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Key stabilizing elements of protein structure identified through pressure and temperature perturbation of its hydrogen bond network

Abstract

Hydrogen bonds are key constituents of biomolecular structures, and their response to external perturbations may reveal important insights about the most stable components of a structure. NMR spectroscopy can probe hydrogen bond deformations at very high resolution through hydrogen bond scalar couplings (HBCs). However, the small size of HBCs has so far prevented a comprehensive quantitative characterization of protein hydrogen bonds as a function of the basic thermodynamic parameters of pressure and temperature. Using a newly developed pressure cell, we have now mapped pressure- and temperature-dependent changes of 31 hydrogen bonds in ubiquitin by measuring HBCs with very high precision. Short-range hydrogen bonds are only moderately perturbed, but many hydrogen bonds with large sequence separations (high contact order) show greater changes. In contrast, other high-contact-order hydrogen bonds remain virtually unaffected. The specific stabilization of such topologically important connections may present a general principle with which to achieve protein stability and to preserve structural integrity during protein function.

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Figure 1: Pressure and temperature stability of proteins according to Hawley's theory.
Figure 2: High-sensitivity quantitative detection of hydrogen bonds in human ubiquitin by h3JNC′ correlation spectroscopy.
Figure 3: Pressure-induced variations of all detected hydrogen-bond correlations in ubiquitin.
Figure 4: Combined pressure and temperature dependence of representative hydrogen-bond correlations in ubiquitin.
Figure 5: Pressure and temperature derivatives of stability of h3JNC′ as quantitative measures of hydrogen-bond stability.
Figure 6: Immediate vicinity of high- and low-stability hydrogen bonds in β-sheet β3/β5.

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Acknowledgements

The authors acknowledge H.-R. Kalbitzer for introducing them to high-pressure NMR technology and R. Peterson (Daedalus Innovations) for many helpful discussions. This work was supported by SNF grant 31-132857 (to S.G.) and a stipend from the Boehringer Ingelheim Fonds (to L.N.). This article is dedicated to Anna and Joachim Seelig, celebrating their 40 years of science and life at the Biozentrum Basel.

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L.N. and S.G. performed the experiments, analysed the data and wrote the Article.

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Correspondence to Stephan Grzesiek.

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Nisius, L., Grzesiek, S. Key stabilizing elements of protein structure identified through pressure and temperature perturbation of its hydrogen bond network. Nature Chem 4, 711–717 (2012). https://doi.org/10.1038/nchem.1396

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