Jensen G M, Warshel A, Stephens P J
Department of Chemistry, University of Southern California, Los Angeles 90089.
Biochemistry. 1994 Sep 13;33(36):10911-24. doi: 10.1021/bi00202a010.
Calculations of the redox potentials of the 2-/3-couples of [Fe4S4Cys4] clusters in the iron-sulfur proteins Peptococcus aerogenes ferredoxin (PaFd), Azotobacter vinelandii ferredoxin I (AvFdI) and Chromatium vinosum high potential iron protein (CvHiPIP) based on the Protein Dipoles Langevin Dipoles (PDLD) method are reported. The structures of these proteins have been determined by X-ray crystallography; in the case of PaFd the structure has recently been revised due to a change in the sequence close to Cluster II. The large differences between the potentials of the [Fe4S4Cys4] clusters of PaFd and AvFdI and the potential of the [Fe4S*4Cys4] cluster of CvHiPIP are successfully modeled and originate principally in differences in the configuration of main-chain amide groups near the clusters. The small difference between the potentials of PaFd and AvFdI is also satisfactorily modeled in the case of Cluster I of PaFd. Solvent dipoles close to the cluster in PaFd are an important contributor to its higher potential. The two X-ray structures of PaFd yield similar results for Cluster I of PaFd. In contrast, the results for Cluster II differ substantially; for reasons not yet clear, the recently revised structure leads to results in worse agreement with experiment.
报道了基于蛋白质偶极子朗之万偶极子（PDLD）方法对铁硫蛋白产气消化球菌铁氧化还原蛋白（PaFd）、棕色固氮菌铁氧化还原蛋白I（AvFdI）和嗜硫小红卵菌高电位铁蛋白（CvHiPIP）中[Fe4S4Cys4]簇的2-/3-偶极子氧化还原电位的计算。这些蛋白质的结构已通过X射线晶体学确定；就PaFd而言，由于靠近簇II的序列变化，其结构最近已被修正。成功模拟了PaFd和AvFdI的[Fe4S4Cys4]簇电位与CvHiPIP的[Fe4S*4Cys4]簇电位之间的巨大差异，其主要源于簇附近主链酰胺基团构型的差异。在PaFd的簇I的情况下，也令人满意地模拟了PaFd和AvFdI电位之间的微小差异。PaFd中靠近簇的溶剂偶极子是其较高电位的一个重要贡献因素。PaFd的两种X射线结构对PaFd的簇I产生了相似的结果。相比之下，簇II的结果有很大差异；由于尚不清楚的原因，最近修正的结构导致与实验的一致性更差。
