用 DNA 重新定义蛋白质单晶内的蛋白质界面,Journal of the American Chemical Society

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用 DNA 重新定义蛋白质单晶内的蛋白质界面
Journal of the American Chemical Society ( IF 14.4 ) Pub Date : 2021-06-05 , DOI: 10.1021/jacs.1c04191
Benjamin E Partridge ₁ , Peter H Winegar ₁ , Zhenyu Han ₁ , Chad A Mirkin ₁

Affiliation

蛋白质是精致的纳米级构建模块：分子纯、化学可寻址，并且对其进化功能具有固有的选择性。将蛋白质组织成具有高位置、取向和平移顺序的单晶体会产生可以知道每个原子位置的材料。然而，由于定义天然单晶内蛋白质界面的无数相互作用，控制蛋白质的组织具有挑战性。最近，我们发现在蛋白质表面之间引入单一 DNA-DNA 相互作用会导致单晶体内蛋白质堆积的变化以及由此产生的蛋白质-蛋白质相互作用 (PPI)。然而，修改特定的 PPI 来对蛋白质包装进行有意的改变是一个尚未解决的挑战。在这项工作中，我们假设用 DNA-DNA 相互作用破坏和替换高度保守的 PPI 将使蛋白质包装能够通过利用引入的寡核苷酸的可编程性进行调节。使用刀豆球蛋白 A (ConA) 作为模型蛋白，我们规避了潜在有害的诱变，并利用 ConA 与甘露糖的选择性结合，将 DNA 非共价连接到蛋白质表面。我们证明 DNA 缔合消除了负责天然 ConA 结晶的主要 PPI，从而允许对 DNA 设计（长度、互补性和附着位置）进行微妙的改变，从而对 ConA 包装进行明显的改变，包括实现三种新颖的晶体结构和ConA 堆积沿单个晶轴的有意扩展。这些发现显着增强了我们对 DNA 如何取代天然 PPI 来编程有序材料中的蛋白质包装的理解。

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Redefining Protein Interfaces within Protein Single Crystals with DNA

Proteins are exquisite nanoscale building blocks: molecularly pure, chemically addressable, and inherently selective for their evolved function. The organization of proteins into single crystals with high positional, orientational, and translational order results in materials where the location of every atom can be known. However, controlling the organization of proteins is challenging due to the myriad interactions that define protein interfaces within native single crystals. Recently, we discovered that introducing a single DNA–DNA interaction between protein surfaces leads to changes in the packing of proteins within single crystals and the protein–protein interactions (PPIs) that arise. However, modifying specific PPIs to effect deliberate changes to protein packing is an unmet challenge. In this work, we hypothesized that disrupting and replacing a highly conserved PPI with a DNA–DNA interaction would enable protein packing to be modulated by exploiting the programmability of the introduced oligonucleotides. Using concanavalin A (ConA) as a model protein, we circumvent potentially deleterious mutagenesis and exploit the selective binding of ConA toward mannose to noncovalently attach DNA to the protein surface. We show that DNA association eliminates the major PPI responsible for crystallization of native ConA, thereby allowing subtle changes to DNA design (length, complementarity, and attachment position) to program distinct changes to ConA packing, including the realization of three novel crystal structures and the deliberate expansion of ConA packing along a single crystallographic axis. These findings significantly enhance our understanding of how DNA can supersede native PPIs to program protein packing within ordered materials.

更新日期：2021-06-17

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