alexa Characterization of the distribution of internal motions in the basic pancreatic trypsin inhibitor using a large number of internal NMR probes.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Glycomics & Lipidomics

Author(s): Wagner G

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Abstract The experimental observations described in this article indicated that a distribution of many different fluctuations is present in a globular protein. These fluctuations were characterized by observation of many natural internal probes such as the labile peptide protons and the aromatic side chains. The conditions which are necessary to get reactions of the internal probes have been discussed in detail. The structural interpretation of the data was facilitated by the development and the use of new NMR techniques which provided the identification of the resonances of all the labile peptide protons. With NOE measurements a distinction between correlated and uncorrelated exchange events was obtained. This enabled us to elucidate the exchange mechanism over a wide range of p2H and temperature and to classify different subsets of fluctuations with respect to their lifetimes. It was further demonstrated that a change of external conditions such as temperature, p2H or pressure can change the distribution of fluctuations in the protein. The mechanisms responsible for rotation of internal aromatic side chains were also found to change with temperature, and mechanistic aspects of these fluctuations were discussed. This demonstration of a manifold of spatial fluctuations in a small protein provides an impression on the kind of fluctuations which have to be expected for larger proteins. When studying protein reactions one should therefore consider the presence of a large number of different, transiently formed, spatial structures available for the partner in the reaction, which may pick out only that structure which will optimally perform a particular reaction with the highest efficiency.

  • Open Access
This article was published in Q Rev Biophys and referenced in Journal of Glycomics & Lipidomics

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