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

Abstract

In this study we have described the p-p and cation-p interactions between the porphyrin ring and the protein part of porphyrin-containing proteins to better understand their stabilizing role. The number of pp interactions was higher than that of cation-p interactions in the same set of proteins studied. The pyrrole groups of one porphyrin can be involved in p-p interactions with p systems of another porphyrin in the protein. We have found 5.1% cation-p interactions between porphyrin Fe 2+ metal cations and p systems of surrounding amino acids as well as the pyrrole rings of other porphyrins. We observed that most of the p-p interactions have an energy in the range 20.5 to 22.0 kcal mol 21 , while the cation-p interactions showed an energy in the range 22 to 24 kcal mol 21. Further, an appreciable number of metal/cation-p interaction pairs have an energy in the range 26 to 213 kcal mol 21. The preferred parallel-stacked orientation is found to be more stable than a T-shaped structure for the full set of p-p interaction pairs. In the case of cation-p interactions, it was found that 44% of the cation-p 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 p 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.

Amide-π interactions in active centers of superoxide dismutase

“…There is no significant statistical difference in the  angle distribution between the multiple and the single amide- interactions. The preferred orientations are quite similar to those found in aromatic-aromatic interactions, 47 and T-shaped orientation is observed. In the parallel-stacked case, van der Waals contribution is the dominant effect and the electrostatics contribution is actually repulsive, although small in value (<1 kcal mol -1 ).…”

Elucidating a chemical defense mechanism of Antarctic sponges: A computational study

“…Although aromatic interactions are often grouped together, several distinct types are observed, each with their own characteristic stabilities: sandwiched, parallel displaced, T-shaped, edge-to-face; cation-π interactions also represent stabilizing interactions found in proteins ( Figure 5). 85,86,87,88,89,90,91,92…”

“…Figure 5: Illustration of stabilizing aromatic (π-π, cation-π) interactions with their corresponding estimated stabilization energies. 85,89,87,86,90,91,92 It should be noted that all of the π-π interaction energies shown here were calculated in the gas phase, while the cation-π term was calculated in solution: Commonly seen ring-ring centroid distances between aromatic residues in such clusters are between 5-8Å. 84 Furthermore, they concluded that aromatic substrates should preferentially bind in protein active sites with significant aromatic character.…”

Investigations on the role of cation-π interactions in active centers of superoxide dismutase

“…9,20 Generally the composition of cation- interaction forming residues is similar to other globular proteins. [39][40][41][42] The organization of multicomponent supramolecular assemblies is often governed by multiple noncovalent interactions. 43 Ternary complexes are the…”