Rubredoxin Function: Redox Behavior from Electrostatics
Rubredoxin Function: Redox Behavior from Electrostatics
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DOI：
10.1021/ct100476h
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发表时间：
2011-03-01
影响因子：
5.5
通讯作者：
Knapp, E. W.
中科院分区：
文献类型：
--
作者：
Gamiz-Hernandez, Ana Patricia;Kieseritzky, Gernot;Knapp, E. W.
应用连续静电理论来计算红氧还蛋白 (Rd) 蛋白的氧化还原电位。我们使用了 Rd 晶体结构的多个侧链构象异构体、优化的盐桥几何形状、突变残基以及铁硫络合物 (FeS 络合物) 附近的残基，对于给定的溶剂 pH 和氧化还原电位自洽。讨论了以下对 Rd 氧化还原电位的贡献：侧链构象、FeS 配合物的氢键几何形状、介电环境、带电残基和盐桥。我们考虑了 15 种不同的 Rd（不同物种/菌株和突变体），它们具有可用的晶体结构，其氧化还原电位在 -86 mV 和 +31 mV 之间变化。计算出的氧化还原电位与测量值的均方根偏差 (RMSD) 偏差小于 16 mV。酰胺氢键几何形状被认为对于 Rd 氧化还原电位的变化至关重要。为了测试这一假设，我们考虑了 14 个突变体 Rd，我们根据 WT 巴氏梭菌 (Cp) 的 Rd 对其结构进行建模，留下 FeS 复合物不变的酰胺氢键几何形状。在这里，我们获得了仅 14 mV 的 RMSD，测量值表明酰胺 H 键几何形状不可能是决定 Rd 氧化还原电位的主要因素。我们分析了决定中温和嗜热 Rd 的 Rd 氧化还原电位相差近 90 mV 的因素，我们发现差异的一半是由于序列，一半是由于主链变化。尽管这两个 Rd 之间的盐桥网络差异很大，并且被认为是热稳定性差异的原因，但它们对 Rd 氧化还原电位的总体影响很小。
Continuum electrostatic theory was applied to compute redox potentials of rubredoxin (Rd) proteins. We used multiple side chain conformers of Rd crystal structures, optimized geometries of salt bridges, mutated residues, and residues in the neighborhood of the iron sulfur complex (FeS complex) self-consistently for given solvent pH and redox potential. The following contributions to Rd redox potentials are discussed: side chain conformations, H-bond geometries of the FeS complex, dielectric environment, charged residues, and salt bridges. We considered 15 different Rd's (of different species/strains and mutants) with available crystal structures whose redox potentials vary between -86 mV and +31 mV. The computed redox potentials deviated by less than 16 mV, root-mean-square deviation (RMSD), from measured values. The amide H-bond geometry is considered to be crucial for the variation of Rd redox potentials. To test this assumption, we considered 14 mutant Rd's for which we modeled the structures based on Rd from WT Clostridium pasterianum (Cp) leaving the amide H-bond geometry of the FeS complex invariant. Here, we obtained an RMSD of only 14 mV with measured values demonstrating that the amide H bond geometries cannot be a major factor determining Rd redox potentials. We analyzed the factors determining the Rd redox potentials of a mesophilic and a thermophilic Rd differing by nearly 90 mV We found that half of the difference is due to sequence and half is due to backbone variations. Albeit salt-bridge networks vary considerably between these two Rd's and are considered to be responsible for differences in thermostability, their overall influence on Rd redox potentials is small.