title: Memetic algorithms for ligand expulsion from protein cavities.
abstract: Ligand diffusion through a protein interior is a fundamental process governing biological signaling and enzymatic catalysis. A complex topology of channels in proteins leads often to difficulties in modeling ligand escape pathways by classical molecular dynamics simulations. In this paper, two novel memetic methods for searching the exit paths and cavity space exploration are proposed: Memory Enhanced Random Acceleration (MERA) Molecular Dynamics (MD) and Immune Algorithm (IA). In MERA, a pheromone concept is introduced to optimize an expulsion force. In IA, hybrid learning protocols are exploited to predict ligand exit paths. They are tested on three protein channels with increasing complexity: M2 muscarinic G-protein-coupled receptor, enzyme nitrile hydratase, and heme-protein cytochrome P450cam. In these cases, the memetic methods outperform simulated annealing and random acceleration molecular dynamics. The proposed algorithms are general and appropriate in all problems where an accelerated transport of an object through a network of channels is studied.
authors.affiliation: Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland.
authors.forename: J
authors.initials: J
authors.lastname: Rydzewski
authors.affiliation: Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland.
authors.forename: W
authors.initials: W
authors.lastname: Nowak
mesh_terms: D000465:Algorithms; D002164:Camphor / Q000737:chemistry; D019475:Camphor 5-Monooxygenase / Q000378:metabolism*; D003035:Cobalt / Q000737:chemistry; D004058:Diffusion; D006418:Heme / Q000378:metabolism; D006836:Hydro-Lyases / Q000378:metabolism*; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009536:Niacinamide / Q000737:chemistry; D011485:Protein Binding; D011813:Quinuclidinyl Benzilate / Q000737:chemistry; D043585:Receptor, Muscarinic M2 / Q000378:metabolism*
chemical_list: D008024:Ligands; D043585:Receptor, Muscarinic M2; D009536:Niacinamide; D003035:Cobalt; D006418:Heme; D011813:Quinuclidinyl Benzilate; D002164:Camphor; D019475:Camphor 5-Monooxygenase; D006836:Hydro-Lyases; C048831:nitrile hydratase