Structure and dynamics of inactive and active MARK4: conformational switching through the activation process

Abstract

Microtubule affinity-regulating kinase 4 (MARK4) is a serine/threonine protein kinase belonging to a highly-conserved group of PAR proteins that phosphorylate microtubule-associated proteins (tau, MAP2 and MAP4) and regulate cell polarity. MARK4 isoform is mainly found in brain tissue, causing microtubule destabilization in neuronal cells and also tau-protein phosphorylation seen in Alzheimer’s disease. In this study, the dynamic behavior of inactive and active structures of human MARK4 was studied by modeling and molecular dynamics simulations and motions of the protein through activation process were interpolated. Structure and dynamics of the protein active state in presence of Mg-ATP were also studied. The results suggest for occlusion of ATP binding site by activation loop, as the main inactivation mechanism. Data also justify the necessity of UBA (ubiquitin-associated) domain auto-inhibitory role. Within the inactive and active state, G-loop is highly fluctuating and assumes an open conformation and away from Mg-ATP complex. This behavior raises the assumption that this loop may experience other stabilizing interactions with residues out of the kinase core which help its stabilization during the phospho-transfer reaction. Mg-ATP complex localization is well preserved within the catalytic cleft through the electrostatic interactions. However, minor rearrangements of water molecules around this complex are allowed, which may further refine the delicate position of this complex for phospho-transfer reaction.Communicated by Ramaswamy H. Sarma