Abstract
Metabolic pathway analysis is one of the tools used in biology and medicine in order to understand reaction cycles in living cells. A shortcoming of the approach, however, is that reactions are analysed only at a level corresponding to what is known as the ’collective token view’ in Petri nets, i.e., summarising the number of atoms of certain types in a compound, but not keeping track of their identity.
In this paper we propose a refinement of pathway analysis based on hypergraph grammars, modelling reactions at a molecular level. We consider as an example the citric acid cycle, a classical, but non-trivial reaction for energy utilisation in living cells. Our approach allows the molecular analysis of the cycle, tracing the flow of individual carbon atoms based on a simulation using the graph transformation tool AGG.
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References
Attributed Graph Grammar (AGG) Tool Environment (2006), http://tfs.cs.tu-berlin.de/agg
Cardelli, L., Pradalier, S.: Where Membranes Meet Complexes. In: Proceedings of BioConcur (2005)
Claus, V., Ehrig, H., Rozenberg, G. (eds.): Graph Grammars 1978. LNCS, vol. 73, pp. 389–400. Springer, Heidelberg (1979)
Cotton, F.A.: Chemical Applications of Group Theory. Wiley, Chichester (1990)
IUPAC Basic Terminology of Stereochemistry. Pure & Applied Chemistry 68(12), 2193–2222 (1996)
Löwe, M.: Algebraic Approach to Single-Pushout Graph Transformation. Theoretical Computer Science 109(1&2), 181–224 (1993)
McCaskill, J.S., Niemann, U.: Graph Replacement Chemistry for DNA Processing. In: Condon, A., Rozenberg, G. (eds.) DNA 2000. LNCS, vol. 2054, pp. 103–116. Springer, Heidelberg (2001)
Mesecar, A.D., Koshland Jr., D.E.: A new model for protein sterospecificity. Nature 403, 614–615 (2000)
Rosselló, F., Valiente, G.: Graph Transformation in Molecular Biology. In: Kreowski, H.-J., Montanari, U., Orejas, F., Rozenberg, G., Taentzer, G. (eds.) Formal Methods in Software and Systems Modeling. LNCS, vol. 3393, pp. 116–133. Springer, Heidelberg (2005)
Rosselló, F., Valiente, G.: Analysis of Metabolic Pathways by Graph Transformation. In: Ehrig, H., Engels, G., Parisi-Presicce, F., Rozenberg, G. (eds.) ICGT 2004. LNCS, vol. 3256, pp. 70–82. Springer, Heidelberg (2004)
Taentzer, G.: AGG: A Graph Transformation Environment for Modeling and Validation of Software. In: Pfaltz, J.L., Nagl, M., Böhlen, B. (eds.) AGTIVE 2003. LNCS, vol. 3062, pp. 446–453. Springer, Heidelberg (2004), http://tfs.cs.tu-berlin.de/agg
Yadav, M.K., Kelley, B.P., Silverman, S.M.: The Potential of a Chemical Graph Transformation System. In: Ehrig, H., Engels, G., Parisi-Presicce, F., Rozenberg, G. (eds.) ICGT 2004. LNCS, vol. 3256, pp. 83–95. Springer, Heidelberg (2004)
Zubay, G.L., Parson, W.W., Vance, D.E.: Principles of Biochemisty, vol. 2 (1995)
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Ehrig, K., Heckel, R., Lajios, G. (2006). Molecular Analysis of Metabolic Pathway with Graph Transformation. In: Corradini, A., Ehrig, H., Montanari, U., Ribeiro, L., Rozenberg, G. (eds) Graph Transformations. ICGT 2006. Lecture Notes in Computer Science, vol 4178. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11841883_9
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DOI: https://doi.org/10.1007/11841883_9
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