Cytochrome C
Created by Sooin Lee
The main physiological role of
Cytochrome c is to transport electrons across the membranes of mitochondria (6). It is an essential component of the electron transport chain which ultimately supports ATP generation inside a cell. Another major role of Cytochrome C is to trigger programmed cell death through apoptosis upon apoptotic stimulus (1). Therefore, a deficiency of Cytochrome c will cause embryonic lethality and attenuate stress induced apoptosis since apoptosis is responsible for DNA damage and other cell stress responses (7).
Cytochrome c has a molecular weight of 11572.35 g/mol and an isoelectric point at a pH of 9.52. Cytochrome c consists of 104 amino acids in a single chain A and has a
secondary structure including both alpha helices and beta sheets. It is composed of 40% alpha helices including 5 helices among 42 residues, 1% beta sheet including 2 strands on 2 residues, and 59% random coils. ( However, 1% of beta sheet is not recognized by the software and will not be shown in the secondary structure link.) Since there is only one subunit, Cytochrome c is not an oligomer. There are nine hydrogen bonds in Cytochrome c. A hydrogen bond between two residues,
Cysteine-14 and Histidine-18, is known to be one of the most critical hydrogen bonds for protein stability as it plays an important role in orienting side chains for heme ligation (3).
Cytochrome c is a hemeprotein with a
prosthetic group that consists of an iron atom contained in the center of a porphyrin, a large heterocyclic organic ring (3). Cytochrome c originates from Heme C, which is different from other heme proteins due to two
thioether linkages between C-14 and C-17(2). Since heme is an asymmetrical structure, the covalent bonds between the vinyl groups of the porphyrin and cysteine residues should be specifically oriented to be recognized by an enzyme that catalyzes the formation of the covalent attachment of the porphyrin ligand (2). The role of heme moiety in the native conformation of Cytochrome c is to form an ordered complex in order to maintain a thermodynamically favorable state (2). As a prosthetic group, Cytochrome c has iron as an associated metal ion. This iron atom is essential for the enzymatic function and stabilization of the structure (3). The iron atom which is located in the center of the heme molecule is responsible of transporting electron through the respiratory chain where iron atom exists in the ferrous state when Cytochrome c is reduced until it becomes oxidized again (3). The coordination of iron to Methionine-80 and Histidine-18 also plays an important role in the formation of the gross structure of Cytochrome c (2).
There is a HEME ligation associated with Cytochrome, which is a Protoporphyrin IX containing an
Fe atom. HEME has a formula of C34H32FeN4O4 and a molecular weight of 616.49 g/mol. This iron protoporphyrin IX is an active site which is connected to one or two protein-donated axial ligands which influence the reactivity of the heme iron (4). The heme iron is six-coordinate and low-spin with axial ligands derived specifically from histidine, lysine, or methionine (4). In cytochrome c, this ligand is coordinated to a protein-donated
Histidine 18 and Methionine 80 residues (4). The heme axial ligation is designed to mimic oxygen activation chemistry (4).
Cytochrome C exhibits its electron transport activity through the formation of complexes with its redox partners: reductase (complex III) and oxidase (complex IV) (5). The universal site of the cytochrome c interaction with two complexes consists of the central hydrophobic domain and the electrostatic domain (5). While electrostatic interactions determine the correct spatial orientation of the contacting proteins, the hydrophobic interactions are often considered to be the main force for protein stabilization (5). Therefore, the electrostatic interactions between positively charged lysine residues on the surface of Cytochrome c around the heme cavity and negatively charged residues of amino acids on subunits play a significant role in forming complexes of Cytochrome c and complex III or complex IV of the respiratory chain(5).
Moreover, residue
Lysine-72 plays a significant role in the apoptotic pathway and is a second major function of Cytochrome c. When the cell detects an apoptotic stimulus, the intrinsic apoptotic pathway is triggered, and mitochondrial cytochrome c is released into the cytosol to engage the APAF1, an apoptotic protease-activating factor-1(1). Lysine-72 is important because it provides stability to the cytochrome c and APAF interactions (1). Any mutations of the Lysine 72 will result in a decrease in the apoptotic activity depending on its substitutes for Lysine 72, however, there is no known disease directly associated with this mutation(1).
In addition, two proteins with similar structure from the Deli Structural Alignment test were selected for a structure comparison. The
first protein is a complex protein called an
anti-Cytochrome c antibody (PDB ID = 1WEJ) consisting of E8 antibodies from Mus musculus and Cytochrome c from Equus caballus has three
subunits.
Chain F consists of 105 residues with 40% alpha helices including 5 helices among 43 residues and 1% beta sheets including 2 strands on 2 residues. It also has a modified residue of ACE 0 (Acetyl group).
Chain H is an E8 antibody with 223 residues including 8% alpha helices including 6 helices among 19 residues and 49% beta sheets including 21 strands on 110 residues.
Chain L is an E8 antibody with 214 residues including 6% alpha helices including 3 helices among 13 residues and 52% beta sheets including 21 strands on 113 residues. The presence of two E8 antibodies adds an important immunological and biochemical function as it has the ability to recognize a specific antigen (8). Since cytochrome c is a paradigm in the study of antibody-antigen interactions, it is widely used as a model protein antigen, combined with E8 antibodies for further research in the conformation of antigen (8).
The
second protein is cytochrome c (PDB IS = 1CRC) from Equus caballus (common name-horse). This protein has two
subunits where only one unique sequence exists for both chains. Both
Chain A and
Chain B consist of 105 residues with 40% alpha helices, including five helices among 43 residues and 1% beta sheets including two strands. The only difference between cow cytochrome c and horse cytochrome c is the modified residue of ACE 0 (8). This protein has basically the same function as cytochrome c from a cow in the intermembrane space of mitochondria (9). Important residues such as 61, 83, and 87-89 are responsible for enzymatic interaction with the multiple redox partners, while
Tyr-48 and Trp-59 are the main components for forming the native environment for the buried heme (9).