Agent-based model of the budding yeast cell cycle regulatory network

Abstract

Kinetic parameters are a crucial aspect when studying reactions involving proteins. Unfortunately, these are often unknown or hard to measure in the laboratory. Therefore, modeling phenomena involving protein reactions without using kinetic parameters can be a significant advantage. In this work, an agent-based model of the budding yeast (Saccharomyces cerevisiae) cell cycle was created based on a cell cycle regulatory network, to obtain the correct sequence of states of the regulatory proteins. Comparing the results to a Boolean network model, having similar results, following the correct sequence of phases and reaching in 71% of the cases the biological G1 stationary state of the cell. Yeast cell cycle is highly conservated among other eukaryotes, meaning that is regulators works similar than the ones in humans; knowing that, yeast cells can be mutated to have behavior related to a specific tumor and then treated with different drugs to check which is better to kill that particular tumor. This model could be a starting point for being used in the development of cancer drugs adding cell cycle mutations that match a specific type of tumor cell cycle and an agent representing the medication or treatment.