These chains are known to interact with the BDNF/ NT-4/5 protein. The two monomer chain of TrkB-D5 (chains X and Y) are identical. The asymmetric unit of the crystal structure contains a single copy of the TrkB-D5:NT-4/5 complex, comprising one homodimer of NT-4/5 bound to two monomers of TrkB-D5. Crystal structure of the extracellular D5 domain of the TrkB which exhibits binding with the human Neurotrophin-4/5 (NT-4/5) ligand (PDB id: 1HCF) was selected from the protein databank. The primary structure of TrkB receptor and its various domains were examined. Molecular modeling and generation of TrkB binding region
Chemdraw ultra ball and stick model software#
The chemical properties of CTXB was calculated by ACD (Advanced Chemistry Development, Canada) labs Chemsketch software and the data is presented in Table 1. The molecule was further subjected to re-optimization via MOPAC (Molecular Orbital Package) method until the RMS gradient attained a value lesser than 0.0001 kcal/mol Å. Extensive energy minimization was performed using the Austin Model-1 (AM1) programme until the root mean square (RMS) gradient value became smaller than 0. The two dimensional (2D) and three dimensional (3D) structure of the CTXB was built using ChemDraw Ultra 8.0 (Cambridgesoft, Waltham, MA, USA) ( Fig. The primary structure of the peptide is known and in this manuscript we report for the first time the putative three dimensional structure of the peptide ( Fig. Cyclization is important to provide stability to the peptide macromolecule. It is an inhibitor of the TrkB receptor activation and its downstream signalling pathway mediated by BDNF binding,. Selection and preparation of cyclotraxin B, TrkB inhibitorĬyclotraxin B (CTXB) is a cyclic peptide chain of 10 amino acid linked by a disulphide bridge. The molecular model of CTXB has been generated and it’s docking with TrkB domain carried out to determine the critical residues involved in the protein peptide interaction.Ģ.1. This article reports for the first time binding mechanism and interaction parameters of CTXB with the TrkB receptor. Cyclotraxin B (CTXB) is a disulphide bridge linked cyclic peptide molecule that interacts with TrkB receptor and inhibits the BDNF/TrkB downstream signalling. The data presented here is related to the research article entitled “Brain Derived neurotrophic factor is involved in the regulation of glycogen synthase kinase 3β (GSK3β) signalling”. Identification of various activators and inhibitors of the TrkB receptor and greater understanding their binding mechanisms is critical to elucidate the biochemical and pharmacological pathways and analyse various protein crystallization studies. TrkB is a high affinity receptor for the brain derived neurotrophic factor (BDNF) and its phosphorylation stimulates activation of several intracellular signalling pathways linked to cellular growth, differentiation and maintenance.