title: Understanding the molecular basis of substrate binding specificity of PTB domains.
abstract: Protein-protein interactions mediated by phosphotyrosine binding (PTB) domains play a crucial role in various cellular processes. In order to understand the structural basis of substrate recognition by PTB domains, multiple explicit solvent atomistic simulations of 100ns duration have been carried out on 6 PTB-peptide complexes with known binding affinities. MM/PBSA binding energy values calculated from these MD trajectories and residue based statistical pair potential score show good correlation with the experimental dissociation constants. Our analysis also shows that the modeled structures of PTB domains can be used to develop less compute intensive residue level statistical pair potential based approaches for predicting interaction partners of PTB domains.
authors.affiliation: Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India.
authors.forename: Neetu
authors.initials: N
authors.lastname: Sain
authors.affiliation: Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India.
authors.forename: Garima
authors.initials: G
authors.lastname: Tiwari
authors.affiliation: Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India.
authors.forename: Debasisa
authors.initials: D
authors.lastname: Mohanty
mesh_terms: D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D019000:Phosphotyrosine / Q000378:metabolism*; D011485:Protein Binding; D000072417:Protein Domains; D013379:Substrate Specificity
chemical_list: D019000:Phosphotyrosine