%0 Journal Article %1 Verma2012Domino %A Verma, Malkhey %A Zakhartsev, Maksim %A Reuss, Matthias %A Westerhoff, Hans V. %D 2012 %J Biochimica et biophysica acta %K metabolism regulation %R 10.1016/j.bbabio.2012.09.014 %T 'Domino' systems biology and the 'A' of ATP. %U http://dx.doi.org/10.1016/j.bbabio.2012.09.014 %X We develop a strategic 'domino' approach that starts with one key feature of cell function and the main process providing for it, and then adds additional processes and components only as necessary to explain provoked experimental observations. The approach is here applied to the energy metabolism of yeast in a glucose limited chemostat, subjected to a sudden increase in glucose. The puzzles addressed include (i) the lack of increase in ATP upon glucose addition, (ii) the lack of increase in ADP when ATP is hydrolyzed, and (iii) the rapid disappearance of the 'A' (adenine) moiety of ATP. Neither the incorporation of nucleotides into new biomass, nor steady de novo synthesis of AMP explains. Cycling of the 'A' moiety accelerates when the cell's energy state is endangered, another essential domino among the seven required for understanding of the experimental observations. This new domino analysis shows how strategic experimental design and observations in tandem with theory and modeling may identify and resolve important paradoxes. It also highlights the hitherto unexpected role of the 'A' component of ATP. Copyright \copyright 2012. Published by Elsevier B.V.

@article{Verma2012Domino, abstract = { We develop a strategic 'domino' approach that starts with one key feature of cell function and the main process providing for it, and then adds additional processes and components only as necessary to explain provoked experimental observations. The approach is here applied to the energy metabolism of yeast in a glucose limited chemostat, subjected to a sudden increase in glucose. The puzzles addressed include (i) the lack of increase in {ATP} upon glucose addition, (ii) the lack of increase in {ADP} when {ATP} is hydrolyzed, and (iii) the rapid disappearance of the 'A' (adenine) moiety of {ATP}. Neither the incorporation of nucleotides into new biomass, nor steady de novo synthesis of {AMP} explains. Cycling of the 'A' moiety accelerates when the cell's energy state is endangered, another essential domino among the seven required for understanding of the experimental observations. This new domino analysis shows how strategic experimental design and observations in tandem with theory and modeling may identify and resolve important paradoxes. It also highlights the hitherto unexpected role of the 'A' component of {ATP}. Copyright {\copyright} 2012. Published by Elsevier {B.V}. }, added-at = {2018-12-02T16:09:07.000+0100}, author = {Verma, Malkhey and Zakhartsev, Maksim and Reuss, Matthias and Westerhoff, Hans V.}, biburl = {https://www.bibsonomy.org/bibtex/255782217b3f772178e31cc799d511a6f/karthikraman}, citeulike-article-id = {11548965}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.bbabio.2012.09.014}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/23031542}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=23031542}, day = 29, doi = {10.1016/j.bbabio.2012.09.014}, interhash = {6606dd364a50e34ea538f139995c7aaa}, intrahash = {55782217b3f772178e31cc799d511a6f}, issn = {0006-3002}, journal = {Biochimica et biophysica acta}, keywords = {metabolism regulation}, month = sep, pmid = {23031542}, posted-at = {2012-10-26 05:26:20}, priority = {2}, timestamp = {2018-12-02T16:09:07.000+0100}, title = {'Domino' systems biology and the 'A' of {ATP}.}, url = {http://dx.doi.org/10.1016/j.bbabio.2012.09.014}, year = 2012 }