Native heme proteins cover a broad range of biological functions, including those which show redox-active ligand complexes. Therefore, it is of great interest to understand the role of the protein environment in modulating the heme cofactor's properties. Different orientations of the imidazole rings relative to heme can shift the heme redox potential and control the coordination of substrates to heme proteins and cytochromes. The molecular model systems built with the minimalistic structural requirements can help further to sort out the different factors and control mechanisms. The entire RCSB PDB database was searched to reveal these factors, and the heme proteins with at least one histidine ligand were analyzed. We analyzed a total of 693 hemes in 432 different crystal structures of heme proteins. The exhaustive analysis of available crystal structures of heme proteins has shown that two major factors determine the orientation of axial histidine ligands: (1) the interaction of the imidazole ring with the heme propionic acids and (2) the interaction with its histidine backbone. The results of the PDB study have been interpreted by a molecular force field and quantum-chemical computations, confirming that the emphasized interactions are mainly of electrostatic origin. The protein environment offers a sufficient number and different oriented hydrogen-bond acceptor groups, as was found in several detailed case studies. Surprisingly, based on the same analysis, the orientation of the ΝοΗ group of imidazole axially coordinated to heme does not often depend on a specific hydrogen-bond pattern with acceptor groups of the protein. Thus, the hydrogen-bond pattern is not often decisive, and it is probably the natural pathway to fine-tune the orientation of the ligated imidazoles. DFT computations revealed two main factors determining the imidazole orientation: (1) the direct intramolecular electrostatic interactions of propionic groups with the polar ΝοΗ groups of imidazole, and (2) the electrostatic interaction of the total dipole moment of the imidazole-heme complex with the reaction field. The theoretical and computational outstanding challenges in this area were also discussed. One of the purposes of the presented study is to shed some light on the histidine orientation in proteins and find a set of rales that control or govern histidine orientation.
Đorđević et al. (Sat,) studied this question.