Shifting the Hydrolysis Equilibrium of Substrate Loaded Acyl Carrier Proteins

Unique recognition of the microalgal plastidial glycerol-3-phosphate acyltransferase for acyl-ACP

Plastidial glycerol-3-phosphate acyltransferases (GPATs) catalyze acyl-ACP and glycerol-3-phosphate to synthesize lysophosphatidic acid in vivo, which initiates the formation of various glycerolipids. Although the physiological substrates of plastidial GPATs are acyl-ACPs, acyl-CoAs have been commonly studied on the GPATs in vitro. However, little is known whether there are any distinct features of GPATs towards acyl-ACP and acyl-CoA. In this study, the results showed that the microalgal plastidial GPATs preferred acyl-ACP to acyl-CoA, while surprisingly, the plant-derived plastidial GPATs showed no obvious preferences towards these two acyl carriers. The key residues responsible for the distinct feature of microalgal plastidial GPATs were compared with plant-derived plastidial GPATs in their efficiency to catalyze acyl-ACP and acyl-CoA. Microalgal plastidial GPATs uniquely recognized acyl-ACP as compared to with other acyltransferases. The structure of the acyltransferases-ACP complex highlights only the involvement of the large structural domain in ACP in microalgal plastidial GPAT while in the other acyltransferases, both large and small structural domains were involved in the recognition process. The interaction sites on the plastidial GPAT from the green alga Myrmecia incisa (MiGPAT1) with ACP turned out to be K204, R212 and R266. A unique recognition between the microalgal plastidial GPAT and ACP was elucidated.

Using NMR Titration Experiments to Study E. coli FAS-II- and AcpP-Mediated Protein-Protein Interactions

Acyl carrier proteins (ACPs) are central to many primary and secondary metabolic pathways. In E. coli fatty acid biosynthesis (FAB), the central ACP, AcpP, transports intermediates to a suite of partner proteins (PP) for iterative modification and elongation. The regulatory protein-protein interactions that occur between AcpP and the PP in FAB are poorly understood due to the dynamic and transient nature of these interactions. Solution-state NMR spectroscopy can reveal information at the atomic level through experiments such as the 2D heteronuclear single quantum coherence (HSQC). The following protocol describes NMR HSQC titration experiments that can elucidate biomolecular recognition events.

Probing Substrate-Loaded Carrier Proteins by Nuclear Magnetic Resonance

Carrier proteins (CPs) are central actors in nonribosomal peptide synthetases (NRPSs) as they interact with all catalytic domains, and because they covalently hold the substrates and intermediates leading to the final product. Thus, how CPs and their partner domains recognize and engage with each other as a function of CP cargos is paramount to understanding and engineering NRPSs. However, rapid hydrolysis of the labile thioester bonds holding substrates challenges molecular and biophysical studies to determine the molecular mechanisms of domain recognition. In this chapter, we describe a protocol to counteract hydrolysis and study loaded carrier proteins at the atomic level with nuclear magnetic resonance (NMR) spectroscopy. The method relies on loading CPs in situ, with adenylation domains in the NMR tube, to reach substrate-loaded CPs at steady state. We describe controls and experimental readouts necessary to assess the integrity of the sample and maintain loading on CPs. Our approach provides a basis to conduct subsequent NMR experiments and obtain kinetic, thermodynamic, dynamic, and structural parameters of substrate-loaded CPs alone or in the presence of other domains.

Decoding allosteric regulation by the acyl carrier protein

Enzymes in multistep metabolic pathways utilize an array of regulatory mechanisms to maintain a delicate homeostasis [K. Magnuson, S. Jackowski, C. O. Rock, J. E. Cronan, Jr, Microbiol. Rev. 57, 522-542 (1993)]. Carrier proteins in particular play an essential role in shuttling substrates between appropriate enzymes in metabolic pathways. Although hypothesized [E. Płoskoń et al., Chem. Biol. 17, 776-785 (2010)], allosteric regulation of substrate delivery has never before been demonstrated for any acyl carrier protein (ACP)-dependent pathway. Studying these mechanisms has remained challenging due to the transient and dynamic nature of protein-protein interactions, the vast diversity of substrates, and substrate instability [K. Finzel, D. J. Lee, M. D. Burkart, ChemBioChem 16, 528-547 (2015)]. Here we demonstrate a unique communication mechanism between the ACP and partner enzymes using solution NMR spectroscopy and molecular dynamics to elucidate allostery that is dependent on fatty acid chain length. We demonstrate that partner enzymes can allosterically distinguish between chain lengths via protein-protein interactions as structural features of substrate sequestration are translated from within the ACP four-helical bundle to the protein surface, without the need for stochastic chain flipping. These results illuminate details of cargo communication by the ACP that can serve as a foundation for engineering carrier protein-dependent pathways for specific, desired products.

Type I fatty acid synthase trapped in the octanoyl-bound state

De novo fatty acid biosynthesis in humans is accomplished by a multidomain protein, the Type I fatty acid synthase (FAS). Although ubiquitously expressed in all tissues, fatty acid synthesis is not essential in normal healthy cells due to sufficient supply with fatty acids by the diet. However, FAS is overexpressed in cancer cells and correlates with tumor malignancy, which makes FAS an attractive selective therapeutic target in tumorigenesis. Herein, we present a crystal structure of the condensing part of murine FAS, highly homologous to human FAS, with octanoyl moieties covalently bound to the transferase (MAT—malonyl‐/acetyltransferase) and the condensation (KS—β‐ketoacyl synthase) domain. The MAT domain binds the octanoyl moiety in a novel (unique) conformation, which reflects the pronounced conformational dynamics of the substrate‐binding site responsible for the MAT substrate promiscuity. In contrast, the KS binding pocket just subtly adapts to the octanoyl moiety upon substrate binding. Besides the rigid domain structure, we found a positive cooperative effect in the substrate binding of the KS domain by a comprehensive enzyme kinetic study. These structural and mechanistic findings contribute significantly to our understanding of the mode of action of FAS and may guide future rational inhibitor designs.