dorsal/arxiv
View SchemaDirected Ligand Passage Over the Surface of Diffusion-Controlled Enzymes: A Cellular Automata Model
| Authors | Mehrdad Ghaemi, Nasrollah Rezaei-Ghaleh, Mohammad-Nabi Sarbolouki |
|---|---|
| Categories | |
| ArXiv ID | physics/0411242 |
| URL | https://arxiv.org/abs/physics/0411242 |
| Journal | Lecture Notes in Computer Science, 2004, 3305, 719-724 |
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.
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"abstract": "The rate-limiting step of some enzymatic reactions is a physical step, i.e.\ndiffusion. The efficiency of such reactions can be improved through an increase\nin the arrival rate of the substrate molecules, e.g. by a directed passage of\nsubstrate (ligand) to active site after its random encounter with the enzyme\nsurface. Herein, we introduce a cellular automata model simulating the ligand\npassage over the protein surface to its destined active site. The system is\nsimulated using the lattice gas automata with probabilistic transition rules.\nDifferent distributions of amino acids over the protein surface are examined.\nFor each distribution, the hydration pattern is achieved and the mean number of\niteration steps needed for the ligand to arrive at the active site calculated.\nComparison of results indicates that the rate at which ligand arrives at the\nactive site is clearly affected by the distribution of amino acids outside the\nactive side. Such a process can facilitate the ligand diffusion towards the\nactive site thereby enhancing the efficiency of the enzyme action.",
"arxiv_id": "physics/0411242",
"authors": [
"Mehrdad Ghaemi",
"Nasrollah Rezaei-Ghaleh",
"Mohammad-Nabi Sarbolouki"
],
"categories": [
"physics.bio-ph",
"physics.comp-ph",
"q-bio.BM"
],
"journal_ref": "Lecture Notes in Computer Science, 2004, 3305, 719-724",
"title": "Directed Ligand Passage Over the Surface of Diffusion-Controlled Enzymes: A Cellular Automata Model",
"url": "https://arxiv.org/abs/physics/0411242"
},
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