Faculty

Solution NMR spectroscopy can simultaneously address, at an atomic level of resolution, aspects of structure, dynamics, interactions and energetics of complexes of biomacromolecules in solution.

Our group of around six graduate students and post-docs is involved in all of these aspects, doing in-depth fundamental structural biology studies on a limited number of systems.
Protein folding in human cells is mediated by chaperone proteins of the Hsp70 class. Using multi-dimensional multi-nuclear NMR, we elucidate the structure and mechanism of these important proteins, applying the most recent methods with our 800 MHz equipment. In addition, we study complexes (up to 80 kDa) of the chaperone proteins with target proteins and co-factors in binary and tertiary assemblies, which are essential to the in-vivo protein folding process.

Dynamics (local motions) is an essential component of biological functioning. Our credo is "where it matters it moves," expressing the common finding that enzyme active sites and intermolecular intraction interfaces are most often dynamical. The group is working on the fundamental problem of the experimental delineation of such local motions. In dynamical NMR studies on the ribonuclease Binase, the group has found evidence for extensive dynamics in the active site of the protein that likely is the rate-determining step in the cataylic process. Many more proteins are being investigated with these techniques. The results are compared with theoretical molecular dynamics studies and quantum chemistry calculations.

In collaboration with other labs, the group studies the conformational changes, kinetics and thermodynamics of allosteric enzymes and maps the interaction interfaces between proteins in large complexes. We have detected large differences between protein structure in the crystal and protein structure in solution for some of the systems we study.

The laboratory uses NMR instruments dedicated to biophysical research at 800, 600 and 500 MHz, and will have access to the new top-of-the-line 900 MHz system in the Michigan Life Sciences Corridor. Several instruments are equipped with cryogenic probes that boost NMR sensitivity three-fold. We have wet-labs for protein mutagenesis, expression, purification and sample preparation.

Awards

Fellow of the American Association for the Advancement of Science

Representative Publications

1. Wang, T., Cai, S. and Zuiderweg, E.R.P., "Temperature Dependence of Anisotropic Protein Backbone Dynamics", J. Am. Chem. Soc., 2003, 125, 8639.

2. Kern, D. and Zuiderweg, E.R.P., "The Role of Dynamics in Allosteric Regulation", Curr. Opinion Struct. Biol., 2003, 13, 748.

3. Revington, M. and Zuiderweg, E.R.P., "NMR Study of Nucleotide-induced Changes in the Nucleotide Binding Domain of Thermus Thermophilus Hsp70 Chaperone DnaK: Implications for the Allosteric Mechanism", J. Biol. Chem., 2004, 279, 33958.

4. Yip, G. and Zuiderweg, E.R.P., "A Phase Cycle Scheme that Significantly Suppresses Offset-dependent Artifacts in the R2-CPMG 15N Relaxation Experiment", J. Magn. Reson., 2004, 171, 25.

5. Zhang, Y. and Zuiderweg, E.R.P., "The Hsc70 Chaperone Nucleotide Binding Domain in Solution Unveiled as a Molecular Machine that Can Reorient its Functional Subdomains", Proc. Natl. Acad. Sci. USA, 2004, 101, 10272.

6. Wang, T, King Frederick, K., Igumenova, T.I., Wand, A.J. and Zuiderweg, E.R.P., "Changes in Calmodulin Backbone Dynamics upon Ligand Binding Revealed by Cross-correlated NMR Relaxation Measurements", J. Am. Chem. Soc., 2005, 127, 828-829.

7. Revington, M., Zhang, Y., Kurochkin, A.V. and Zuiderweg, E.R.P., "NMR Investigations of Allosteric Processes in a Two-domain, 55 kDa Thermus Thermophilus DnaK Molecular Chaperone", J. Mol. Biol., 2005, 349, 163-183.