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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.


Occurrence rate of the hub Ala for each SCOP class level. Comparing these plots to Figure 7, it appears that the amino acid Ala corresponds to the higher occurrence rate.
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fig9: Occurrence rate of the hub Ala for each SCOP class level. Comparing these plots to Figure 7, it appears that the amino acid Ala corresponds to the higher occurrence rate.

Mentions: These two observations lead us to compute only the occurrence rate of the most frequently encountered hub Ala according to its position; see Figure 9. By comparing the Figures 7 and 9, it appears clearly that the highest occurrence rate for the four classes corresponds to the position of the amino acid Ala. Therefore, we can establish a relation between the amino acid position in the primary structure and the hub apparition. Thus, the amino acids Ala, Cys, Gly, Leu, and Val act as hub because they are localized in the protein sequence in favorable regions which involve a high interaction within the folded structure. This tendency is actually a consequence of the amino acid hydrophobicity and more globally it is a consequence of the formation of a hydrophobic core in the folded proteins.


A topological description of hubs in amino Acid interaction networks.

Gaci O - Adv Bioinformatics (2010)

Occurrence rate of the hub Ala for each SCOP class level. Comparing these plots to Figure 7, it appears that the amino acid Ala corresponds to the higher occurrence rate.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig9: Occurrence rate of the hub Ala for each SCOP class level. Comparing these plots to Figure 7, it appears that the amino acid Ala corresponds to the higher occurrence rate.
Mentions: These two observations lead us to compute only the occurrence rate of the most frequently encountered hub Ala according to its position; see Figure 9. By comparing the Figures 7 and 9, it appears clearly that the highest occurrence rate for the four classes corresponds to the position of the amino acid Ala. Therefore, we can establish a relation between the amino acid position in the primary structure and the hub apparition. Thus, the amino acids Ala, Cys, Gly, Leu, and Val act as hub because they are localized in the protein sequence in favorable regions which involve a high interaction within the folded structure. This tendency is actually a consequence of the amino acid hydrophobicity and more globally it is a consequence of the formation of a hydrophobic core in the folded proteins.

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.