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A topological description of hubs in amino Acid interaction networks.

Gaci O - Adv Bioinformatics (2010)

Bottom Line: Once we have compared this type of graphs to the general model of scale-free networks, we analyze the existence of nodes which highly interact, the hubs.We describe these nodes taking into account their position in the primary structure to study their apparition frequency in the folded proteins.Finally, we observe that their interaction level is a consequence of the general rules which govern the folding process.

View Article: PubMed Central - PubMed

Affiliation: Le Havre University, LITIS EA 4108, BP 540, 76058 Le Havre, France.

ABSTRACT
We represent proteins by amino acid interaction networks. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. Once we have compared this type of graphs to the general model of scale-free networks, we analyze the existence of nodes which highly interact, the hubs. We describe these nodes taking into account their position in the primary structure to study their apparition frequency in the folded proteins. Finally, we observe that their interaction level is a consequence of the general rules which govern the folding process.

No MeSH data available.


Each time a hub interacts, we add one to its occurrence score and then deduce an occurrence probability for the amino acids to act as a hub in an SSE-IN. We repeat the process grouping the SSE-INs by their family and also by their structural class. The probability of an amino acid Ala being a hub is the stronger independently of the protein classifications.
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fig6: Each time a hub interacts, we add one to its occurrence score and then deduce an occurrence probability for the amino acids to act as a hub in an SSE-IN. We repeat the process grouping the SSE-INs by their family and also by their structural class. The probability of an amino acid Ala being a hub is the stronger independently of the protein classifications.

Mentions: We also compute the occurrence level of hubs, that is their number of appearances on each protein SSE-IN. We accumulated this score at the SCOP class level to obtain the probability for each amino acid to be a hub in a protein SSE-IN; see Figure 6. We can remark the existence of peaks which show clearly a strong tendency of amino acids Ala, Cys, Gly, Leu, and Val to have a high interactivity within the folded protein. Thus, there are the same amino acids which play the role of hubs independently of structural families.


A topological description of hubs in amino Acid interaction networks.

Gaci O - Adv Bioinformatics (2010)

Each time a hub interacts, we add one to its occurrence score and then deduce an occurrence probability for the amino acids to act as a hub in an SSE-IN. We repeat the process grouping the SSE-INs by their family and also by their structural class. The probability of an amino acid Ala being a hub is the stronger independently of the protein classifications.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2877201&req=5

fig6: Each time a hub interacts, we add one to its occurrence score and then deduce an occurrence probability for the amino acids to act as a hub in an SSE-IN. We repeat the process grouping the SSE-INs by their family and also by their structural class. The probability of an amino acid Ala being a hub is the stronger independently of the protein classifications.
Mentions: We also compute the occurrence level of hubs, that is their number of appearances on each protein SSE-IN. We accumulated this score at the SCOP class level to obtain the probability for each amino acid to be a hub in a protein SSE-IN; see Figure 6. We can remark the existence of peaks which show clearly a strong tendency of amino acids Ala, Cys, Gly, Leu, and Val to have a high interactivity within the folded protein. Thus, there are the same amino acids which play the role of hubs independently of structural families.

Bottom Line: Once we have compared this type of graphs to the general model of scale-free networks, we analyze the existence of nodes which highly interact, the hubs.We describe these nodes taking into account their position in the primary structure to study their apparition frequency in the folded proteins.Finally, we observe that their interaction level is a consequence of the general rules which govern the folding process.

View Article: PubMed Central - PubMed

Affiliation: Le Havre University, LITIS EA 4108, BP 540, 76058 Le Havre, France.

ABSTRACT
We represent proteins by amino acid interaction networks. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. Once we have compared this type of graphs to the general model of scale-free networks, we analyze the existence of nodes which highly interact, the hubs. We describe these nodes taking into account their position in the primary structure to study their apparition frequency in the folded proteins. Finally, we observe that their interaction level is a consequence of the general rules which govern the folding process.

No MeSH data available.