Elucidating the Molecular interaction of Zebrafish (<i>Danio rerio</i>) Peptidoglycan recognition protein 2 with Diaminopimelic acid and Lysine type Peptidoglycans using <i>in-silico</i> Approaches
Creators: name: Ajaya Kumar Rout
name: Paramanik, Sunanda
name: Budheswar Dehury
name: Acharya, Varsha
name: Himanshu Sekhar Swain
name: Sukanta Kumar Pradhan
name: Behera, Bhaskar
name: Pati, Soumen Kumar
name: Bijay Kumar Behera
name: Basanta Kumar Das
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: FOS: Computer and information sciences
subject: Inorganic Chemistry
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences

description: Peptidoglycan recognition proteins (PGRPs) are the important members of pattern recognition receptors (PRRs) family and represents major constituent of innate immunity. Although PGRPs are structurally conserved through evolution; their involvement in innate immunity are different in vertebrates and invertebrates. They are highly specific for the recognition and in some cases, 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 zPGRP. Therefore to fill the research gap, we inferred the three-dimensional architecture of the zPGRP2 through theoretical modeling and investigated the conformational and dynamic properties through molecular dynamics simulations. Docking information of microbial ligands i<i>.e.,</i> muramyl pentapeptide-DAP (MPP-Dap), muramyl pentapeptide-LYS (MPP-Lys), muramyl tripeptide-DAP (MTP-Dap), muramyl tripeptide-Lys (MTP-Lys), muramyl tetrapeptide-DAP (MTr-Dap), muramyl tetrapeptide-LYS (MTr-Lys) and tracheal cytotoxin (TCT) in Autodock Vina revealed β1, α2, α4, β4, and loops connecting β1 − α2, α2 − β2, β3 − β4, and α4 − α5 as the key interacting domains participate in ligand recognition. Several conserved amino acids <i>i.e.,</i> 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.