Issue No. 05 - Sept.-Oct. (2012 vol. 9)
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.66
Eugen Czeizler , Dept. of Inf. & Comput. Sci., Aalto Univ., Aalto, Finland
Vladimir Rogojin , Fac. of Med., Helsinki Univ., Helsinki, Finland
Ion Petre , Dept. of Inf. Technol., Abo Akademi Univ., Turku, Finland
The heat shock response is a well-conserved defence mechanism against the accumulation of misfolded proteins due to prolonged elevated heat. The cell responds to heat shock by raising the levels of heat shock proteins (hsp), which are responsible for chaperoning protein refolding. The synthesis of hsp is highly regulated at the transcription level by specific heat shock (transcription) factors (hsf). One of the regulation mechanisms is the phosphorylation of hsf's. Experimental evidence shows a connection between the hyper-phosphorylation of hsfs and the transactivation of the hsp-encoding genes. In this paper, we incorporate several (de)phosphorylation pathways into an existing well-validated computational model of the heat shock response. We analyze the quantitative control of each of these pathways over the entire process. For each of these pathways we create detailed computational models which we subject to parameter estimation in order to fit them to existing experimental data. In particular, we find conclusive evidence supporting only one of the analyzed pathways. Also, we corroborate our results with a set of computational models of a more reduced size.
proteins, biothermics, cellular biophysics, genetics, molecular biophysics, parameter estimation, parameter estimation, phosphorylation, heat shock factor, heat shock response, well-conserved defence mechanism, misfolded protein accumulation, cell, chaperoning protein refolding, specific heat shock factors, transcription factors, hsp-encoding genes, computational models, Computational modeling, Heating, Electric shock, Proteins, Biological system modeling, Kinetic theory, Numerical models, quantitative refinement., Simulation, modeling, computing methodologies, biology and genetics, computer applications, heat shock response, protein phosphorylation
V. Rogojin, E. Czeizler and I. Petre, "The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. , pp. 1326-1337, 2012.