title: Exploration of the binding modes of buffalo PGRP1 receptor complexed with meso-diaminopimelic acid and lysine-type peptidoglycans by molecular dynamics simulation and free energy calculation.
abstract: The peptidoglycan recognition proteins (PGRPs) are the key components of innate-immunity, and are highly specific for the recognition of bacterial peptidoglycans (PGN). Among different mammalian PGRPs, the PGRP1 binds to murein PGN of Gram-positive bacteria (lysine-type) and also have bactericidal activity towards Gram-negative bacteria (diaminopimelic acid or Dap-type). Buffaloes are the major sources of milk and meat in Asian sub-continents and are highly exposed to bacterial infections. The PGRP activates the innate-immune signaling, but their studies has been confined to limited species due to lack of structural and functional information. So, to understand the structural constituents, 3D model of buffalo PGRP1 (bfPGRP1) was constructed and conformational and dynamics properties of bfPGRP1 was studied. The bfPGRP1 model highly resembled human and camel PGRP structure, and shared a highly flexible N-terminus and centrally placed L-shaped cleft. Docking simulation of muramyl-tripeptide, tetrapeptide, pentapeptide-Dap-(MTP-Dap, MTrP-Dap and MPP-Dap) and lysine-type (MTP-Lys, MTrP-Lys and MPP-Lys) in AutoDock 4.2 and ArgusLab 4.0.1 anticipated β1, α2, α4, β4, and loops connecting β1-α2, α2-β2, β3-β4 and α4-α5 as the key interacting domains. The bfPGRP1-ligand complex molecular dynamics simulation followed by free binding energy (BE) computation conceded BE values of -18.30, -35.53, -41.80, -25.03, -24.62 and -22.30 kJ mol(-1) for MTP-Dap, MTrP-Dap, MPP-Dap, MTP-Lys, MTrP-Lys and MPP-Lys, respectively. The groove-surface and key binding residues involved in PGN-Dap and Lys-type interaction intended by the molecular docking, and were also accompanied by significant BE values directed their importance in pharmacogenomics, and warrants further in vivo studies for drug targeting and immune signaling pathways exploration.
authors.affiliation: Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India; Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, Osaka Prefecture 5650871, Japan. Electronic address: bikash.bioinformatics@gmail.com.
authors.forename: Bikash Ranjan
authors.initials: BR
authors.lastname: Sahoo
authors.affiliation: Immunology Frontier Research Centre, Osaka University, Osaka Prefecture 5650871, Japan. Electronic address: prvndubey@ifrec.osaka-u.ac.jp.
authors.forename: Praveen Kumar
authors.initials: PK
authors.lastname: Dubey
authors.affiliation: RIKEN Center for Life Science Technologies, Yokohama 2300045, Japan.
authors.forename: Shubham
authors.initials: S
authors.lastname: Goyal
authors.affiliation: Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India.
authors.forename: Gopal Krushna
authors.initials: GK
authors.lastname: Bhoi
authors.affiliation: Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India.
authors.forename: Santosh Kumar
authors.initials: SK
authors.lastname: Lenka
authors.affiliation: Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India; Biotechnology Laboratory, Central Inland Fisheries Research Institute, Kolkata, West Bengal 700120, India.
authors.forename: Jitendra
authors.initials: J
authors.lastname: Maharana
authors.affiliation: Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751001, India.
authors.forename: Sukanta Kumar
authors.initials: SK
authors.lastname: Pradhan
authors.affiliation: Division of Animal Biotechnology, National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
authors.forename: Ranjit Singh
authors.initials: RS
authors.lastname: Kataria
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002020:Buffaloes; D002162:Camelus; D002352:Carrier Proteins / Q000737:chemistry / Q000378:metabolism*; D003960:Diaminopimelic Acid / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D008239:Lysine / Q000737:chemistry; D051379:Mice; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D010457:Peptidoglycan / Q000737:chemistry / Q000378:metabolism*; D025341:Principal Component Analysis; D011485:Protein Binding; D016415:Sequence Alignment
chemical_list: D002352:Carrier Proteins; D010457:Peptidoglycan; C118897:peptidoglycan recognition protein; D003960:Diaminopimelic Acid; D008239:Lysine
keywords: Buffalo; Innate immunity; MM/PBSA; Molecular dynamics; PGRP