Applying the Tuple Space-Based Approach to the Simulation of the Caspases, an Essential Signalling Pathway Maura Cárdenas-García 1 , Pedro Pablo González-Pérez 2,* 1 Benemérita Universidad Autónoma de Puebla, Sur 2702, Puebla, 72410, México, http://www.buap.mx 2 Universidad Autónoma Metropolitana, Departamento de Matemáticas Aplicadas y Sistemas, Avenida Constituyentes 647, México, D.F., 11810, México, http://www.cua.uam.mx Summary Apoptotic cell death plays a crucial role in development and homeostasis. This process is driven by mitochondrial permeabilization and activation of caspases. In this paper we adopt a tuple spaces-based modelling and simulation approach, and show how it can be applied to the simulation of this intracellular signalling pathway. Specifically, we are working to explore and to understand the complex interaction patterns of the caspases apoptotic and the mitochondrial role. As a first approximation, using the tuple spaces- based in silico approach, we model and simulate both the extrinsic and intrinsic apoptotic signalling pathways and the interactions between them. During apoptosis, mitochondrial proteins, released from mitochondria to cytosol are decisively involved in the process. If the decision is to die, from this point there is normally no return, cancer cells offer resistance to the mitochondrial induction. 1 Introduction Apoptosis is a type of cell death to eliminate unnecessary or damaged cells in a perfectly controlled manner that minimizes damage to neighbouring cells. The resulting cell debris, which are always surrounded by plasma membrane are removed by phagocytosis, preventing inflammation in the area. The cell dying by apoptosis undergoes a series of morphological changes, reducing its volume. The membrane is altered and displays protuberances ("blebbing"), cytoplasm and cell organelles are condensed inside release factors, which promote mitochondrial death. When the mechanisms that regulate apoptosis fail, this balance is disturbed and may originate excess and defect, various pathologies. Resistance to apoptosis is one of the characteristics that contribute to the generation of a tumour and may also be the cause of some autoimmune diseases. Otherwise, excessive apoptosis could be related to neurodegenerative diseases. One of the most important features of apoptosis is the nucleus condensation and DNA fragmentation. Moreover, many proteins undergo cell rupture or proteolysis generally catalysed by caspases. All caspases (cysteine proteases) have a cysteine in its active centre and proteins produced cuts right behind the amino acid Asp. There are two major pathways of apoptosis activation and three pathways of activation of caspases and therefore apoptosis: * To whom correspondence should be addressed. Email: pgonzalez@correo.cua.uam.mx Journal of Integrative Bioinformatics, 10(1):225, 2013 http://journal.imbio.de doi:10.2390/biecoll-jib-2013-225 1 Copyright 2013 The Author(s). Published by Journal of Integrative Bioinformatics. This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License (http://creativecommons.org/licenses/by-nc-nd/3.0/).