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通过实验和计算方法揭示 METP3 中四面体金属结合位点的结构。

Unravelling the Structure of the Tetrahedral Metal-Binding Site in METP3 through an Experimental and Computational Approach.

机构信息

Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy.

Istituto di Biostrutture e Bioimmagini (IBB), National Research Council (CNR), Via Mezzocannone 16, 80134 Napoli, Italy.

出版信息

Molecules. 2021 Aug 28;26(17):5221. doi: 10.3390/molecules26175221.

DOI:10.3390/molecules26175221
PMID:34500655
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8434281/
Abstract

Understanding the structural determinants for metal ion coordination in metalloproteins is a fundamental issue for designing metal binding sites with predetermined geometry and activity. In order to achieve this, we report in this paper the design, synthesis and metal binding properties of METP3, a homodimer made up of a small peptide, which self assembles in the presence of tetrahedrally coordinating metal ions. METP3 was obtained through a redesign approach, starting from the previously developed METP molecule. The undecapeptide sequence of METP, which dimerizes to house a Cys tetrahedral binding site, was redesigned in order to accommodate a CysHis site. The binding properties of METP3 were determined toward different metal ions. Successful assembly of METP3 with Co(II), Zn(II) and Cd(II), in the expected 2:1 stoichiometry and tetrahedral geometry was proven by UV-visible spectroscopy. CD measurements on both the free and metal-bound forms revealed that the metal coordination drives the peptide chain to fold into a turned conformation. Finally, NMR data of the Zn(II)-METP3 complex, together with a retrostructural analysis of the Cys-X-X-His motif in metalloproteins, allowed us to define the model structure. All the results establish the suitability of the short METP sequence for accommodating tetrahedral metal binding sites, regardless of the first coordination ligands.

摘要

理解金属离子在金属蛋白中的配位结构决定因素对于设计具有预定几何形状和活性的金属结合位点是一个基本问题。为了实现这一目标，我们在本文中报告了 METP3 的设计、合成和金属结合特性，METP3 是由一个小肽组成的同源二聚体，它在四面体配位金属离子存在下自组装。METP3 是通过重新设计方法从先前开发的 METP 分子获得的。为了容纳 CysHis 位点，对 METP 的十一肽序列进行了重新设计，该序列二聚化以容纳 Cys 四面体结合位点。通过紫外可见光谱确定了 METP3 与不同金属离子的结合特性。用 Co(II)、Zn(II)和 Cd(II)成功组装了 METP3，其化学计量比和四面体几何形状均为 2:1，这得到了证明。对游离态和金属结合态的 CD 测量表明，金属配位促使肽链折叠成转角构象。最后，Zn(II)-METP3 配合物的 NMR 数据以及对金属蛋白中 Cys-X-X-His 基序的回溯分析，使我们能够确定模型结构。所有结果都证明了短 METP 序列适合容纳四面体金属结合位点，而与第一配位配体无关。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/5c69da3ac1c0/molecules-26-05221-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/99a7c5d48b06/molecules-26-05221-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/6e765313a93c/molecules-26-05221-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/228ff6dac3cc/molecules-26-05221-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/6563ab09e117/molecules-26-05221-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/086f151b1406/molecules-26-05221-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/95a3bd1791c1/molecules-26-05221-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/03b816550279/molecules-26-05221-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/76a5fabfb166/molecules-26-05221-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/497138dfc2d2/molecules-26-05221-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/5c69da3ac1c0/molecules-26-05221-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/99a7c5d48b06/molecules-26-05221-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/6e765313a93c/molecules-26-05221-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/228ff6dac3cc/molecules-26-05221-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/6563ab09e117/molecules-26-05221-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/086f151b1406/molecules-26-05221-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/95a3bd1791c1/molecules-26-05221-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/03b816550279/molecules-26-05221-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/76a5fabfb166/molecules-26-05221-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/497138dfc2d2/molecules-26-05221-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2ea0/8434281/5c69da3ac1c0/molecules-26-05221-g010.jpg

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