XH/π interactions with the π system of porphyrin ring in porphyrin-containing proteins

Abstract

Searching structures of porphyrin-containing proteins from the Protein Data Bank revealed that the pi system of every porphyrin ring is involved in XH/pi interactions, with most of the porphyrins having several interactions. Both five-membered pyrrole rings and six-membered chelate rings are involved in XH/pi interactions; the number of interactions with five-membered rings is larger than the number of interactions with six-membered rings. We found interactions with C-H and N-H groups as hydrogen-atom donors; however, the number of CH/pi interactions is much larger than the number of NH/pi interactions. The amino acids involved in the interactions show a high conservation score. Our results that every porphyrin is involved in XH/pi interactions and that amino acids involved in these interactions are highly conserved demonstrate that XH/pi interactions play an important role in porphyrin-protein stability.

Hydrogen Bonds and Hydrophobic Interactions of Porphyrins in Porphyrin-Containing Proteins

“…In order to find out the importance of different noncovalent interactions of the porphyrin ring in proteins, in our previous work we studied the conservation of the residues involved in the interactions [23]. The data about the average conservation scores are calculated for four groups of amino acids in binding pocket; for the amino acids involved in the XH/ (X = N, C) interactions with porphyrin ring, in hydrogen bonds, in hydrophobic interactions, and for the amino acids that are not involved in any type of the interactions with the porphyrin [23].…”

“…Searching structures of porphyrincontaining proteins from the Protein Data Bank it was revealed that -system of every porphyrin ring is involved in CH/ interactions and most of the porphyrins are making several interactions. The amino acids involved in the interactions show high conservation score indicating that CH/ interactions play an important role in the porphyrinprotein stability [23].…”

“…In our previous work we showed that porphyrin -system in metal complexes and in proteins could be involved in CH/ interactions [22,23]. Searching structures of porphyrincontaining proteins from the Protein Data Bank it was revealed that -system of every porphyrin ring is involved in CH/ interactions and most of the porphyrins are making several interactions.…”

Noncovalent Interactions of π‐Systems in Crystal Structures of Transition‐Metal Complexes

“…. .π and stacking interactions of chelate rings [8,[18][19][20][21][22][23][24][25][26][27][28]. Other groups have reported CH.…”

“…These chelate ring π -systems can potentially be involved in CH-π interactions. Such interactions have been identified in the crystal structures of transition-metal complexes [21,22] and in structures of porphyrin-containing proteins [23]. A summary is presented below.…”