Allosteric regulation of the inactive to active state conformational transition in CDPK1 protein of Plasmodium falciparum

Abstract

The aim of the current study is to investigate the role of the CAD domain in the activation mechanism of calcium dependent protein kinase-1 of Plasmodium falciparum (PfCDPK1) and explore the possibility of allosteric inhibition of this kinase. PfCDPK1 belongs to CDPK family of apicomplexan kinases which have a C-terminal CAD domain. Microsecond scale MD simulations were performed on modeled structures of complete PfCDPK1 and its kinase domain alone. The simulations revealed that in absence of CAD the salt bridge between Glu116 in αC-helix and Lys85 in β3-sheet of kinase breaks after 200 ns resulting in inactive conformation of the kinase, but the salt bridge stays intact in the complete protein stabilizing it in active conformation. These results highlight the novel CAD mediated allosteric stabilization of the crucial salt bridge which is a hallmark of active conformation of kinase domains. The mechanistic details of the allosteric activation revealed by our study, opens up the possibility for design of allosteric inhibitors of PfCDPK1 kinase by disrupting the kinase:CAD interactions. Using a combination of machine learning and structure-based in silico screening, we have identified novel PPI modulators for allosteric inactivation of PfCDPK1 kinase.