the ligand recognition site comprised of β1, α2, α4, β4 and loops connecting β1 ? α2, α2 ? β2, β3 ? β4 and α4 ? α5. Conserved His31, His32, Ala34, Ile35, Pro36, Lys38, Asp60, Trp61, Trp63, Ala89, His90, Asp106, His143 and Arg144 are predicted to essential for binding and provides stability to these zPGRP–PGN complexes. Our study provides basic molecular information for further research on the immune mechanisms of PGRP’s in Zebrafish. The plasticity of the zPGRP’s binding site revealed by these microbial ligands suggests an intrinsic capacity of the innate immune system to rapidly evolve specificities to meet new microbial challenges in the future.

Communicated by Ramaswamy H. Sarma     

Computational Analysis of “-omics” Data to Identify Transcription Factors Regulating Secondary Metabolism in Rauvolfia serpentina

Plant Molecular Biology Reporter - Rauvolfia serpentina has been known to produce therapeutically important indole alkaloids used in treatment of various diseases. Despite its medicinal importance,...     

Effects of dextrose, verapamil and magnesium during hypoxia in myocardial tissue

We studied the effects of superfusion of canine heart muscle tissue with a solution that mimicks hypoxia, acidosis and hyperkalemia (altered Tyrode's solution). Contracture (rise in resting tension) develops much sooner (5.2 +/- 0.8 vs. 30-40 min in 5 mM dextrose) in the absence of dextrose. High dextrose (55 mM) stabilizes the rise in tonic tension and protects against the action potential shortening during such superfusion. Presence of verapamil (1-1.5 microM) during altered Tyrode's superfusion considerably lessens the magnitude of the increase in tonic tension (31.7 +/- 8.6 vs. 129.5 +/- 32.6 mg in the control). Presence of high magnesium (5 mM) during altered Tyrode's superfusion also offers some protection against tonic tension increase (12.6 +/- 3.6 mg rise in tonic tension vs. 129.5 +/- 3.2 mg in the control), action potential shortening, and amplitude decrease. These results suggest that (a) magnesium and verapamil both have significant effects on the cellular calcium uptake, and (b) anaerobic metabolism utilizing either glycogen or exogenous glucose is capable of preventing contracture during ischemia.