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Time-resolved crystallography reveals allosteric communication aligned with molecular breathing
(2019)
A comprehensive understanding of protein function demands correlating structure and dynamic changes. Using time-resolved serial synchrotron crystallography, we visualized half-of-the-sites reactivity and correlated molecular-breathing motions in the enzyme fluoroacetate dehalogenase. Eighteen time points from 30 milliseconds to 30 seconds cover four turnover cycles of the irreversible reaction. They reveal sequential substrate binding, covalent-intermediate formation, setup of a hydrolytic water molecule, and product release. Small structural changes of the protein mold and variations in the number and placement of water molecules accompany the various chemical steps of catalysis. Triggered by enzyme-ligand interactions, these repetitive changes in the protein framework’s dynamics and entropy constitute crucial components of the catalytic machinery.
We present a ‘hit-and-return’ (HARE) method for time-resolved serial synchrotron crystallography with time resolution from milliseconds to seconds or longer. Timing delays are set mechanically, using the regular pattern in fixed-target crystallography chips and a translation stage system. Optical pump-probe experiments to capture intermediate structures of fluoroacetate dehalogenase binding to its ligand demonstrated that data can be collected at short (30 ms), medium (752 ms) and long (2,052 ms) intervals.
The surface tension and dilational surface visco-elasticity of the individual solutions of the biopolymer DNA and the azobenzene-containing cationic surfactant AzoTAB, as well as their mixtures were measured using the drop profile analysis tensiometry. The negatively charged DNA molecules form complexes with the cationic surfactant AzoTAB. Mixed DNA + AzoTAB solutions exhibit high surface activity and surface layer elasticity. Extremes in the dependence of these characteristics on the AzoTAB concentration exist within the concentration range of 3 x 10(-6)-5 x 10(-5) M. The surface tension of the mixture shows a minimum with a subsequent maximum. In the same concentration range the elasticity shows first a maximum and then a subsequent minimum. A recently developed thermodynamic model was modified to account for the dependence of the adsorption equilibrium constant of the adsorbed complex on the cationic surfactant concentration. This modified theory shows good agreement with the experimental data both for the surface tension and the elasticity values over the entire range of studied AzoTAB concentrations. (C) 2016 Elsevier B.V. All rights reserved.