Probing subunit communication via a singly ligated state of dimeric thymidylate synthase Public Deposited

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  • March 20, 2019
Creator
  • Falk, Bradley
    • Affiliation: School of Medicine, Department of Biochemistry and Biophysics
Abstract
  • Enzymes are highly dynamic molecules that undergo motions on a wide variety of timescales that are linked to all aspects of their function from mediating substrate binding and enabling chemistry to facilitating regulation by effector ligands. NMR studies on a handful of small monomeric enzymes have highlighted the role of dynamics in simple systems, but most enzymes possess added complexity stemming from size, oligomeric structures, multistep and/or multisubstrate mechanisms, and allosteric regulation. In recent years there has been a resurgence of interest in understanding the mechanisms of protein allostery. Canonically, allostery occurs in oligomeric proteins: ligand binding in one subunit alters binding or activity in a symmetry related second subunit. For such systems it is often straightforward to measure cooperative binding thermodynamics, but gaining detailed structural and/or dynamic mechanisms for intersubunit communication has proved to be much more difficult. This work has focused on applying NMR techniques to probe the inner workings of cooperativity and intersubunit communication in a large dimeric enzyme, Escherichia coli thymidylate synthase. A combined ITC and NMR approach showed that binding of substrate dUMP and cofactor mTHF occurs in both binding sites and dUMP binds with equal affinity. However, the two dUMP binding events are characterized by slightly different ΔCp showing that the two binding sites are not formally equivalent and presenting evidence for intersubunit communication. To probe this inequivalence a pair of mixed labeled dimers were created that can only bind substrate in one subunit and can be labeled on either subunit for NMR studies. These mixed labeled dimers enabled an NMR approach to distinguish the step-wise effects of ligand binding to this dimeric enzyme with subunit specificity. Binding studies revealed an asymmetric response to the two dUMP binding events and evidence of an extreme state in the singly bound form. The mixed dimers allow for visualization of singly bound peak positions which are typically elusive for dimeric systems. In thymidylate synthase these singly bound peaks fall in unexpected patterns that yield new insight into intersubunit communication.
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Rights statement
  • In Copyright
Advisor
  • Traut, Thomas
  • Carter, Charles
  • Pielak, Gary J.
  • Zhang, Qi
  • Lee, Andrew
Degree
  • Doctor of Philosophy
Degree granting institution
  • University of North Carolina at Chapel Hill Graduate School
Graduation year
  • 2017
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