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Title: Docking site dynamics of ba3-cytochrome c oxidase from thermus thermophilus
Authors: Soulimane, Tewfik 
Varotsis, Constantinos 
Koutsoupakis, Constantinos 
Keywords: Enzymes;Cytochrome oxidase;Fourier transform infrared spectroscopy;Photodissociation;Ligands;Protein binding;Solvents
Issue Date: 2003
Publisher: The American Society for Biochemistry and Molecular Biology
Source: Journal of biological chemistry, 2003, Volume 278, Issue 38, Pages 36806-36809
Abstract: Ligand trajectories trapped within a docking site or within an internal cavity near the active site of proteins are important issues toward the elucidation of the mechanism of reaction of such complex systems, in which activity requires the shuttling of oriented ligands to and from their active site. The ligand motion within ba3-cytochrome c oxidase from Thermus thermophilus has been investigated by measuring time-resolved stepscan Fourier transform infrared difference spectra of photodissociated CO from heme a 3 at ambient temperature. Upon photodissociation, 15-20% of the CO is not covalently attached to CuB but is trapped within a docking site near the ring A of heme a3propionate. Two trajectories of CO that are distinguished spectroscopically and kinetically (Vco = 2131 cm-1, td = 10-35 μs and vco= 2146 cm -1, td = 85 μs) are observed. At later times (t d = 110 μs) the docking site reorganizes about the CO and quickly establishes an energetic barrier that facilitates equilibration of the ligand with the protein solvent. The time-dependent shift of the CO trajectories we observe is attributed to a conformational motion of the docking site surrounding the ligand. The implications of these results with respect to the ability of the docking site to constrain ligand orientation and the reaction dynamics of the docking site are discussed herein
ISSN: 00219258
DOI: 10.1074/jbc.M307117200
Rights: Copyright © 2013 by American Society for Biochemistry and Molecular Biology
Type: Article
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