title: Viscosity-dependent relaxation significantly modulates the kinetics of CO recombination in the truncated hemoglobin TrHbN from Mycobacterium tuberculosis.
abstract: Kinetic traces were generated for the nanosecond and slower rebinding of photodissociated CO to trHbN in solution and in porous sol-gel matrices as a function of viscosity, conformation, and mutation. TrHbN is one of the two truncated hemoglobins from Mycobacterium tuberculosis. The kinetic traces were analyzed in terms of three distinct phases. These three phases are ascribed to rebinding: (i) from the distal heme pocket, (ii) from the adjacent apolar tunnel prior to conformational relaxation, and (iii) from the apolar tunnel subsequent to conformational relaxation. The fractional content of each of these phases was shown to be a function of the viscosity and, in the case of the sol-gel-encapsulated samples, sample preparation history. The observed kinetic patterns support a model consisting of the following elements: (i) the viscosity and conformation-sensitive dynamics of the Tyr(B10) side chain facilitate diffusion of the dissociated ligand from the distal heme pocket into the adjacent tunnel; (ii) the distal heme pocket architecture determines ligand access from the tunnel back to the heme iron; (iii) the distal heme pocket architecture is governed by a ligand-dependent hydrogen bonding network that limits the range of accessible side chain positions; and (iv) the apolar tunnel linking the heme site to the solvent biases the competition between water and ligand for occupancy of the vacated polar distal heme pocket greatly toward the nonpolar ligand. Implications of these finding with respect to biological function are discussed.
authors.affiliation: Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
authors.forename: David
authors.initials: D
authors.lastname: Dantsker
authors.forename: Uri
authors.initials: U
authors.lastname: Samuni
authors.forename: Yannick
authors.initials: Y
authors.lastname: Ouellet
authors.forename: Beatrice A
authors.initials: BA
authors.lastname: Wittenberg
authors.forename: Jonathan B
authors.initials: JB
authors.lastname: Wittenberg
authors.forename: Mario
authors.initials: M
authors.lastname: Milani
authors.forename: Martino
authors.initials: M
authors.lastname: Bolognesi
authors.forename: Michel
authors.initials: M
authors.lastname: Guertin
authors.forename: Joel M
authors.initials: JM
authors.lastname: Friedman
mesh_terms: D001665:Binding Sites; D002248:Carbon Monoxide / Q000737:chemistry*; D018360:Crystallography, X-Ray; D005990:Glycerol / Q000737:chemistry; D006418:Heme / Q000737:chemistry; D006454:Hemoglobins / Q000737:chemistry*; D007700:Kinetics; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D011995:Recombination, Genetic; D013696:Temperature; D013997:Time Factors; D054793:Truncated Hemoglobins; D014867:Water / Q000737:chemistry
chemical_list: D006454:Hemoglobins; D008024:Ligands; D054793:Truncated Hemoglobins; D014867:Water; D006418:Heme; D002248:Carbon Monoxide; D005990:Glycerol