Molecular modeling and docking characterization of Dectin-1 (PAMP) receptor of Bubalus bubalis.
Dectin-1, is a type II transmembrane receptor protein which contains a single extracellular CTLD (C-type lectin domain), stalk, transmembrane domain and an ITAM (immunoreceptor tyrosine-based activation motifs) in its cytoplasmic tail. Dectin-1 has the ability to recognize fungal β-glucans, which are carbohydrate PAMPs found predominantly in fungal cell walls. The recognition of fungal β-glucans by Dectin-1 helps in a variety of cellular responses, like host protection, such as fungal uptake and killing, and the production of inflammatory cytokines and chemokines. In this study we predicted the 3D (three dimensional) structure of Dectin-1 receptor based on homology modeling using MODELLER 9v8 software. The TMHMM server was used for the prediction of transmembrane helices. DALI, PROFUNC, Q-Site Finder, PINTS servers and PASS software used for the prediction of functional sites in the modeled Dectin-1 receptor. The docking investigation of Dectin-1 receptor with β-glucan suggests that ASP150, ASP113, GLY106, and GLU196 amino acids are the catalytic residues which form a shallow groove in the protein surface and bind to ligand β-glucan. We hope that this work will help in in-silico screening, structure-based design, and in understanding the structural basis of ligand binding to the Dectin-1 receptor.
Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar 243122, India. brijeshbioinfo@gmail.com
Brijesh S
BS
Yadav
Vijay
V
Tripathi
Ajeet
A
Kumar
Md Faheem
MF
Khan
Abhijit
A
Barate
Ajay
A
Kumar
Bhaskar
B
Sharma
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002020:Buffaloes / Q000378:metabolism*; D002473:Cell Wall / Q000378:metabolism; D005658:Fungi / Q000378:metabolism*; D037181:Lectins, C-Type / Q000737:chemistry / Q000378:metabolism*; D008024:Ligands; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D047071:beta-Glucans / Q000737:chemistry / Q000378:metabolism*; D000099181:Dectin-1
D037181:Lectins, C-Type; D008024:Ligands; D008565:Membrane Proteins; D047071:beta-Glucans; D000099181:Dectin-1