Abstract
Acyl carrier protein (ACP) is an essential co-factor protein in fatty acid biosynthesis that shuttles covalently bound fatty acyl intermediates in its hydrophobic pocket to various enzyme partners. To characterize acyl chain-ACP interactions and their influence on enzyme interactions, we performed 19 molecular dynamics (MD) simulations of Escherichia coli apo-, holo-, and acyl-ACPs. The simulations were started with the acyl chain in either a solvent-exposed or a buried conformation. All four short-chain (< or = C10) and one long-chain (C16) unbiased acyl-ACP MD simulation show the transition of the solvent-exposed acyl chain into the hydrophobic pocket of ACP, revealing its pathway of acyl chain binding. Although the acyl chain resides inside the pocket, Thr-39 and Glu-60 at the entrance stabilize the phosphopantetheine linker through hydrogen bonding. Comparisons of the different ACP forms indicate that the loop region between helices II and III and the prosthetic linker may aid in substrate recognition by enzymes of fatty acid synthase systems. The MD simulations consistently show that the hydrophobic binding pocket of ACP is best suited to accommodate an octanoyl group and is capable of adjusting in size to accommodate chain lengths as long as decanoic acid. The simulations also reveal a second, novel binding mode of the acyl chains inside the hydrophobic binding pocket directed toward helix I. This study provides a detailed dynamic picture of acyl-ACPs that is in excellent agreement with available experimental data and, thereby, provides a new understanding of enzyme-ACP interactions.
Highlights
There are two main types of machineries that perform this process, known as the type I fatty acid synthase (FAS) systems found in mammals and fungi and the type II systems existing in bacteria and eukaryotic plastids [2]
The acyl chain intermediates in Fatty acid (FA) synthesis are bound covalently by means of a prosthetic linker on acyl carrier protein (ACP) that is derived from coenzyme A in an enzymatic reaction catalyzed by ACP synthase (ACPS) (Fig. 1)
Long range electrostatic interactions were calcu- Asn-24, Ala-26, and Phe-28 with the backbone atoms of Glnlated according to Fast Particle-Mesh Ewald (PME) electrostat- 66, Val-65, and Thr-63, respectively, immediately preceding ics [25] with a cutoff of 0.9 nm
Summary
There are two main types of machineries that perform this process, known as the type I fatty acid synthase (FAS) systems found in mammals and fungi and the type II systems existing in bacteria and eukaryotic plastids [2]. Considering that ACP makes up ϳ0.25% of all soluble protein in E. coli suggests that there are mechanisms for enzymes to recognize what type of acyl-ACP is bound [17] To understand this process, it is essential that a dynamic picture of the substrate behavior attached to ACP is obtained. If the pathway of substrate binding by ACP is revealed, potential drug target sites that are not apparent from static structures alone may be identified To evaluate these questions we performed extensive molecular dynamics (MD) simulations of apo-, holo-, and saturated acylACPs ranging from 4 to 18 carbon groups in length. Our findings are substantiated by excellent agreement with experimental data in the literature
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