Iso-1-Cytochrome C (PB ID: 4MU8) from Saccharomyces Cerevisiae
Created by: Nicholas
Ruloff
Cytochrome
C is a mobile protein in the mitochondria of bacteria that participates in the
electron transport chain. Usually, cytochrome is embedded in the membrane of
the cells and creates a gradient potential across the membrane (1). Iso-1-cytochrome C of saccharomyces cerevisiae, also known as yeast, which has a
PDB-ID of 4MU8, participates in the electron transport chain, which is involved
in ATP synthesis, but it also specifically participates in apoptosis, the protein
driven death of a cell (2,3). Iso-1-cytochrome C was crystallized at its
isoelectric point at a pH of 8.8 for study, and each protein weighs 12,182 Daltons
(4). Iso-1-cytochrome C of yeast has four major ligands: Glycerol, Sulfate
ions, tert-butyl alcohol and Protoporphyrin IX with iron. Glycerol and
tert-butyl alcohol participate in the crystallization of iso-1-cytochrome C.
The sulfate ions participate in the activation and deactivation of particular
residues. Protoporphyrin IX with iron is the key ligand that participates in
the electron transport chain (2).
Iso-1-cytochrome
C has two subunits. Both subunits are the same, and contain the same types and
amount of ligands. The subunits do not contain any beta sheets, however, random coils are present and each subunit has four alpha helices. Since both subunits
are the same, they perform the same function in the electron transport chain.
Also contained within each subunit is a water channel. His-18, Asn-52, Met-64, and
Leu-85 interact with water in this water channel. Additionally, water residue 119 and Tyr-67
interact with the water channel, specifically with Asn-52. These three residues control the closing and therefore the opening scheme of the water channel (2). Cytochrome
C has a large involvement with water, as water is used to remove protons from a
cell through the membrane. Cytochrome C uses water for its electron transport
chain participation (3). The Protoporphyrin IX with iron and specific water residues 114, 126, 136, and 149 form the buried water channel (2). The water channel
is used to create an electrochemical proton gradient that then allows for ATP
synthesis within the cell.
The sulfate
ion is an activating ligand. It interacts with Arg-38 by activating and stabilizing the protein from this residue (2). This activation then allows for
Protoporphyrin IX with iron to either be oxidized or reduced to move electrons
in the electron transport chain and create a gradient across the membrane. The Protoporphyrin IX with iron complex is crucial to the electron transport chain
because of its ability to be oxidized to iron(III) or reduced to iron(II).
Specifically, for oxidation, peroxidase activity is crucial and is defined as
the catalysis of oxidation of iron(II) to iron(III) by the decomposition of an
organic peroxide (5). The ability of Protoporphyrin IX with iron to be oxidized
and reduced allows for the transfer of charges through the water channel to
create an electrochemical proton gradient. Protoporphyrin IX with iron can be
determined as the most important ligand within the protein because of its
activity, and similarly found ligands can be seen in comparable proteins.
There are
two conformations of Iso-1-cytochrome C. In the extended conformation,
peroxidase activity is effective, and the electron transport chain continues.
In its compact conformation, peroxidase activity is not seen and the electron
transport chain stops (2). The activation by the sulfate ion allows for the
protein to alter its conformation between the extended and compact
conformations to induce or stop the electron transport chain. The differences
between conformations, along with the closing scheme that can occur between
residues Asn-52, Water-119 and Tyr-67, demonstrates two different styles of activating
and deactivating the electron transport chain (2). These two checkpoints for
the activation of the electron transport chain indicate two requirements of the
electron transport chain. Water must be present for the electron transport
chain to be active, otherwise hydrogen bonding between Asn-52, Water-119 and Tyr-67
close the water channel in order to keep water levels regular in the yeast
cell. But it also mainly stops the water channels function for the formation of
an electrochemical gradient to synthesize ATP. Sulfate ions must also be
present, and in high enough concentration for the activation of Arg-38,
otherwise the protein will not make the correct conformation and peroxidase
activity with end. Cell activity generally has multiple requirements, but these
requirements indicate whether the cell is healthy and has the nutrients to
participate in the electron transport chain. If the cell happens to be
unhealthy, then electron transport can be mitigated until balance is reassured
inside of the cell membrane, otherwise the water channel would be used to
continuously create an electrochemical gradient that would be unnecessary when
ATP synthesis is unable to occur.
Apoptosis
occurs when a cell is determined to be inefficient and cell death must occur
(3). Cell division rapidly occurs throughout an organism, and without a method
of removal of old cells, the organism would keep its multiplying cells and
grown larger. However, cells become ineffective over time, and therefore a
method of removal is necessary, and this is done through intercellular and
intracellular regulation by apoptosis. The mitochondria release the cytochrome
c into the cytosol and the protein binds to another protein, signaling to begin
the intracellular programmed death (3). By this method, a cell can
self-determine by its effectiveness whether or not it is beneficial to the
organism. If it is ineffective, then the Iso-1-cytochrome C can activate the
destruction of the cell so that surrounding cells can use the nutrients left in
the cytosol.
Other
proteins have extreme similarities to Iso-1-cytochrome C, and these
similarities are found through comparisons of the sequence of the proteins and
comparisons of the structure of the proteins. Two programs perform these
comparisons: PSI-BLAST and the Dali server. The purpose of PSI-BLAST is to find
similarity in the sequences of proteins in order to compare those proteins with
similar primary structure, while the purpose of the Dali Server is to compare
three-dimensional structures of proteins in the protein data bank by comparing
the intramolecular distances of two proteins when superimposed upon one another
(6,7). The PSI-BLAST program ranks protein similarities with an E value. The
lower the E value is, the higher the similarities are between the compared
proteins. The Dali server, however, ranks protein similarities with a Z value,
and the higher the Z value is indicative of higher similarity in the
three-dimensional structures of the compared proteins. Ferricytochrome C is a
protein that demonstrated both a high Z value and a low E value, meaning that
its sequence and three-dimensional structure are very comparable to
Iso-1-cytochrome C.
Ferricytochrome C, with a PDB-ID of 1CCR, is a protein that is found in rice, and is also part
of the electron transport chain (8). In comparison to Iso-1-cytochrome C, it
has an E and Z value of 6 x 10-51 and 20.6 respectively, and has a
mass of 12,271 Daltons (9). Ferricytochrome C contains only one subunit, in
which there are many similarities to Iso-1-Cytochrome C including only
containing alpha helices and random coils. Ferricytochrome C, however, does not
require sulfate ions to be activated and therefore peroxidase activity is more
readily active. Even though Ferricytochrome C is only one subunit, which is
extremely similar to both subunits of Iso-1-Cytochrome C, it only has an eighth
of the water molecules as ligands compared to Iso-1-Cytochrome C. This means
that the water channel for Ferricytochrome C is much shorter than in
Iso-1-cytochrome C, and therefore an electrochemical proton gradient would be
easier to make because the transfer of charges occurs over a shorter distance.
Ferricytochrome C also has a proton ligand to the Protoporphyrin IX with iron
complex that interacts with iron, which is not seen in Iso-1-Cytochrome C.
Another
comparable protein is Cytochrome C found in mice, which has a PDB-ID of 2AIU
and a mass of 11,714 Daltons (10,11). With E and Z scores of 3 x 10-52
and 21.3 respectively, Cytochrome C in mice has more similarities with
iso-1-cytochrome C than Ferricytochrome C. Similarly seen in the cytochrome
proteins before, Cytochrome C in mice also contains Protoporphyrin IX with
iron, and therefore undergoes similar processes in the electron transport chain
as both Iso-1-cytochrome C and Ferricytochrome C. Differently from
Ferricytochrome C, Cytochrome C in mice has a phosphate ion activation that is
comparable to the sulfate ion activation in Iso-1-cytochrome C. This, however,
means that Cytochrome C found in mice and Iso-1-cytochrome C are activated by
differing signaling methods, and the use of a phosphate ion as a signal would
be useful for the synthesis of ATP since the compound contains three phosphate
ion groups.
Human cells
also contain Cytochrome C that interacts in the electron transport chain. A mutant protein of human Cytochrome C, with a PDB-ID of 3ZOO, that was
crystalized and had its structure determined was also extremely similar to
Iso-1-cytochrome C (12). The E and Z scores for the PSI-BLAST and Dali server
were 1 x 10-50 and 21.6 respectively. The mutant protein of human
Cytochrome C has a mass of 11,749 Daltons (13). This indicates that the mutant
human Cytochrome C has a more similar three-dimensional structure to
Iso-1-cytochrome C than Cytochrome C in mice and Ferricytochrome in rice,
however, the sequence of amino acids has a higher differentiation to
Iso-1-cytochrome C than the other two comparable proteins.
The
importance of Iso-1-cytochrome C is the same as the three other compared
proteins: to participate in the electron transport chain. The electron
transport chain creates an electrochemical proton gradient across the membrane
for the formation of ATP. The crucial parts of all three of these proteins are
the water channels formed and the Protoporphyrin IX with iron complex. The
water channel brings the reagents necessary to create a gradient across the
membrane, while the protein as a whole acts as a parent catalyst that align the
molecules necessary for reaction with the Protoporphyrin IX with iron complex.
Without this protein, the electron transport chain cannot occur because of the
unlikelihood of the reactions around the Protoporphyrin IX with iron complex
without the guidance of Iso-1-Cytochrome C.