Carbon Content and Half Life of Proteins

Sneha Nirmala John, Anisha Jayakumar, AN.Kaarthik, J.Jannet Vennila and E.Rajasekaran*
Department of Bioinformatics, School of Biotechnology and Health Sciences
Karunya University, Coimbatore– 641114
Tamil Nadu, India. *email: ersekaran@gmail.com

Abstract— Carbon is the single most element in protein

responsible for hydrophobic interaction. Carbon distribution
and its relevance to half life are investigated here. One of the
shortest lived proteins ornithine carboxylase is taken for this
purpose. The result reveals that high carbon content along this
protein sequence make the protein to misfold that causes the
reduction of half life. Reduction of carbon content might
improve the stability and half life of this shot lived protein. A
stretch of sequence that is unfolded is also considered
responsible for instability or short life. Carbon accumulation
leads to misfolding and reduces half life. Similarly reduction of
carbon content leads to unfolding that also reduces half life. In
another term, protein which has higher carbon content is
generally labile, less stable and less half life and protein with
less carbon content is hydrophilic and has less half life. It is
recommended that a uniform distribution with optimum level
of carbon content will give a long life. Also addition of
III. RESULTS AND DISCUSSION
Hydrophobicity seems to be responsible for half life of a
protein. The distribution of carbon along the sequence is very
important towards this hydrophobicity. The carbon
distribution profile of two short half life proteins (ornithine
carbylase and clusterin) and a normal (proteasome) protein is
studied here. The figures 1-3 show the carbon distribution
profile of these proteins. A line at 31.45% indicates the
optimum value of carbon. Distribution around this value
leads stability of the protein that gives long half life.
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% of Carbon

hydrophobic residue at N-terminal might increase the half life 33

of a protein.
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Keywords- carbon distribution; protein half-life; carbon
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profile; proteasome; ornithine carboxylase; hydrophobicity;

I. INTRODUCTIOMN 30

The form of hydrophobic interaction in folding and 29

binding of protein is dominated by carbon element alone. 0 200 Residue 400
Number 600
This carbon distribution makes the protein to fold in some
fashion to have a particular structure to carry out a Fig 1. Carbon content in ornithine carboxylase, a short lived protein.
biochemical reaction. Proteins are continually produced and High carbon content leads to misfolding and labile.
degraded in cells. The time taken for degradation of proteins
varies from one protein to another. This is measured as half- 35
life a protein. The physical nature (misfold or unfold) in
protein reduces half life. What is the factor then that 34
determines the misfold or unfolds? To address this problem a 33
carbon distribution study has been taken up here.
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II. METHODOLOGY
The protein sequences of ornithine carboxylase, clusterin 30
and proteasome are collected from the NCBI. The carbon 29
distributions profiles are obtained from CARBANA program 0 50 100 150 200 250 300 350 400 450
available online which uses the principle of 31.45% of
carbon. The step value of 17 and 500 atoms for statistical
average are considered in this analysis. The results on carbon
percentage versus amino acid number are plotted as shown in Fig.2. Carbon content in clusterin protein of human. Reduction of carbon
figures. content in a long portion of the sequence leads to nonfolding and short half
life.

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0 100 200
Fig.3. Carbon content in proteasome protein of human (normal protein)
Ornithine carboxylase is a shortest lived protein. Its
stability is determined by arrangement of three dimensional
structure. The carbon distribution (fig 1) is responsible for
this. Any misfolded or unfolded proteins are generally less
stable. Ornithine carboxylase shows vary high carbon
content all along the sequence. Due to this there are strains
in the protein that makes the protein to misfolded and
degrades quickly. Figure 2 shows the carbon distribution in
clusterin protein of human, a short half life protein. This
protein shows up a long hydrophilic unfold region (20-107).
This region makes the protein to unstable. The reduction of
half life is due to this region. The tension in this region can
be reduced by adding hydrophobic groups. The region
between 177 and 275 contain rich of carbon content. This is
again causing misfolding that reduces half life this protein.
The region between 275 and 330 is also hydrophilic in
nature, causing unfolding that reduces half life. The carbon
distribution in proteasome (degradation responsible protein)
is reported in figure 3. The carbon distribution profile is
normal. This is a typical example of normal protein for
comparison. There is no abnormality.
All these investigation results are applicable to globular
protein. A proteins which has small half life is either labile
(containing higher carbon content) or unstable (containing
less carbon content). The hydrophobic residue at N-terminal
is also a factor that decides half life. Upon burial of this end
residue acid, it is not available for interaction.
IV. CONCLUSION
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Carbon distribution in protein plays a vital role
misfolding and half life. Carbon accumulation leads to
misfolding and reduces the half life a protein. Similarly
reduction of carbon leads to unfolding that also reduces half
life. In another term, protein which has higher carbon
content is generally labile, less stable and short half life and
protein with less carbon content, hydrophilic and again short
half life. It is recommended that a uniform distribution with
optimum level of carbon content will give a long half life.
REFERENCE
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