Asymmetric Dynamics of the Acyl-Carrier Protein Inside the Fungal Fatty-Acid Mega-Synthase

Abstract

Fatty-acid mega-synthases (FAS) are large multifunctional protein complexes responsible for the synthesis of fatty acids. In fungi, FAS features two distinct reaction chambers with three-fold symmetry, each of which includes all enzymes necessary to catalyze the iterative elongation of fatty acids, together with three acyl-carrier proteins (ACP), used for covalent substrate shuttling. Flexible linkers double-tether the ACPs to FAS scaffold to facilitate the delivery of chemical intermediates. However, the actual shuttling mechanism is still unknown; several contribution factors have been proposed, e.g. linker length and elasticity, electrostatics complementarity between the ACPs and the catalytic centers, etc.To assess these and other factors, we have analyzed the dynamics of ACP within the FAS reaction chamber, using multi-scale molecular dynamics (MD) simulations. We have adopted a novel model, which comprises a coarse-grained (CG), semi-rigid-body representation of the ACPs; a CG, flexible representation of the ACP-chamber linkers; a grid-based representation of the FAS chamber; and an implicit description of solvent.It was found that ACP dynamics is not hindered by the linker length nor its flexibility. Indeed, each ACP domain is able to visit all catalytic sites. Nonetheless, the probability of ACP encounters with the catalytic sites was found to differ between adjacent sub-chambers. It was found that this asymmetry arises from the steric hindrance imposed on the ACPs by the linkers. In conclusion, the dynamics of ACP within FAS appears to be essentially stochastic, and not limited by the native linker length; instead, it is modulated by volume-exclusion effects due to ‘molecular crowding’and by electrostatic steering towards the chamber walls. It follows that residence times at each catalytic site will be primarily determined by their individual binding affinities for the ACP domain and its substrate.