title: Analysis of ligand binding to proteins using molecular dynamics simulations.
abstract: This work aims to explore theoretically the molecular mechanisms of ligand binding to proteins through the use of molecular dynamics simulations. The binding of sodium dodecyl sulfate (SDS) to cobra cardio toxin A3 (CTX A3) and thiourea (TOU) to lysozyme have been chosen as the two model systems. Data acquisitions were made by Gromacs software. To begin with, the collisions of ligand molecules with every residue of CTX A3 and lysozyme were evaluated. With this information in hand, the average numbers of collisions with each residue was defined and then assessed. Next, a measure of the affinity of a residue, P(i), referred to as conformational factor, toward a ligand molecule was established. Based on the results provided, all site-making residues for CTX A3 and lysozyme were identified. The results are in good agreement with the experimental data. Finally, based on this method, all site-making residues of bovine carbonic anhydrase (BCA) toward the SDS ligand were predicted.
authors.affiliation: Biophysical Chemistry Laboratory, Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, P.O. Box 91775-1436, Mashhad, Iran. mhousaindokht@science1.um.ac.ir
authors.forename: M R
authors.initials: MR
authors.lastname: Housaindokht
authors.forename: M R
authors.initials: MR
authors.lastname: Bozorgmehr
authors.forename: M
authors.initials: M
authors.lastname: Bahrololoom
mesh_terms: D000818:Animals; D001665:Binding Sites; D002256:Carbonic Anhydrases / Q000378:metabolism; D004179:Cobra Cardiotoxin Proteins / Q000378:metabolism; D003198:Computer Simulation; D008024:Ligands; D008958:Models, Molecular; D009113:Muramidase / Q000378:metabolism; D011485:Protein Binding; D011506:Proteins / Q000378:metabolism*; D012967:Sodium Dodecyl Sulfate / Q000378:metabolism; D013890:Thiourea / Q000378:metabolism
chemical_list: D004179:Cobra Cardiotoxin Proteins; D008024:Ligands; D011506:Proteins; D012967:Sodium Dodecyl Sulfate; D009113:Muramidase; D002256:Carbonic Anhydrases; D013890:Thiourea