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Biophys J. 2018 Jan 9;114(1):10-14. doi: 10.1016/j.bpj.2017.10.030. Epub 2017 Nov 15.

Thermodynamic Coupling Function Analysis of Allosteric Mechanisms in the Human Dopamine Transporter.

Author information

1
Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York; HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York. Electronic address: mil2037@med.cornell.edu.
2
Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York; HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York.
3
Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York.

Abstract

Allostery plays a crucial role in the mechanism of neurotransmitter-sodium symporters, such as the human dopamine transporter. To investigate the molecular mechanism that couples the transport-associated inward release of the Na+ ion from the Na2 site to intracellular gating, we applied a combination of the thermodynamic coupling function (TCF) formalism and Markov state model analysis to a 50-μs data set of molecular dynamics trajectories of the human dopamine transporter, in which multiple spontaneous Na+ release events were observed. Our TCF approach reveals a complex landscape of thermodynamic coupling between Na+ release and inward-opening, and identifies diverse, yet well-defined roles for different Na+-coordinating residues. In particular, we identify a prominent role in the allosteric coupling for the Na+-coordinating residue D421, where mutation has previously been associated with neurological disorders. Our results highlight the power of the TCF analysis to elucidate the molecular mechanism of complex allosteric processes in large biomolecular systems.

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