School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom.
Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, India.
PLoS One. 2019 Jul 10;14(7):e0219435. doi: 10.1371/journal.pone.0219435. eCollection 2019.
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.
载体蛋白是由四个螺旋组成的束，它们将代谢物和次生代谢物（如脂肪酸、聚酮和非核糖体肽）共价结合。这些蛋白质介导了许多具有重要药用价值的化合物的产生，包括抗生素和抗癌剂。酰基载体蛋白（ACP）可以作为多结构域多肽的一部分（I 型 ACP），或者作为多蛋白复合物的一部分（II 型）。这里主要关注的是 I 型反式 AT 聚酮合酶 MmpA 的 ACP2 和 ACP3 这两个结构域，它们是抗生素莫匹罗星生物合成途径的核心组成部分。在它们的 apo、holo 和酰基形式的分子动力学模拟中，ACP2 和 ACP3 都形成了一个底物结合的表面凹槽。与这个表面凹槽结合的底物的酰基链上有极性基团暴露出来，并与溶剂形成氢键。所有 ACP 中都存在的 GXDS 基序中的大体积疏水残基，以及螺旋 III 上的类似残基，似乎阻止了 I 型 ACP 和来自聚酮合酶的 II 型 ACP 形成深隧道。相比之下，在 II 型脂肪酸合酶的 ACP 中，等效位置有小的丙氨酸残基，它们确实形成了一个深的溶剂排除的底物结合隧道。在模拟中，带有 I61A L36A W44L 突变的 ACP3 形成了一个深隧道，可以将一个饱和的底物完全埋藏在 ACP 的核心中，与野生型 ACP3 的表面凹槽形成对比。同样，在 II 型 ACP 大肠杆菌脂肪酸合酶的 ACP 中，突变可以使配体结合从深隧道转变为表面凹槽，从而证明了改变几个残基如何可以改变配体结合的可能性。
