Banci L, Carloni P, Savellini G G
Department of Chemistry, University of Florence, Italy.
Biochemistry. 1994 Oct 18;33(41):12356-66. doi: 10.1021/bi00207a002.
Molecular dynamics (MD) calculations are performed on cytochrome c peroxidase (CcP) and on horseradish peroxidase, isoenzyme C (HRP), and its substrate adduct with p-cresol. For CcP, a refinement in solution of the X-ray structure is obtained which indicates that in solution the protein structure is very similar to that in the crystal. For HRP, the X-ray structure is not available. We have generated a model of this protein based on the recently reported structure of the similar lignin peroxidase (LiP) protein. This model involves the entire system as all the amino acid residues match the sequence. This HRP model was refined through energy minimization and MD calculations. A refined structural model for HRP, for the first time involving the entire protein, is therefore now available. The tertiary structure of HRP is close to that of LiP, and also the active site in the two proteins has significantly similar structures. The well-ordered water molecules and the extensive H-bond network present in the X-ray structure of CcP is maintained in the dynamics without any constraints, indicating that the active site residues produce a field strong enough to make all these interactions quite stable. Interestingly, also in HRP a network of ordered water molecules and H-bonds is present, again without constraints. This is consistent with the similarities of the active sites in the two proteins. Finally, we have calculated the MD structure of the adduct of HRP and a substrate molecule, p-cresol. This structural model is compared with the NMR data, which are in fairly good agreement. The binding site and the protein-substrate interactions are discussed.
对细胞色素c过氧化物酶（CcP）、辣根过氧化物酶同工酶C（HRP）及其与对甲酚的底物加合物进行了分子动力学（MD）计算。对于CcP，获得了其X射线结构在溶液中的优化结果，表明在溶液中蛋白质结构与晶体中的非常相似。对于HRP，尚无X射线结构。我们基于最近报道的类似木质素过氧化物酶（LiP）蛋白的结构生成了该蛋白的模型。该模型涵盖了整个系统，因为所有氨基酸残基都与序列匹配。通过能量最小化和MD计算对该HRP模型进行了优化。因此，现在首次有了一个涵盖整个蛋白质的优化的HRP结构模型。HRP的三级结构与LiP的接近，并且两种蛋白质的活性位点结构也明显相似。在动力学过程中，CcP的X射线结构中存在的有序水分子和广泛的氢键网络得以无约束地维持，这表明活性位点残基产生了足够强的场，使所有这些相互作用相当稳定。有趣的是，在HRP中也存在有序水分子和氢键网络，同样没有约束。这与两种蛋白质活性位点的相似性一致。最后，我们计算了HRP与底物分子对甲酚加合物的MD结构。将该结构模型与NMR数据进行了比较，二者相当吻合。讨论了结合位点和蛋白质 - 底物相互作用。
