Structure, function and dynamics in acyl carrier proteins

Abstract

Carrier proteins are four-helix bundles that covalently hold metabolites and secondary metabolites, such as fatty acids, polyketides and non-ribosomal peptides. These proteins mediate the production of many pharmaceutically important compounds including antibiotics and anticancer agents. Acyl carrier proteins (ACPs) can be found as part of a multi-domain polypeptide (Type I ACPs), or as part of a multiprotein complex (Type II). Here, the main focus is on ACP2 and ACP3, domains from the type I trans -AT polyketide synthase MmpA, which is a core component of the biosynthetic pathway of the antibiotic mupirocin. During molecular dynamics simulations of their apo, holo and acyl forms ACP2 and ACP3 both form a substrate-binding surface-groove. The substrates bound to this surface-groove have polar groups on their acyl chain exposed and forming hydrogen bonds with the solvent. Bulky hydrophobic residues in the GXDS motif common to all ACPs, and similar residues on helix III, appear to prohibit the formation of a deep tunnel in type I ACPs and type II ACPs from polyketide synthases. In contrast, the equivalent positions in ACPs from type II fatty acid synthases, which do form a deep solvent-excluded substrate-binding tunnel, have the small residue alanine. During simulation, ACP3 with mutations I61A L36A W44L forms a deep tunnel that can fully bury a saturated substrate in the core of the ACP, in contrast to the surface groove of the wild type ACP3. Similarly, in the ACP from E . coli fatty acid synthase, a type II ACP, mutations can change ligand binding from being inside a deep tunnel to being in a surface groove, thus demonstrating how changing a few residues can modify the possibilities for ligand binding.

Elucidation of transient protein-protein interactions within carrier protein-dependent biosynthesis

“…For example, recent studies have demonstrated that engineering enzyme specificity for a non-native AcpP-dependent enzyme can be accomplished by modifying the PPI residues for improved binding 25 . Even single atom changes in the identity of AcpP-bound cargo have been demonstrated to impart perturbations to the structure of acyl-AcpP 26 , 27 .

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Probing the structure and function of acyl carrier proteins to unlock the strategic redesign of type II polyketide biosynthetic pathways

“…Tsai et al. recently developed a force field to model the Ppant arm and Ppant-bound intermediates, starter units, and extender units ( 83 , 87 ). Together, these advances provide an exciting framework for applying force fields capable of modeling ACPs in their holo - and acyl -states.…”

“…Recent progress toward the parameterization of the Ppant arm and its cargo has paved the way for a new era of type II PKS ACP research in which MD simulations can be used hand-in-hand with structural and biochemical approaches. Tsai et al recently developed a force field to model the Ppant arm and Ppant-bound intermediates, starter units, and extender units (83,87). Together, these advances provide an exciting framework for applying force fields capable of modeling ACPs in their holoand acyl-states.…”

Decoding Protein Gas‐Phase Stability with Alanine Scanning and Collision‐Induced Unfolding Ion Mobility Mass Spectrometry

“…Acyl carrier proteins (ACPs) are a group of structurally homologous proteins found in fatty acid synthases (FASs), polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs). [32][33][34][35] Comprised of four alpha-helices, their function is to tether and transfer the growing natural product intermediate between enzymatic domains via a phosphopantetheine moiety, which is post-translationally appended to a conserved serine residue on the ACP. Although ACPs are structurally homologous, they have low sequence similarity, even within related biosynthetic pathways.…”