Directed Ligand Passage over the Surface of Diffusion-Controlled Enzymes: A Cellular Automata Model

DOI10.1007/978-3-540-30479-1_74zbMATH Open1116.92311arXivphysics/0411242OpenAlexW1570527346MaRDI QIDQ5464166FDOQ5464166

Nasrollah Rezaei-Ghaleh, Mehrdad Ghaemi, Mohammad-Nabi Sarbolouki

Publication date: 17 August 2005

Published in: Lecture Notes in Computer Science (Search for Journal in Brave)

Abstract: The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of substrate (ligand) to active site after its random encounter with the enzyme surface. Herein, we introduce a cellular automata model simulating the ligand passage over the protein surface to its destined active site. The system is simulated using the lattice gas automata with probabilistic transition rules. Different distributions of amino acids over the protein surface are examined. For each distribution, the hydration pattern is achieved and the mean number of iteration steps needed for the ligand to arrive at the active site calculated. Comparison of results indicates that the rate at which ligand arrives at the active site is clearly affected by the distribution of amino acids outside the active side. Such a process can facilitate the ligand diffusion towards the active site thereby enhancing the efficiency of the enzyme action.

Full work available at URL: https://arxiv.org/abs/physics/0411242

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Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Cellular automata (computational aspects) (68Q80)

Cited In (1)

• Docking and Molecular Dynamics Simulation of Complexes of High and Low Reactive Substrates with Peroxidases

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