Natural selection based on coordination chemistry: computational assessment of [4Fe–4S]-maquettes with non-coded amino acids
Natural selection based on coordination chemistry: computational assessment of [4Fe–4S]-maquettes with non-coded amino acids
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基于配位化学的自然选择：使用非编码氨基酸对 [4Fe−4S]-模型进行计算评估
DOI：
10.1098/rsfs.2019.0071
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发表时间：
2019
期刊：
影响因子：
4.4
通讯作者：
McGlynn, Shawn E.
中科院分区：
文献类型：
--
作者：
Szilagyi, Robert K.;Hanscam, Rebecca;Shepard, Eric M.;McGlynn, Shawn E.
半胱氨酸是生物学中唯一含有巯基的编码氨基酸。去质子化的硫醇盐对于锚定铁-硫（[Fe-S]）簇是必不可少的，作为蛋白质基质的辅基。[Fe-S]金属蛋白和金属酶参与生物电子传递、自由基化学、小分子活化和信号传导。这些是最早的生物体中可能存在的关键代谢和调节过程。在生命理论出现的背景下，半胱氨酸特异性R-CH 2-SH侧链的选择和进化是一个令人着迷的问题。我们进行了计算[4Fe-4S]-模型建模方法，以评估侧链长度如何影响短7聚体和长16聚体肽中[Fe-S]簇的结合和稳定性，其中含有硫代甘氨酸，半胱氨酸或同型半胱氨酸。基于力场的分子动力学模拟[4Fe-4S]簇巢的形成补充了密度泛函理论计算的配体交换反应之间的预组装簇和肽。二级结构分析表明，与半胱氨酸的肽被发现有更大的频率嵌套绑定预先形成的[4Fe-4S]簇。此外，与硫代甘氨酸或高半胱氨酸配体相比，半胱氨酸配体中单个亚甲基的存在减轻了空间体积，保持了H-键合和偶极网络，并提供了共价Fe-S（硫醇盐）键，其一起为[4Fe-4S]簇结合创造了最佳的电子和几何结构条件。我们的理论工作通过配位化学形成了半胱氨酸自然选择的实验可检验的假设。
Cysteine is the only coded amino acid in biology that contains a thiol functional group. Deprotonated thiolate is essential for anchoring iron–sulfur ([Fe–S]) clusters, as prosthetic groups to the protein matrix. [Fe–S] metalloproteins and metalloenzymes are involved in biological electron transfer, radical chemistry, small molecule activation and signalling. These are key metabolic and regulatory processes that would likely have been present in the earliest organisms. In the context of emergence of life theories, the selection and evolution of the cysteine-specific R–CH2–SH side chain is a fascinating question to confront. We undertook a computational [4Fe–4S]-maquette modelling approach to evaluate how side chain length can influence [Fe–S] cluster binding and stability in short 7-mer and long 16-mer peptides, which contained either thioglycine, cysteine or homocysteine. Force field-based molecular dynamics simulations for [4Fe–4S] cluster nest formation were supplemented with density functional theory calculations of a ligand-exchange reaction between a preassembled cluster and the peptide. Secondary structure analysis revealed that peptides with cysteine are found with greater frequency nested to bind preformed [4Fe–4S] clusters. Additionally, the presence of the single methylene group in cysteine ligands mitigates the steric bulk, maintains the H-bonding and dipole network, and provides covalent Fe–S(thiolate) bonds that together create the optimal electronic and geometric structural conditions for [4Fe–4S] cluster binding compared to thioglycine or homocysteine ligands. Our theoretical work forms an experimentally testable hypothesis of the natural selection of cysteine through coordination chemistry.
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影响因子：
8
作者：
Ho, BK;Thomas, A;Brasseur, R
通讯作者：
Brasseur, R
[FenSn(SPh)4]2- (n = 2, 4) 在水基介质中的组装
DOI：
--
发表时间：
1984
期刊：
影响因子：
--
作者：
D. Kurtz;W. Stevens
通讯作者：
W. Stevens
影响因子：
8.4
作者：
Lagardère L;Jolly LH;Lipparini F;Aviat F;Stamm B;Jing ZF;Harger M;Torabifard H;Cisneros GA;Schnieders MJ;Gresh N;Maday Y;Ren PY;Ponder JW;Piquemal JP
通讯作者：
Piquemal JP
DOI：
10.1016/j.bbamcr.2014.11.001
发表时间：
2015-06
影响因子：
5.1
作者：
Outten, F. Wayne
通讯作者：
Outten, F. Wayne
[FenSn(SR)4]2− (n=2, 4) 在水介质中由铁盐、硫醇、硫、硫化物或硫代硫酸盐加硫氰酸组装而成
DOI：
--
发表时间：
1985
期刊：
影响因子：
--
作者：
F. Bonomi;M. Werth;D. Kurtz
通讯作者：
D. Kurtz