Human diseases may be caused by the malfunction of an intact protein. Hydrogen bond (h-bond) is one of the key interactions in maintaining the structure of a protein and facilitating its function. The presence and extent of h-bond cooperativity in proteins remains a fundamental question, and quantitative analysis of h-bond cooperativity is still lacking.
The Modelling and Simulation Group from the Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT) of the Chinese Academy Sciences, led by Professor YAO Lishan, demonstrated the quantitative analysis of the h-bond cooperativity in an intact (or natural) protein.
This study was conducted by a modified hydrogen/deuterium (i.e. H/D) exchange NMR (Nuclear Magnetic Resonance) spectroscopy method. The method is based on the fact that the substitution of NH by ND in a backbone amide group slightly weakens the N−H•••O−C h-bond. Such a substitution impacts the h-bonds nearby as reflected by their 1H and 15N chemical shift changes of the NMR spectra. The fitting of the chemical shifts of the nearby residues to the exchange rates provides new quantitative insights into the cooperativity of h-bonds in the protein.
In Figure 1, the experimental results showed that the H/D exchange at amide sites i−3 to i+3 all perturbs the h-bond at amide site i of α-helix, suggesting a positive cooperativity between these 6 h-bonds and the h-bond at amide site i. The quantum mechanical (QM) calculations demonstrated that the cooperativity is originated from the electrostatic polarization which affects the peptide plane electric dipole moment and thus the h-bond strength. In brief, the experimental and theoretical results implied very good consistence.
This work is the first study detecting the h-bond cooperativity in an intact protein α‑helix. This approach can also be employed to study h-bond cooperativity in β-sheets (another important structure unit within a protein, besides α‑helix, see Figure 1) of a protein or other biomolecules such as DNA and RNA. It is supposed that such studies may provide fundamental understanding for practical or diagnostic applications in future. This study was published on Journal of the American Chemical Society.
| Figure 1. Perturbation of a backbone hydrogen bond creates a response of nearby hydrogen bonds (Image by QIBEBT) |
Observation of α-Helical Hydrogen-Bond Cooperativity in an Intact Protein, Journal of the American Chemical Society, 2016, 138, 1824-1827.
Contacts: Prof. YAO Lishan
Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences