The evolution of dynamic amino acid interaction networks around the catalytic cycle of α tryptophan synthase

Abstract

Networks of noncovalent interactions play important roles in the structural dynamics of globular proteins. Allosteric signals can propagate from the surface of an enzyme into its active site through these amino acid interaction networks. We used nuclear magnetic resonance (NMR) chemical shift covariance analyses1 on a catalytically inactive variant of the alpha subunit of tryptophan synthase to map amino acid interaction networks across its entire catalytic cycle. We used site‐specific Ala‐to‐Gly substitutions at loop residues to generate small network perturbations2. The amino acid substitutions lead to chemical shift changes both local and remote from the site(s) of perturbations. Residues with covarying chemical shift changes across this series of perturbations are proposed to be involved in the same conformational change, and thus belong to the same amino acid interaction network3.Our studies indicate that different enzyme states have different sets of chemical shift correlations, the chemical shift correlations change as a function of the catalytic cycle, and the changes in chemical shift correlations are coordinated with each other. These studies indicate that long‐range interaction networks systematically strengthen (or weaken) as a function of catalytic cycle progression.Most residues identified in these networks are dynamic on the μs‐ms timescale according to NMR 15N R2 relaxation dispersion studies4. Amino acid substitutions at surface‐exposed, network positions lead to the suppression of these structural dynamics and abrogate the stimulation of the alpha subunit's catalytic activity by the beta subunit. The evolving long‐range interaction networks are likely important in positioning catalytic machinery, controlling protein structural dynamics, and coordinating functional interactions with the beta subunit. In general, amino acid interaction networks offer opportunities to modify state‐specific enzyme function and regulation.Support or Funding InformationNSF MCB‐1615032This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.