title: Transient ligand docking sites in Cerebratulus lacteus mini-hemoglobin.
abstract: The monomeric hemoglobin of the nemertean worm Cerebratulus lacteus functions as an oxygen storage protein to maintain neural activity under hypoxic conditions. It shares a large, apolar matrix tunnel with other small hemoglobins, which has been implicated as a potential ligand migration pathway. Here we explore ligand migration and binding within the distal heme pocket, to which the tunnel provides access to ligands from the outside. FTIR/TDS experiments performed at cryogenic temperatures reveal the presence of three transient ligand docking sites within the distal pocket, the primary docking site B on top of pyrrole C and secondary sites C and D. Site C is assigned to a cavity adjacent to the distal portion of the heme pocket, surrounded by the B and E helices. It has an opening to the apolar tunnel and is expected to be on the pathway for ligand entry and exit, whereas site D, circumscribed by TyrB10, GlnE7, and the CD corner, most likely is located on a side pathway of ligand migration. Flash photolysis experiments at ambient temperatures indicate that the rate-limiting step for ligand binding to CerHb is migration through the apolar channel to site C. Movement from C to B and iron-ligand bond formation involve low energy barriers and thus are very rapid processes in the wt protein.
authors.affiliation: Institute of Biophysics, University of Ulm, Albert-Einstein-Allee 11, D-89081 Ulm, Germany.
authors.forename: Pengchi
authors.initials: P
authors.lastname: Deng
authors.forename: Karin
authors.initials: K
authors.lastname: Nienhaus
authors.forename: Pasquale
authors.initials: P
authors.lastname: Palladino
authors.forename: John S
authors.initials: JS
authors.lastname: Olson
authors.forename: George
authors.initials: G
authors.lastname: Blouin
authors.forename: Luc
authors.initials: L
authors.lastname: Moens
authors.forename: Sylvia
authors.initials: S
authors.lastname: Dewilde
authors.forename: Eva
authors.initials: E
authors.lastname: Geuens
authors.forename: G Ulrich
authors.initials: GU
authors.lastname: Nienhaus
mesh_terms: D019943:Amino Acid Substitution; D000596:Amino Acids / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000818:Animals; D001665:Binding Sites; D002248:Carbon Monoxide / Q000737:chemistry / Q000378:metabolism; D006418:Heme / Q000737:chemistry / Q000378:metabolism; D006454:Hemoglobins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006860:Hydrogen Bonding; D007448:Invertebrates / Q000737:chemistry*; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D009154:Mutation; D010100:Oxygen / Q000737:chemistry / Q000378:metabolism; D010108:Oxyhemoglobins / Q000737:chemistry; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017550:Spectroscopy, Fourier Transform Infrared; D013696:Temperature; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D006454:Hemoglobins; D008024:Ligands; D010108:Oxyhemoglobins; D006418:Heme; D002248:Carbon Monoxide; D010100:Oxygen