Professor, Biological Chemistry
M.Sc., University of Amsterdam, Netherlands
Ph.D., University of Nijmegen (Hilbers), Netherlands
Postdoctoral, University of Groningen (Kaptein), Netherlands
Postdoctoral, ETH Zurich (Wuthrich), Switzerland
Research Profile
NMR studies of Biomacromolecular Conformation, Dynamics and Interactions in Solution
The NMR methodolgy has now matured to the point that the systems up to 100 kDa can be studied at atomic level. The proteins are in solution and carry out the conformational changes and dynamic interactions necessary for function while the NMR experiments are running.
Our group applies all aspects of these methodologies to study Hsp70 protein-folding chaperone proteins in solution. Hsp70's mediate trafficking, triaging, folding, unfolding and refolding of other proteins in vivo, from bacteria to man. The group's high-resolution solution structure determinations of Hsp70 domains, as well as studies of atom-resolved dynamics and ligand interactions, have led to the formulation of an allosteric mechanism for these proteins. These mechanisms are being investigated in depth with large constructs (up to 60 kDa) that have become accessible for TROSY NMR studies by using 800 MHz equipment. We discover that these active allosteric constructs in solution change their conformation in upon ligand binding, while such is not the case in the crystal. We are also investigating complexes of chaperone and co-chaperone proteins in different allosteric states.
Dynamics (local motion) is an essential component of biological functioning. Without motion, proteins cannot accomodate ligands, carry out chemistry, be allosterically active or be thermally stable. The group is working on the fundamental problem of the modeling of local motions. In several small proteins, the group has found evidence for correlated motions, for conformational change dynamics in enzyme active sites and for large changes in entropy contained in the dynamics of the protein backbone upon ligand binding.
In collaboration with other labs, the group studies the allosteric enzyme GCTase; maps the interaction interface between protein domains; and complements X-ray structure determinations of proteins with a relevant solution structure, dynamical and ligand-binding data.
The laboratory has dedicated 500 and 600 MHz NMR spectrometers, and we are main users of a another 600 MHz and a 800 MHz NMR spectrometer. The state-of-the-art instruments are equipped with four radio-frequency channels and (cryogenic) triple-resonance gradient probes for the execution of the most modern multi-dimensional NMR experiments. A large Silicon Graphics / P.C. computer cluster is available for data processing, spectral interpretation and structure display. We have two wet-labs for protein mutagenesis, expression, purification and sample preparation.
Our group is housed in the Chemesitry builiding on Central Campus. Together with two other biological NMR groups in that builiding (Al-Hashimi and Ramamoorthy) we form a vibrant NMR research community of about twenty-five students and post-docs, with combined group meetings, parties and specialized seminars.
Awards
1980-1982 Postdoctoral Research Fellowship, Netherlands Organization for the Advancement of Pure Research (ZWO), The Hague, The Netherlands
1982-1983 Postdoctoral Research Fellowship, The Roche Foundation, Basel, Switzerland
1982-1983 Postdoctoral Research Fellowship, The Federation of European Biological Societies
2002 Pfizer Research Award
2004 Fellow of the American Association for the Advancement of Science
Representative publications
Zuiderweg, E.R.P., Kaptein, R. and Wuthrich, K.: Secondary structure of the lac-repressor DNA binding domain by two dimensional 1H NMR in solution. Proc. Natl. Acad. Sci. USA 1983; 80: 5837-5841.
Zuiderweg, E.R.P., Scheek, R.M., Boelens, R., Van Gunsteren, W.F. and Kaptein, R.: Determination of protein structures from nuclear magnetic resonance data using a restrained molecular dynamics approach: the lac-repressor DNA binding domain. Biochimie 1985; 67: 707-715.
Zuiderweg, E.R.P. and Fesik, S.W.: Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a. Biochemistry, 1989; 28: 2387-2391.
Morshauser, R.C., Wang, H., Flynn, G.C and Zuiderweg, E.R.P. The peptide binding domain of the chaperone-protein Hsc70 has an unusual secondary structure topology. Biochemistry, 1995; 34, 6261-6266
Fischer, M.W.F., Zeng, L., Majumdar, A. and Zuiderweg, E.R.P., Characterizing Semi-Local Motions in Proteins by NMR Relaxation Studies, Proc. Natl. Acad. Sci, USA, 95, 8016-8019 (1998)
Morshauser, R.C., Hu, W., Wang, H., Pang, Y., Flynn, G.C. and Zuiderweg, E.R.P. High resolution solution structure of the 18 kda substrate binding domain of the mammalian chaperone protein hsc70. J. Mol. Biol, 289, 1387-1403 (1999)
Pellecchia, M., Stevens, S.Y., Vander Kooi, C.W., Montgomery, D.H., Feng, E.H., Gierasch, L.M., and Zuiderweg, E.R.P. Structural insights into substrate binding by the molecular chaperone DnaK. Nature Structural Biology,7, 298- 303 (2000)
Wang, L., Pang, Y., Holder, T., Brender, J.R., Kurochkin, A, Zuiderweg, E.R.P. Functional Dynamics in the active site of the ribonuclease Binase, Proc. Natl. Acad. Sci. USA, 98, 7684-7689 (2001)
Stevens, S.Y., Sanker, S., Kent, C. and Zuiderweg, E.R.P. Delineation of the allosteric mechanism for a cytidylyltransferase exhibiting negative cooperativity, Nature Structural Biology 8, 947-952 (2001). http://proquest.umi.com.proxy.lib.umich.edu/pqdweb?index=6&did=1013301291&SrchMode=1&sid=1&Fmt=6&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1231779966&clientId=17822
Kern, D. and Zuiderweg, E.R.P. The role of dynamics in allosteric regulation, Current Opinion in Structural Biology, 13, 748-757 (2003)
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, 101:10272-10277, (2004). http://www.pnas.org.proxy.lib.umich.edu/content/101/28/10272.full.pdf+html?sid=6e7e505b-3c01-4b6a-bddc-6dbbecec22d1
Deep, S., Im, S.C., Zuiderweg, E.R.P., and Waskell, L. Characterization and Calculation of a cytochrome c-cytochrome b5 complex using NMR data. Biochemistry 44, 10654-10668 (2005). http://pubs.acs.org.proxy.lib.umich.edu/doi/abs/10.1021/bi050482x?journalCode=bichaw&quickLinkVolume=44&quickLinkPage=10654&volume=44
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. 127, 828-829 (2005).http://pubs.acs.org.proxy.lib.umich.edu/action/doSearch?searchText=zuiderweg&searchSub=Search&publication=40001010
Revington, M., Zhang, Yip, G.N.B., Kurochkin, A.V. and Zuiderweg, E.R.P. NMR investigations of allosteric processes in a two-domain Thermus Thermophilus Hsp70 molecular chaperone, J. Mol. Biol. 349, 163-183 (2005) http://www.sciencedirect.com.proxy.lib.umich.edu/science?_ob=ArticleListURL&_method=list&_ArticleListID=851518949&_sort=d&view=c&_acct=C000007678&_version=1&_urlVersion=0&_userid=99318&md5=cf984758219c8ae506c84a12c9deef3a
Bertelsen, E.B., Chang, L., Gestwicki, J.E. and Zuiderweg, E.R.P. Solution conformation of E.coli Hsp70 complexed with ADP and substrate, Proc. Natl. Acad. Sci. USA in the press (2009).