Is a malleable protein necessarily highly dynamic? The hydrophobic core of the nuclear coactivator binding domain is well ordered.

Abstract

The nuclear coactivator binding domain of CREB binding protein folds into remarkably different structures in complex with different ligands. To understand the mechanism of the structural adaptability in the nuclear coactivator binding domain (NCBD), we have compared the dynamics of the hydrophobic core of NCBD in the ligand-free state and in a well-folded complex with the ligand activator for thyroid hormone and retinoid receptors using multiple NMR methods including methyl chemical shifts, coupling constants, and methyl order parameters. From all NMR measures, the aliphatic side chains in the hydrophobic core are slightly more dynamic in the free protein than in the complex, but have mobility comparable to the hydrophobic cores of average folded proteins. Urea titration monitored by NMR reveals that all parts of the protein, including the side-chain packing in the hydrophobic core, denatures in a single cooperative process. The molten globule characteristics of NCBD are thus restricted to a slowly fluctuating tertiary structure. Consequently, the conformational plasticity of the protein is most likely related to its low overall stability rather than an intrinsically flexible protein structure. The well-defined structure supports a model of molecular recognition dominated by conformational selection, whereas only minor structural adjustments are necessary after the association.