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Biological Sciences Division
Research Highlights

February 2008

New NMR Method to Characterize Proteins

A metal-amino acid motif is found to be involved in catalytic reaction

Portrait of Paul Ellis
Paul Ellis

Results: Scientists at Pacific Northwest National Laboratory used solid-state nuclear magnetic resonance methods to develop a method to understand the structure-function relationships in metallo-proteins. They found that a metal-amino acid motif once thought to only play a structural role in proteins can, in special cases, be reactive.  The scientists' methods are helping to understand when the zinc and sulfur-containing thiol groups in the amino acid cysteine (Cys) play a structural role in proteins or are involved in the catalysis of alkyl group transfer. 

Why it matters: Alkyl groups, which are composed of carbon and hydrogen atoms arranged in a chain, are very common in organic molecules and are important to biological systems.  For example, alkyl group transfer is important to DNA repair and protein synthesis.  Only one particular arrangement of zinc and Cys—when one zinc atom is coordinated with four Cys molecules—has been found to be involved in catalysis of alkyl group transfer. This arrangement represents a new class of biological zinc sites.  Depending on the thiol environment of the zinc atom—how the sulfur atoms in the Cys are coordinated to the zinc—the site may or may not play a catalytic role.

Methods: The research team used a 900-MHz NMR spectrometer and supercomputer at the Department of Energy's Environmental Molecular Sciences Laboratory, a national scientific user facility located at PNNL. They also used NWChem, computational chemistry software developed at PNNL, to perform experimental measurements and apply computational models to five known compounds. In one of these, zinc is coordinated to four sulfurs, including one compound that is a synthetic analogue of Ada, a known alkyl-transfer and DNA-repair protein.

Peptide
Scientists are developing a method to understand proteins better, merging NMR experiments and theory to study compounds containing zinc (pink) and sulfur (yellow). Enlarged View

The team employed a two-step process: they first used solid-state 67Zn NMR to correlate known structural details about each complex to its NMR parameters.  They then compared their experimental findings with molecular theory performed at varying levels of detail to determine what method best predicted the NMR characteristics. Their results, published in the Journal of the American Chemical Society, show the zinc-Cys system to be sensitive to small structural changes and illustrate the level of theory adequate for predicting NMR results.

What's next: In the future, the team's approach could be used to model and characterize proteins whose structure-function relationship is not well understood, such as Ada. 

Acknowledgments: This work was funded by the National Institutes of Health, and the NMR experiments were performed in EMSL. The research team included Dr. Andrew Lipton and Dr. Paul Ellis, PNNL, in collaboration with Prof. Gerard Parkin of Columbia University and Prof. Daniel Reger of the University of South Carolina.

Reference

Lipton AS and PD Ellis.  2007.  "Modeling the metal center of cys4 zinc proteins."  Journal of the American Chemical Society 129(29):9192-9200.


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