title: How maltose influences structural changes to bind to maltose-binding protein: results from umbrella sampling simulation.
abstract: A well-studied periplasmic-binding protein involved in the abstraction of maltose is maltose-binding protein (MBP), which undergoes a ligand-induced conformational transition from an open (ligand-free) to a closed (ligand-bound) state. Umbrella sampling simulations have been us to estimate the free energy of binding of maltose to MBP and to trace the potential of mean force of the unbinding event using the center-of-mass distance between the protein and ligand as the reaction coordinate. The free energy thus obtained compares nicely with the experimentally measured value justifying our theoretical basis. Measurement of the domain angle (N-terminal-domain - hinge - C-terminal-domain) along the unbinding pathway established the existence of three different states. Starting from a closed state, the protein shifts to an open conformation during the initial unbinding event of the ligand then resides in a semi-open conformation and later resides predominantly in an open-state. These transitions along the ligand unbinding pathway have been captured in greater depth using principal component analysis. It is proposed that in mixed-model, both conformational selection and an induced-fit mechanism combine to the ligand recognition process in MBP.
authors.affiliation: Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, D-70569 Stuttgart, Germany.
authors.forename: Nahren Manuel
authors.initials: NM
authors.lastname: Mascarenhas
authors.forename: Johannes
authors.initials: J
authors.lastname: Kästner
mesh_terms: D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D008024:Ligands; D008320:Maltose / Q000737:chemistry* / Q000378:metabolism*; D058619:Maltose-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D025341:Principal Component Analysis; D011485:Protein Binding; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D029968:Escherichia coli Proteins; D008024:Ligands; D058619:Maltose-Binding Proteins; D008320:Maltose