Prediction of GABARAP interaction with the GABA type A receptor

• Published in: Proteins, structure, function, and bioinformatics Vol. 86; no. 12; pp. 1251 - 1264
• Main Authors: Irwin, B.W.J., Vukovič, Siniša, Payne, M.C., ElGamacy, Mohammad, Chau, P.‐L.
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01.12.2018; Wiley Subscription Services, Inc
• Subjects: Adaptor Proteins, Signal Transducing - chemistry; Apoptosis Regulatory Proteins; Binding Sites; Databases, Protein; Docking; free energy change; GABAA receptor; GABARAP; GABARAP protein; Humans; Identification methods; Microtubule-Associated Proteins - chemistry; Molecular Docking Simulation; Protein Conformation; Protein Multimerization; Proteins; Receptors, GABA-A - chemistry; Thermodynamics; GABAA receptor; free energy change; GABARAP
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.25589

We have performed docking simulations on GABARAP interacting with the GABA type A receptor using SwarmDock. We have also used a novel method to study hydration sites on the surface of these two proteins; this method identifies regions around proteins where desolvation is relatively easy, and these are possible locations where proteins can bind each other. There is a high degree of consistency between the predictions of these two methods. Moreover, we have also identified binding sites on GABARAP for other proteins, and listed possible binding sites for as yet unknown proteins on both GABARAP and the GABA type A receptor intracellular domain.