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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.


We assign to each node a number so that the H extremity has the number 100. We sum the occurrence score of hubs according to their positions and normalize. We observe favorable regions when the occurrence rate is high.
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fig7: We assign to each node a number so that the H extremity has the number 100. We sum the occurrence score of hubs according to their positions and normalize. We observe favorable regions when the occurrence rate is high.

Mentions: Now, we want to describe the way in which the hubs appear in the folded protein. Then, we study the distribution of hub positions as a function of the SSE-IN structural class to identify variations dependent or not on the biological function of proteins. To lead this study, we attribute to the nodes an incremental position so that the H extremity has a position 100. Then, each time a hub exists in an SSE-IN, we increment its occurrence number by position and finally normalize by the maximum to obtain the occurrence ratio of hubs according to their positions in the SSE-IN; see Figure 7. The results show the existence of favorable regions in which the hub apparition is higher than somewhere else. This favorable localization is strongly visible for the All α class where the hubs have a tendency to interact around the positions 20, 40, or 80. The distribution of hub positions is the most homogeneous for the α/β class. It involves dependence on the SSE-IN topology since it is not possible to find more than one strong favorable area which appears around the position 60.


A topological description of hubs in amino Acid interaction networks.

Gaci O - Adv Bioinformatics (2010)

We assign to each node a number so that the H extremity has the number 100. We sum the occurrence score of hubs according to their positions and normalize. We observe favorable regions when the occurrence rate is high.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig7: We assign to each node a number so that the H extremity has the number 100. We sum the occurrence score of hubs according to their positions and normalize. We observe favorable regions when the occurrence rate is high.
Mentions: Now, we want to describe the way in which the hubs appear in the folded protein. Then, we study the distribution of hub positions as a function of the SSE-IN structural class to identify variations dependent or not on the biological function of proteins. To lead this study, we attribute to the nodes an incremental position so that the H extremity has a position 100. Then, each time a hub exists in an SSE-IN, we increment its occurrence number by position and finally normalize by the maximum to obtain the occurrence ratio of hubs according to their positions in the SSE-IN; see Figure 7. The results show the existence of favorable regions in which the hub apparition is higher than somewhere else. This favorable localization is strongly visible for the All α class where the hubs have a tendency to interact around the positions 20, 40, or 80. The distribution of hub positions is the most homogeneous for the α/β class. It involves dependence on the SSE-IN topology since it is not possible to find more than one strong favorable area which appears around the position 60.

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.