π–π and cation–π interactions in protein–porphyrin complex crystal structures

Abstract

In this study we have described the π–π and cation–π interactions between the porphyrin ring and the protein part of porphyrin-containing proteins to better understand their stabilizing role. The number of π–π interactions was higher than that of cation–π interactions in the same set of proteins studied. The pyrrole groups of one porphyrin can be involved in π–π interactions with π systems of another porphyrin in the protein. We have found 5.1% cation–π interactions between porphyrin Fe²⁺ metal cations and π systems of surrounding amino acids as well as the pyrrole rings of other porphyrins. We observed that most of the π–π interactions have an energy in the range −0.5 to −2.0 kcal mol⁻¹, while the cation–π interactions showed an energy in the range −2 to −4 kcal mol⁻¹. Further, an appreciable number of metal/cation–π interaction pairs have an energy in the range −6 to −13 kcal mol⁻¹. The preferred parallel-stacked orientation is found to be more stable than a T-shaped structure for the full set of π–π interaction pairs. In the case of cation–π interactions, it was found that 44% of the cation–π interactions involved planar stacking, 37% of the interactions belonged to the oblique category, and the remaining 19% of the interactions were of the orthogonal type. The separation distance between the cation group and the aromatic ring decreases as the interplanar angle decreases. Furthermore, in the present study we have found that 10.4% of π residues and 3.9% of cationic residues were found to have one or more stabilization centers. Amino acids deployed in the environment of porphyrin rings are deposited in helices and coils. The results from this study might be used for structure-based porphyrin protein prediction and as scaffolds for future porphyrin-containing protein design.