Cytochrome c
created by Salman Humayon
Cytochrome c (pdb ID 2B4Z) from bovine heart is a heme protein that is found in the mitochondria and is involved the electron chain transfer. Acting as an intermediate cytochrome c accepts electrons from Mitochondrial Electron Transport Complex III and transfers it to Mitochondrial Electron Transport Complex IV (Grisham, 652). Cytochrome c is also involved in the process of apoptosis which is the programmed death of cells (Miles, 7). The molecular weight of cytochrome c is 11572.35 Da (Expasy).
The structure of cytochrome c is directly linked with its function. Its primary structure is composed of 104 residues (Mirkin, 3). The tertiary structure’s most important role is that it has the heme group which interacts with its residues. Three residues of interest are Gln-12, Gln16, and Gln-42 which are susceptible to deaminidation (Mirkin, 86). These are symmetry-related molecules that are in close contact with their neighboring amino acids in the crystal phase. Gln-12 is 5.5 Å from Lys-39, Gln-16 is 4.9 Å from Glu-61, and Gln-42 is 3.49 Å from Lys-73 (Mirkin, 86). Deaminidation is often referred to as deamination and is the removal of an amine group from a molecule for an OH group (Mcllwain, 100). The heme group contained in cytochrome c interacts axially with His-18 and Met-80 (Mirkin 86). This heme group contains a heme c which is an iron protoporphyrin IX with covalent cysteine attachments (Grisham, 652). 40% of the structure of cytochrome c is helical and 1% is beta sheet.
Cytochrome c which is found inside the mitochondria is responsible for apoptosis. Cytochrome c is associated with cardiolipin (diphosphatidylglycerol) and when peroxidase activity of cytochrome c oxidizes the cardiolipin lipid chain the cytochrome c is released from the cardiolipin membrane. Then cytochrome c binds to an apoptic protease-activating factor 1 (Apaf-1) molecule in its locked form and experiences dATP hydrolysis. Then after seven of these structures combine in a spherical form “the opening of pores in the outer membrane, induced by a variety of triggering agents, releases cytochrome c to the cytosol, where it initiates the events of apoptosis” (Grisham, 675).
A comparison between the cytochrome c in the bovine heart and the cytochrome c in horse heart can be made. The horse heart cytochrome c is similar except that its glutamines residues, Gln-12, Gln-16, and Gln-42, are further apart from its neighbors. For horse heart cytochrome c the Gln 12-is 6 Å from Lys-39, Gln-16 is 8.52 Å from Glu-61, and Gln-42 is 3.94 Å from Lys-73 (Mirkin, 87). The most notable change in distances is the Gln-16 to Glu-61 which is about as twice as big as the distance found for the bovine heart cytochrome c.
The glutamines that are susceptible to deaminidation allow for better electrical charge transfer and allow for easier crystallization (Markin, 87). These glutamines, Gln-12, Gln-16, and Gln-42, are easily crystalized. Crystallization is wanted because it can transfer electrons more efficiently. The secondary structure of cytochrome c is important for this reason. It enables the glutamines to be exposed and be susceptible to deamidination. The tertiary structure holds the iron protoporphyrin IX with covalent cysteine attachments, the heme group, in the position where it can help with electron transfer (by axially interacting with His-18 and Met-80). The heme group’s electron facilitation confirms it to be a promising biosensor (Mirkin, 89). Biosensor is a device that allows for simple quantitative measurements of a biological signal from something it is in direct contact with (Tokas, Slide 2).
The deaminidation effect in horse heart cytochrome c is not as effective as the bovine heart cytochrome c and so the consequences for the bovine heart cytochrome c are greater (Mirkin, 87). The longer distance between glutamine residues and their neighbors in the horse heart cytochrome c do not allow for as easy deaminidation. This results in less crystallization and less efficiency in electron transfer. The tertiary structure still facilitates electron transfer with the use of iron protoporphyrin IX with covalent cysteine attachments.
PSI-Blast (Blast) server was used to find protein structures that are similar to bovine heart cytochrome c. Blast uses the primary structure of a protein and finds proteins with the closest similarity in primary structure (Blast). After finding proteins with similar primary structure it assigns them an “E” value. The E value has an inverse relationship with how similar the primary structure of the query protein is to the subject protein (the protein that came as a result of the search). E value is increased for every difference or gap between the two primary structures and is decreased for similar primary structure. An important distinction then to make is that mutations will increase the E value. After running a search on Blast the cytochrome c protein from horse heart had an E value of 3e^-74. This small value indicates that most of the primary structure of the query and subject protein is very similar. There was also a search done with the Dali server which compares the tertiary structure of proteins for similarities with the query protein. Proteins with similar residue distances and therefore similar folds will have a “Z” score above 2 (Dali). After running the sequence on the Dali server the horse heart cytochrome c was found with a Z score of 17.2. This high score is expected because the horse heart cytochrome c was very similar in structure but had larger distances between some residues compared to the query protein. The ExPASy server was used to find the isoelectric point which is 9.52. The isoelectric point is the pH at which the net charge is zero and carries no electrical charge (The Free Dictionary.com, 2012).