title: Ligand binding energy and catalytic efficiency from improved packing within receptors and enzymes.
abstract: Some small molecules bind to their receptors, and transition states to enzymes, so strongly as to defy current understanding. We show that in the binding of biotin to streptavidin, the streptavidin structure becomes better packed. We conclude that this contraction of the streptavidin structure promotes biotin binding. The improved packing is associated with positively cooperative binding, occurring with a benefit in enthalpy and a cost in entropy. Evidence indicating that catalytic efficiency can also originate via improved packing in some enzyme transition states, derived from the work of others, is presented. Negatively cooperative ligand binding is concluded to induce converse effects (less efficient packing, a cost in enthalpy, and a benefit in entropy). It applies to the binding of O(2) to haemoglobin, which indeed occurs with a hitherto unreported loosening of the amide backbones of the haemoglobin monomers.
authors.affiliation: Department of Chemistry, University of Cambridge, UK. dhw1@cam.ac.uk
authors.forename: Dudley H
authors.initials: DH
authors.lastname: Williams
authors.forename: Elaine
authors.initials: E
authors.lastname: Stephens
authors.forename: Min
authors.initials: M
authors.lastname: Zhou
mesh_terms: D000818:Animals; D001665:Binding Sites; D001710:Biotin / Q000737:chemistry / Q000378:metabolism*; D002384:Catalysis; D003198:Computer Simulation; D019277:Entropy; D006454:Hemoglobins / Q000737:chemistry / Q000378:metabolism*; D006736:Horses; D007501:Iron / Q000737:chemistry; D008024:Ligands; D013058:Mass Spectrometry; D008958:Models, Molecular; D008962:Models, Theoretical; D010100:Oxygen / Q000737:chemistry / Q000378:metabolism*; D010434:Pepsin A / Q000378:metabolism; D010455:Peptides / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D019809:Streptavidin / Q000737:chemistry / Q000378:metabolism*
chemical_list: D006454:Hemoglobins; D008024:Ligands; D010455:Peptides; D001710:Biotin; D019809:Streptavidin; D007501:Iron; D010434:Pepsin A; D010100:Oxygen