Principles of Protein Structure - G. Schulz 1982

Protein–ligand interactions
Heme binding sites
Bonds between heme and apoprotein

Sixty apoprotein atoms participate in Structure/103.html">Van der Waals contacts with the porphyrin ring. The primary similarity among Hemoglobins, Cytochromes c, and cytochromes b is that in all these molecules, the heme group resides within a cavity formed by the side chains of nonpolar Amino Acids. In the Hemoglobin subunit, approximately 60 atoms are involved in van der Waals contacts with the atoms of the porphyrin cycle [60].

* Protoheme IX is also referred to as ferriprotoporphyrin IX [633]. For the purposes of our Discussion, the tetrapyrrole ring of this compound can be considered planar. Attached to this cyclic system are eight side chains: four methyl, two vinyl, and two propionate groups (Fig. 10.2). "Proto" refers to the Water/144.html">Origin of the compound, while "IX" designates the order in which the side groups alternate.

The interaction between the heme and apoprotein side chains can occur via all known modes of binding. The heme side chains perform diverse roles in different Hemoproteins. In cytochrome c, both vinyl groups (or only one in exceptional cases [509]) form covalent bonds with Cys-14 and Cys-17 of the apoprotein; one charged propionate group is located on the molecular surface, whereas the second interacts via a Hydrogen bond—likely of functional significance—with the interior of the molecule. One or both propionate groups appear essential for the structure or function (or both) of horseradish peroxidase [641] and cytochrome b from the golden bean [642].

In the cases of cytochrome b₅ and hemoglobin, earlier studies indicated that the side groups play only a minor and nonspecific role [560, 568, 637]. However, The Significance of individual heme side chains has been re-evaluated in light of recent X-Ray Diffraction data [565, 566]. In the heme-containing fragment of cytochrome b₅, for instance, one propionate group may directly participate in the redox cycle by neutralizing the excess positive charge of the iron atom in ferricytochrome b₅ and binding to another cationic group of ferrocytochrome b₅ [556].

The atoms of the His and Met side chains coordinate the heme iron atom.

In cytochrome b₅, the iron atom exhibits a symmetrical coordination geometry formed by six octahedral Ligand positions occupied by the four pyrrole nitrogen atoms of the heme and the two ε-nitrogen atoms of His-39 and His-63 located in axial positions [297]. The δ-nitrogen atoms of His-39 and His-63 form Hydrogen Bonds with the backbone carbonyl oxygen atoms in such a way that both imidazole rings are rigidly anchored by the rigid STRUCTURE OF THE polypeptide backbone.

Hemoglobins and cytochromes c share identical ligands, but their molecules differ in that one of the axial coordination sites is occupied by an O₂ molecule and a Methionine sulfur atom, respectively. In the absence of an O₂ molecule, the sixth coordination site (the "ligand pocket") of hemoglobin remains unoccupied [60, 636, 643]. It is suggested that in bacterial cytochrome c, both axial ligand positions are vacant. Apparently, in this case, the polypeptide chain surrounding the heme adopts a conformation that prevents the binding of potential ligands [644].