Allosteric Response of DNA Recognition Helices of Catabolite Activator Protein to cAMP and DNA Binding

Abstract

The homodimeric catabolite activator protein (CAP) regulates the transcription of several bacterial genes based on the cellular concentration of cyclic adenosine monophosphate (cAMP). The binding of cAMP to CAP triggers allosteric communication between the cAMP binding domains (CBD) and DNA binding domains (DBD) of CAP, which entails repositioning of DNA recognition helices (F-helices) in the DBD to dock favorably to the target DNA. Despite considerable progress, much remains to be understood about the mechanistic details of DNA recognition by CAP and about the map of allosteric pathways involved in CAP-mediated gene transcription. The present study uses molecular dynamics and umbrella sampling simulations to investigate the mechanism of cAMP-and DNAinduced changes in the conformation and energetics of F-helices observed during the allosteric regulation of CAP by cAMP and the subsequent binding to the DNA promoter region. Using novel collective variables, the free energy profiles associated with the orientation and dynamics of F-helices in the unliganded, cAMP-bound, and cAMP-DNA-bound states of CAP are calculated and compared. The binding-induced alterations in the resultant free energy profiles reveal important flexibility constraints imposed on DBD upon cAMP and DNA binding. A comprehensive analysis of residue-wise interaction maps reveals potential allosteric pathways between CBD and DBD that facilitate the allosteric transduction of regulatory signals in CAP. The revelation that the predicted allosteric pathways crisscross the intersubunit interface offers important clues on the microscopic origin of the intersubunit cooperativity and dimer stability of CAP.

Recent Developments in Free Energy Calculations for Drug Discovery

“…Deng ( Deng, 2019 ) compares the double decoupling and PMF approaches in the consideration of small molecule inhibitors in complex with G-quadruplex DNA, and finds that both approaches have errors within 2 kcal/mol of the experimentally determined binding free energies. Further work with DNA includes investigation of alkaloid binding to human telomeric G-quadruplex ( Deng et al, 2019 ), umbrella sampling of catabolite activator protein to identify DNA binding induced conformation changes ( Prabhakant et al, 2020 ), binding of the antiviral netropsin in the DNA minor groove ( Zhang et al, 2018 ), examination of Z-DNA stability with modified cytosine bases ( Vongsutilers et al, 2020 ), and binding recognition and allosteric mechanism of tryptophan-responsive regulatory protein-DNA ( Mariadasse et al, 2020 ). Simulation of RNA features the prediction of riboswitch binding affinities ( Hu et al, 2020 ) and in silico screening of aptamers targeting hepatitis B surface antigen ( Sabri et al, 2019 ).…”