Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
Biochemistry. 2010 Apr 6;49(13):2860-8. doi: 10.1021/bi901713r.
Acyl carrier protein (ACP) is the central player in fatty acid (FA) biosynthesis. It covalently binds all FA intermediates and presents them to the enzymes needed for elongation. Bacterial ACP must interact with a large number of proteins, which raises the question of how different acyl-ACPs are recognized and distinguished from each other. We performed molecular dynamics (MD) simulations of the FA synthase intermediates beta-ketoacyl-, beta-hydroxyacyl, and trans-2-enoyl-ACP spanning from 4 to 18 carbon groups in length. These forms of acyl-ACP have largely yet to be characterized experimentally, and our simulations provide a first insight into these structures. The simulations were conducted with the acyl chain directed into the solvent, as well as in a solvent-protected conformation inside the hydrophobic pocket of Escherichia coli ACP. Spontaneous migration from the solvent-exposed state into the hydrophobic binding pocket of ACP was seen in each of the intermediate classes studied, but not in all the individual simulations. This confirms that the intermediates can enter and utilize the same hydrophobic pockets as saturated acyl chains. In addition, a recurring, novel association of the acyl chains with loop I of ACP was observed that may be occupied transiently before entry into the hydrophobic pocket. The MD simulations of the acyl chains in a solvent-shielded state reveal that the polar functional group in the beta position of the beta-ketoacyl and beta-hydroxyacyl chains anchors these moieties at the cavity entrance, while the chains without a polar group in the beta position lack this additional anchoring atom. This leads to a binding mode in which the beta-ketoacyl and beta-hydroxyacyl chains are positioned further from the bottom of the pocket compared to the saturated and enoyl chains, particularly in short chain (<C12) ACPs. These observations suggest a rationale for how different acyl-ACP intermediates may be distinguished by FA synthase enzymes.
酰基载体蛋白（ACP）是脂肪酸（FA）生物合成的核心。它共价结合所有 FA 中间产物，并将其呈现给需要延伸的酶。细菌 ACP 必须与大量的蛋白质相互作用，这就提出了一个问题，即不同的酰基-ACP 是如何被识别和区分的。我们对长度为 4 到 18 个碳原子的 FA 合酶中间体β-酮酰基、β-羟酰基和反式-2-烯酰基-ACP 进行了分子动力学（MD）模拟。这些形式的酰基-ACP 在很大程度上尚未得到实验表征，我们的模拟为这些结构提供了第一个见解。模拟中，酰基链被导向溶剂中，以及在大肠杆菌 ACP 的疏水性口袋内的溶剂保护构象中进行。在研究的每个中间类中，都观察到从暴露于溶剂的状态自发迁移到 ACP 的疏水性结合口袋中，但并非在所有的单个模拟中都发生。这证实了中间体能进入并利用与饱和酰基链相同的疏水性口袋。此外，观察到酰基链与 ACP 的环 I 之间反复出现的新颖结合，该结合可能在进入疏水性口袋之前短暂占据。在溶剂屏蔽状态下的酰基链的 MD 模拟表明，β-酮酰基和β-羟酰基链的β位上的极性官能团将这些部分锚定在腔入口处，而在β位上没有极性基团的链则缺乏这种额外的锚固原子。这导致了一种结合模式，其中β-酮酰基和β-羟酰基链与口袋底部的距离比饱和和烯酰基链更远，特别是在短链（<C12）ACP 中。这些观察结果为 FA 合酶酶如何区分不同的酰基-ACP 中间产物提供了一个合理的解释。
