Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase
Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase
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DOI：
10.1021/acschembio.9b00290
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发表时间：
2019-08-01
影响因子：
4
通讯作者：
Jongkees, Seino A. K.
中科院分区：
文献类型：
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作者：
Goldbach, Leander;Vermeulen, Bram J. A.;Jongkees, Seino A. K.
使用噬菌体和mRNA展示等选择技术衍生的从头大环肽为具有挑战性的生物学问题提供了独特和意想不到的解决方案。这部分是由于它们不寻常的折叠，能够以规范结构（如α-螺旋和β-折叠）不可用的方式呈现侧链。尽管最近对这些分子的兴趣很大，但它们的折叠和结合行为仍然很难表征。在这项工作中，我们提出了共结晶，对接，和解决方案的NMR结构的三个从头大环肽，所有绑定作为竞争性抑制剂与个位数纳摩尔K-I的人胰腺α-淀粉酶的活性位点。我们表明，在这些短的稳定折叠的基序之一是成核的内部疏水相互作用，否则在溶液中的动态构象。从对接的目标结合的结构的溶液结构的比较表明，通过与靶蛋白结合后的相互作用提供的结合构象的稳定。这三种结构还揭示了令人惊讶的功能收敛，以在肽与酶的关键催化残基的相互作用中呈现夹在两个芳族残基之间的单个精氨酸的基序，尽管几乎没有其他结构同源性。我们的研究结果表明，分子内的疏水相互作用是重要的启动小的大环肽结合到他们的目标和高刚性是不必要的高亲和力。
De novo macrocyclic peptides, derived using selection technologies such as phage and mRNA display, present unique and unexpected solutions to challenging biological problems. This is due in part to their unusual folds, which are able to present side chains in ways not available to canonical structures such as alpha-helices and beta-sheets. Despite much recent interest in these molecules, their folding and binding behavior remains poorly characterized. In this work, we present cocrystallization, docking, and solution NMR structures of three de novo macrocyclic peptides that all bind as competitive inhibitors with single-digit nanomolar K-i to the active site of human pancreatic alpha-amylase. We show that a short stably folded motif in one of these is nucleated by internal hydrophobic interactions in an otherwise dynamic conformation in solution. Comparison of the solution structures with a target-bound structure from docking indicates that stabilization of the bound conformation is provided through interactions with the target protein after binding. These three structures also reveal a surprising functional convergence to present a motif of a single arginine sandwiched between two aromatic residues in the interactions of the peptide with the key catalytic residues of the enzyme, despite little to no other structural homology. Our results suggest that intramolecular hydrophobic interactions are important for priming binding of small macrocyclic peptides to their target and that high rigidity is not necessary for high affinity.