Department of Chemistry, Georgetown University, Washington, District of Columbia, USA.
Biophys J. 2010 Feb 17;98(4):560-8. doi: 10.1016/j.bpj.2009.11.006.
Based on the crystal structures, three possible sequence determinants have been suggested as the cause of a 285 mV increase in reduction potential of the rubredoxin domain of rubrerythrin over rubredoxin by modulating the polar environment around the redox site. Here, electrostatic calculations of crystal structures of rubredoxin and rubrerythrin and molecular dynamics simulations of rubredoxin wild-type and mutants are used to elucidate the contributions to the increased reduction potential. Asn(160) and His(179) in rubrerythrin versus valines in rubredoxins are predicted to be the major contributors, as the polar side chains contribute significantly to the electrostatic potential in the redox site region. The mutant simulations show both side chains rotating on a nanosecond timescale between two conformations with different electrostatic contributions. Reduction also causes a change in the reduction energy that is consistent with a linear response due to the interesting mechanism of shifting the relative populations of the two conformations. In addition to this, a simulation of a triple mutant indicates the side-chain rotations are approximately anticorrelated so whereas one is in the high potential conformation, the other is in the low potential conformation. However, Ala(176) in rubrerythrin versus a leucine in rubredoxin is not predicted to be a large contributor, because the solvent accessibility increases only slightly in mutant simulations and because it is buried in the interface of the rubrerythrin homodimer.
基于晶体结构，提出了三个可能的序列决定因素，认为它们通过调节氧化还原位点周围的极性环境，导致 rubrerythrin 的 rubredoxin 结构域的还原电位相对于 rubredoxin 增加了 285 mV。在这里，使用 rubredoxin 和 rubrerythrin 的晶体结构静电计算和 rubredoxin 野生型和突变体的分子动力学模拟来阐明对增加的还原电位的贡献。与 rubredoxins 中的缬氨酸相比，rubrerythrin 中的 Asn(160)和 His(179)被预测为主要贡献者，因为极性侧链对氧化还原位点区域的静电势有很大贡献。突变体模拟显示，两个侧链在纳秒时间尺度上在两种具有不同静电贡献的构象之间旋转。还原还导致还原能量发生变化，这与由于两种构象的相对分布发生变化而导致的线性响应一致。除此之外，三重突变体的模拟表明侧链旋转大约是反相关的，因此当一个处于高电势构象时，另一个处于低电势构象。然而，与 rubredoxin 中的亮氨酸相比，rubrerythrin 中的 Ala(176)预计不会是一个大的贡献者，因为在突变体模拟中溶剂可及性仅略有增加，并且因为它埋藏在 rubrerythrin 同源二聚体的界面中。
