Clusters of Branched Aliphatic Side Chains Serve As Cores of Stability in the Native State of the HisF TIM Barrel Protein

Imidazole-3-glycerol phosphate synthase is a heterodimeric allosteric enzyme that catalyzes consecutive reactions in imidazole biosynthesis through its HisF and HisH subunits. The unusually slow unfolding reaction of the isolated HisF TIM barrel domain from the thermophilic bacteria, Thermotoga maritima, enabled an NMR-based site-specific analysis of the main-chain hydrogen bonds that stabilize its native conformation. Very strong protection against exchange with solvent deuterium in the native state was found in a subset of buried positions in alpha-helices and pervasively in the underlying beta-strands associated with a pair of large clusters of isoleucine, leucine and valine (ILV) side chains located in the alpha(7)(beta alpha)(8)(beta alpha)(1-2) and alpha(2)(beta alpha)(3-6)beta(7) segments of the (beta alpha)(8) barrel. The most densely packed region of the large cluster, alpha(3)(beta alpha)(4-6)beta(7), correlates closely with the core of stability previously observed in computational, protein engineering and NMR dynamics studies, demonstrating a key role for this cluster in determining the thermodynamic and structural properties of the native state of HisF. When considered with the results of previous studies where ILV clusters were found to stabilize the hydrogen-bonded networks in folding intermediates for other TIM barrel proteins, it appears that clusters of branched aliphatic side chains can serve as cores of stability across the entire folding reaction coordinate of one of the most common motifs in biology. (C) 2013 Elsevier Ltd. All rights reserved.