Use of the conjugate peak refinement algorithm for identification of ligand-binding pathways in globins.
Determination of the three-dimensional structures of the globins led to the problem of determining how the ligands bound to the heme. In many of these structures there was no clear path from the solvent to the ligand-binding site. Even in those structures that appeared to have one or more tunnels from the exterior to the heme, it was not clear that these were the only paths for ligand access. Conjugate peak refinement (CPR) is a computational technique that can provide a minimum energy path between two conformations of a protein. By defining one conformation as the unbound structure with an external ligand and the other as the ligand-bound structure, CPR can be used to determine a pathway for ligand binding.
Golden
Stephen D
SD
Department of Chemistry, Loyola University Chicago, Chicago, Illinois, USA.
Olsen
Kenneth W
KW
D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D004734:Energy Metabolism / Q000502:physiology; D005914:Globins / Q000737:chemistry / Q000378:metabolism*; D008024:Ligands; D008954:Models, Biological; D008958:Models, Molecular; D008962:Models, Theoretical; D009211:Myoglobin / Q000737:chemistry / Q000378:metabolism; D010100:Oxygen / Q000378:metabolism; D011485:Protein Binding; D015398:Signal Transduction / Q000502:physiology; D054793:Truncated Hemoglobins / Q000737:chemistry / Q000378:metabolism
D001426:Bacterial Proteins; D008024:Ligands; D009211:Myoglobin; D054793:Truncated Hemoglobins; D005914:Globins; D010100:Oxygen