Volume 3, Issue 1 (Feb 2015)                   Res Mol Med (RMM) 2015, 3(1): 6-11 | Back to browse issues page

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Amiri Dash Atan N, Farrokhi Yekta R, Koushki M. Study of PKA binding sites in cAMP-signaling pathway using structural protein-protein interaction networks. Res Mol Med (RMM). 2015; 3 (1) :6-11
1- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
2- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran ,
3- Clinical Biochemistry Department, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
Abstract:   (4697 Views)

Backgroud: Protein-protein interaction, plays a key role in signal transduction in signaling pathways. Different approaches are used for prediction of these interactions including experimental and computational approaches. In conventional node-edge protein-protein interaction networks, we can only see which proteins interact but ‘structural networks’ show us how these proteins interact which can give us so much information about the network. Structural networks help us understand the molecular basis of cellular functions and regulatory mechanisms in signaling pathways. In this study, we aimed to construct a structural network for a part of cAMP signaling pathway which has PKA (cAMP-dependent protein kinase catalytic subunit alpha) as the hub.
Materials and Methods: A part of cAMP signaling pathway was selected from kegg database and interactions of PKA as hub protein with some of its partners were achieved using Hex8.00 software. The interfaces of the resulted complexes were predicted by KFC2 server.
Results: Hex8.00, as a docking software, gave us the complexes from the interaction of PKA with 15 proteins of its partners. For each complex, the KFC2 server gave us the amino acid composition of the interfaces. Using this amino acid composition, we draw a structural network which shows the binding sites on PKA surface.
Conclusion: We have constructed a structural network for cAMP signaling pathway which shows how PKA interacts with its partners. This network can be used for understanding the mechanisms of signal transduction and also for drug design purposes.

Full-Text [PDF 1019 kb]   (2019 Downloads)    
Type of Study: Research | Subject: Biology
Received: 2015/01/31 | Accepted: 2015/04/15 | Published: 2015/04/15

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