Skip to ContentSkip to Navigation
About us Latest news News News articles

Protein structure and dynamics by NMR: synergy between biochemistry and pulse sequence design

18 March 2011

PhD ceremony: Mr. R. Otten, 11.00 uur, Academiegebouw, Broerstraat 5, Groningen

Title: Protein structure and dynamics by NMR: synergy between biochemistry and pulse sequence design

Promotor(s): prof. B. Poolman

Faculty: Mathematics and Natural Sciences


Proteins are the molecular machines of a cell and are involved in virtual all cellular processes. To understand the function of these biological macromolecules, it is of critical importance to complement a high-resolution 3-dimensional structure with a detailed insight in its molecular dynamics.

The work described in this thesis focuses on the development of nuclear magnetic resonance (NMR) methods to study protein structure and dynamics, using an approach where novel NMR pulse sequences are designed in concert with specific biochemical labeling patterns. In particular, methyl-containing amino acids are targeted because they are important reporters of protein structure and dynamics. Methodology is described for the residue-specific assignment of methyl-groups and their use in investigating protein dynamics on the micr micro sec time scale. The experiments have been used to study the 34 kDa periplasmic binding protein FepB and the transcriptional activator NtrC. Our results indicate that these methods allow for a comprehensive and cost-effective study of protein structure and dynamics for proteins up to ~40 kDa. Furthermore, we demonstrate the strength of NMR spectroscopy to characterize an important class of proteins, the so-called intrinsically disordered proteins. Their structural characterization is challenging due to the inherent flexibility and NMR is, therefore, the most appropriate technique to study them. A novel experiment to probe the local polypeptide backbone structure is described together with its application to human neuroligin-3. The synergy between developments in biochemistry and NMR methodology are shown to be crucial for the advancement of NMR spectroscopy in the field of structural biology.



Last modified:13 March 2020 01.09 a.m.
View this page in: Nederlands

More news

  • 29 November 2023

    Three FSE researchers receive NWO XS grant

    Three researchers of the Faculty of Science and Engineering have been awarded an ENW-XS grant by the Dutch Research Council (Nederlandse Organisatie voor Wetenschappelijke Onderzoek, NWO): Prof. A.I. Guskov the Groningen Biomolecular Sciences and...

  • 29 November 2023

    UG professor Jayawardhana appointed scientific director DISC

    Bayu Jayawardhana has been appointed scientific director of DISC, the interuniversity research institute and graduate school that unites all university groups in the Netherlands that are active in systems and control theory and engineering. The...

  • 23 November 2023

    Two Major European grants for Groningen researchers

    Researchers Clemens Mayer and Danny Incarnato of the University of Groningen have been awarded an ERC Consolidator Grant.