Amino Acid Networks in a (β/α)₈ Barrel Enzyme Change during Catalytic Turnover

Abstract

Proteins can be viewed as small-world networks of amino acid residues connected through noncovalent interactions. Nuclear magnetic resonance chemical shift covariance analyses were used to identify long-range amino acid networks in the α subunit of tryptophan synthase both for the resting state (in the absence of substrate and product) and for the working state (during catalytic turnover). The amino acid networks observed stretch from the surface of the protein into the active site and are different between the resting and working states. Modification of surface residues on the network alters the structural dynamics of active-site residues over 25 Å away and leads to changes in catalytic rates. These findings demonstrate that amino acid networks, similar to those studied here, are likely important for coordinating structural changes necessary for enzyme function and regulation.

Protein thermal denaturation is modulated by central residues in the protein structure network

“…This proposition is in agreement with previous studies showing that the allosteric modulation of protein function is mediated by the propagation of 'perturbation waves' through pre-existing pathways interconnected by central residues [15,16,20,[24][25][26][27]. Similarly, RIN are relevant for structural changes involved in enzyme function [28]. Eyring plots were used to search for details of the mechanism by which the perturbation of central residues change the thermal denaturation of Sfbgly (Figs 13-15).…”

Uncoupling Catalytic and Binding Functions in the Cyclic AMP-Dependent Protein Kinase A

“…To probe the conformational transitions of the enzyme with the different nucleotides, we mapped the enzyme’s amide fingerprint using [ 1 H, 15 N]-TROSY-HSQC experiments (Pervushin et al, 1997) as the amide chemical shifts are sensitive reporters of allosteric transitions (Figure S5) (Axe et al, 2014; Cembran et al, 2014; Selvaratnam et al, 2011). Although previous crystallographic structures of these complexes were reported to be identical (Johnson et al, 2001), small changes in chemical shifts have been demonstrated to report on subtle changes in conformation and allostery (Boulton et al, 2014; Selvaratnam et al, 2012a; Selvaratnam et al, 2012b).…”

Engineered control of enzyme structural dynamics and function

“…These long‐range networks may also offer means through which enzymes communicate in multi‐enzyme complexes . For example, we used NMR chemical shift covariance analysisamong a series of site‐directed protein variants to identify amino acid interaction networks in the alpha subunit of E. coli tryptophan synthase (αTS) . Our analysis revealed that there are two networks of residues [colored orange and blue in Fig.…”