Modeling of intracellular processes using active charged particles
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MODELING OF INTRACELLULAR PROCESSES USING ACTIVE CHARGED PARTICLES B. O. Biletskyya† and A. M. Gupala‡
UDC 519.217.2
Abstract. A new method to model intracellular reactions coordinated by proteins is discussed. Proteins are described using locally interacting charged particles. The interaction is defined algorithmically, which allows disregarding the physical nature of protein activity in the analysis of the processes. Based on the proposed approach, a modeling software environment was developed and used as an example to analyze the process of formation of the hydrophobic core of a protein globule in water. Keywords: multiagent systems, cellular automata, Markov chain, reactions of cellular metabolism, protein.
Introduction. Many experimental data on intracellular processes have been obtained. All the chemical reactions in a cell are known to be coordinated by proteins, which are highly active organic molecules that perform various functions in the cell. Because of the complexity of their functions, cells are similar to molecular machines or mechanisms [1]. Proteins consist of 20 types of amino acids and are chains of tens to thousands of amino acids. Due to the internal interactions among amino acids of the protein chain and the interactions with environmental molecules, a stable three-dimensional protein structure is formed, which is considered to define its function in the cell. Amino-acid sequences of proteins are encoded in the structure of DNA molecule. If necessary, intracellular processes are triggered by the synthesis of appropriate proteins according to instructions from DNA and stop naturally: in course of time the protein structure, as any thermodynamic system, breaks and splits into separate amino acids and loses its function in the cell. The lifetime of the majority of proteins in nature equals several days. The modern crystallography methods allow arranging the protein structure experimentally up to determining the coordinates of all its atoms; however, a reliable method to determine the protein function based on its structure has not been discovered yet. The main difficulty is that accomplishment of the protein’s function is accompanied by a chain of internal structural transformations that are difficult to trace experimentally. Below we propose a method to model proteins by locally interacting particles, the interactions being specified algorithmically. Such an approach allows investigating intracellular processes disregarding the nature of protein interactions. Additional possibilities for modeling of intracellular processes are provided by the use of potentials, which allow specifying the probability of different particle configurations. The proposed approach is implemented as a software environment for simulating processes in Java language. The developed tool is based on the following model. Configuration. Let us call a countable set A the alphabet of particle types. Denote by K, | K | < ¥, the set of possible locations of a particle. Vector w = ( w1 , K, w | K | ) , w Î A | K | , whose compo
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