Predicting allosteric sites with molecular dynamics simulations and correlation-based tools.

BARRERA GUISASOLA, EXEQUIEL E.; BUSTOS DIEGO M.

Córdoba

Congreso; LI reunión anual de la Sociedad Argentina de Biofísica; 2023

Instituto de Investigaciones Biológicas y Tecnológicas (IIByT)

Inour group, we are captivated by understanding the structural aspectsof the family of 14-3-3. These are hub proteins formed by sevenparalogs that control several biological processes like cellsignaling, transcription, and apoptosis. Accordingly, they also playkey roles in multiple diseases. They participate in protein-proteininteractions by capturing different protein partners in a flexibleregion called amphipathic groove (AG). To study the opening andclosing of the AG that dictates its ability to interact with itsprotein partners, we performed all-atom molecular dynamics (MD)simulations, focusing on three paralogs (ζ, ε, and γ). Despite thehighly conserved sequence of their AGs, we observed different openingrates increasing from paralogs γ to ε to ζ. We employed acorrelation-based method called Shortest Path Map to study theinfluence of the less conserved distal residues on the conformationaltransitions of 14-3-3. This method recognizes residues that undergothe highest correlated movements during the trajectories. Even thougheach paralog differed in their shortest path maps, we observed acommon feature: a node located at the entrance of a small pocketpositioned at the opposite side of the AG. This node corresponds toamino acids F153 (ζ), S154 (ε), and H158 (γ), all of them locatedin the same position of this less-conserved region of 14-3-3. Next,we focused on paralog ζ and observed that a transient hydrophobicinteraction between the side chains of F153 and A171 preceded theopening of the AG. To confirm this sequence of events, we calculatedthe cross-correlation function between the time series of theabove-mentioned events, showing the highest correlation (R=0.82) witha Δt of 0.5 ns between the close up of F153 and A171, and theopening of the amphipathic groove. The interaction with A171 was notobserved in paralogs ε and γ. Complementarily,we performed MD simulations of the complex obtained by dockingcalculations between 14-3-3 ζ and Norharmane. This small moleculebonded between residues F153 and A171, impeding their hydrophobicinteraction and maintaining the amphipathic groove closed. Theseresults strengthen our hypothesis of an allosteric regulation of14-3-3 and open promising pharmaceutical interventions presentingparalog specificity.p { margin-bottom: 0.1in; line-height: 115% }