Controlling the dynamics of the Nek2 leucine zipper by engineering of “kinetic” disulphide bonds

Abstract

Nek2 is a dimeric serine/ threonine protein kinase that belongs to the family of NIMA-related kinases (Neks). Its N-terminal catalytic domain and its C-terminal regulatory region are bridged by a leucine zipper, which plays an important role in the activation of Nek2’s catalytic activity. Unusual conformational dynamics on the intermediary/slow timescale has thwarted all attempts so far to determine the structure of the Nek2 leucine zipper by means of X-ray crystallography and Nuclear Magnetic Resonance (NMR). Disulfide engineering, the strategic placement of non-native disulfide bonds into flexible regions flanking the coiled coil, was used to modulate the conformational exchange dynamics of this important dimerization domain. The resulting reduction in exchange rate leads to substantial improvements of important features in NMR spectra, such as line width, coherence transfer leakage and relaxation. These effects were comprehensively analyzed for the wild type protein, two single disulfide bond-bearing mutants and another double disulfide bonds-carrying mutant. Furthermore, exchange kinetics were measured across a wide temperature range, allowing for a detailed analysis of activation energy (ΔG‡) and maximal rate constant (k’ex). For one mutant carrying a disulfide bond at its C-terminus, a full backbone NMR assignment could be obtained for both conformers, demonstrating the benefits of the disulfide engineering. Our study demonstrates the first successful application of ‘kinetic’ disulfide bonds for the purpose of controlling the adverse effects of protein dynamics. Firstly, this provides a promising, robust platform for the full structural and functional investigation of the Nek2 leucine zipper in the future. Secondly, this work broadens the toolbox of protein engineering by disulfide bonds through the addition of a kinetic option in addition to the well-established thermodynamic uses of disulfide bonds.

Cysteines and Disulfide Bonds as Structure-Forming Units: Insights From Different Domains of Life and the Potential for Characterization by NMR

“…Current NMR and X-ray techniques allow defining the molecular structures of disulfide-rich biomolecules in high resolution. As disulfide bridges constitute the only natural covalent link between polypeptides strands, the acquired knowledge on their contribution to molecular scaffolding supports engineering of new cystine-based compounds with new functional (Nagarajan et al, 2018) or dynamical features (Gutmans et al, 2019), enhanced stability (Dombkowski et al, 2014), ultimately, aiming at improved pharmaco-kinetic and -dynamic properties for new therapies and treatment approaches. However, disulfide bonds tend to be unstable under reducing conditions, i.e., in many physiological situations, which triggered search for therapeutic compounds to make use of chemical modifications to stably replace these bonds.…”