Retrostructural analysis of metalloproteins: Application to the design of a minimal model for diiron proteins
Retrostructural analysis of metalloproteins: Application to the design of a minimal model for diiron proteins
复制标题
DOI：
10.1073/pnas.97.12.6298
复制
发表时间：
2000-06-06
影响因子：
11.1
通讯作者：
DeGrado, WF
中科院分区：
文献类型：
--
作者：
Lombardi, A;Summa, CM;DeGrado, WF
从头设计为构建复杂金属蛋白功能所需的模型提供了一种有吸引力的方法。许多金属蛋白的金属结合位点位于二级结构的多个元件之间，邀请了一种逆转录方法来构建其活性位点的最小模型。通过使用仅具有六个可调参数的简单几何模型，可以将包含锌指、二铁蛋白和红蛋白的金属结合位点的骨架几何形状描述为在约1埃rms偏差内。这些几何模型为金属蛋白的设计提供了极好的起点，如Due Ferro 1（DF 1）的构建所示，Due Ferro 1（DF 1）是双核金属蛋白的Glu-Xxx-Xxx-His类的最小模型。通过使用延伸至2.5埃的数据，通过X射线晶体学合成该蛋白并将其结构表征为二-Zn（II）络合物。这种四螺旋束蛋白由两个非共价缔合的螺旋-环-螺旋基序组成，双核中心由两个桥接Glu和两个螯合Glu侧链以及两个单齿His配体形成，主要配体大部分被埋在蛋白质内部，并且它们的几何形状通过与第二壳配体的氢键网络而稳定。Tyr残基与螯合Glu配体形成氢键，类似于在大肠杆菌核糖核苷酸还原酶的含二铁R2亚基和铁蛋白中发现的基序。DF 1还结合钴和铁离子，并应提供一个有吸引力的模型，为各种二铁蛋白，使用氧的过程，包括铁的存储，自由基的形成，和烃氧化。
De novo protein design provides an attractive approach for the construction of models to probe the features required for function of complex metalloproteins, The metal-binding sites of many metalloproteins lie between multiple elements of secondary structure, inviting a retrostructural approach to constructing minimal models of their active sites. The backbone geometries comprising the metal-binding sites of zinc fingers, diiron proteins, and rubredoxins may be described to within approximately 1 Angstrom rms deviation by using a simple geometric model with only six adjustable parameters. These geometric models provide excellent starting points for the design of metalloproteins, as illustrated in the construction of Due Ferro 1 (DF1), a minimal model for the Glu-Xxx-Xxx-His class of dinuclear metalloproteins, This protein was synthesized and structurally characterized as the di-Zn(ll) complex by x-ray crystallography, by using data that extend to 2.5 Angstrom. This four-helix bundle protein is comprised of two noncovalently associated helix-loop-helix motifs, The dinuclear center is formed by two bridging Glu and two chelating Glu side chains, as well as two monodentate His ligands, The primary ligands are mostly buried in the protein interior, and their geometries are stabilized by a network of hydrogen bonds to second-shell ligands, In particular, a Tyr residue forms a hydrogen bond to a chelating Glu ligand, similar to a motif found in the diiron-containing R2 subunit of Escherichia coli ribonucleotide reductase and the ferritins. DF1 also binds cobalt and iron ions and should provide an attractive model for a variety of diiron proteins that use oxygen for processes including iron storage, radical formation, and hydrocarbon oxidation.