Discovery of intramolecular signal transduction network based on a new protein dynamics model of energy dissipation.

PloS One
Cheng-Wei MaAn-Ping Zeng

Abstract

A novel approach to reveal intramolecular signal transduction network is proposed in this work. To this end, a new algorithm of network construction is developed, which is based on a new protein dynamics model of energy dissipation. A key feature of this approach is that direction information is specified after inferring protein residue-residue interaction network involved in the process of signal transduction. This enables fundamental analysis of the regulation hierarchy and identification of regulation hubs of the signaling network. A well-studied allosteric enzyme, E. coli aspartokinase III, is used as a model system to demonstrate the new method. Comparison with experimental results shows that the new approach is able to predict all the sites that have been experimentally proved to desensitize allosteric regulation of the enzyme. In addition, the signal transduction network shows a clear preference for specific structural regions, secondary structural types and residue conservation. Occurrence of super-hubs in the network indicates that allosteric regulation tends to gather residues with high connection ability to collectively facilitate the signaling process. Furthermore, a new parameter of propagation coefficient is defin...Continue Reading

References

Jun 1, 1984·European Journal of Biochemistry·M G DarlisonJ R Guest
Jun 12, 1998·Nature·D J Watts, S H Strogatz
Oct 16, 1999·Science·A L Barabasi, R Albert
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Mar 30, 2000·Protein Science : a Publication of the Protein Society·S KumarR Nussinov
May 4, 2002·Annual Review of Biophysics and Biomolecular Structure·Irene LuqueErnesto Freire
Aug 31, 2002·Science·E RavaszA L Barabási
Dec 17, 2002·Nature Structural Biology·Gürol M SüelRama Ranganathan
Aug 30, 2003·Science·Stephen J Benkovic, Sharon Hammes-Schiffer
May 1, 1965·Journal of Molecular Biology·J MONODJ P CHANGEUX
Dec 17, 2003·Current Opinion in Structural Biology·Dorothee Kern, Erik R P Zuiderweg
Jan 22, 2004·Nature Reviews. Genetics·Albert-László Barabási, Zoltán N Oltvai
Sep 24, 2004·Proteins·K GunasekaranRuth Nussinov
Jan 20, 2005·Proceedings of the National Academy of Sciences of the United States of America·R August EstabrookNorbert O Reich
Jul 16, 2005·Bioinformatics·Falk Schreiber, Henning Schwöbbermeyer
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
May 11, 2006·Chemical Reviews·Mats H M OlssonArieh Warshel
Aug 15, 2006·Nature Structural & Molecular Biology·Nataliya PopovychCharalampos G Kalodimos
Sep 22, 2006·The Journal of Biological Chemistry·Gregory A Grant
Feb 1, 2008·Physical Review Letters·B JuanicoP De Los Rios
May 3, 2008·Physical Biology·Francesco Piazza, Yves-Henri Sanejouand
Feb 21, 2009·PLoS Computational Biology·Michael D Daily, Jeffrey J Gray
Apr 11, 2009·Science·Robert G Smock, Lila M Gierasch
Nov 17, 2009·Physical Biology·Francesco Piazza, Yves-Henri Sanejouand
Dec 15, 2010·Bioinformatics·Michael E SmootTrey Ideker
May 19, 2011·Science Signaling·Illés J FarkasPeter Csermely
Oct 25, 2011·PloS One·Cheng-Wei MaAn-Ping Zeng

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