Correlation of Structure and Function of Zinc Metalloproteins Via a Combined NMR/Molecular Theory Approach
EMSL Project ID
19834
Abstract
One of the most significant challenges in the metallobiochemistry of Zn2+ is the a priori determination of how the metal center will facilitate a particular chemical reaction. Two examples illustrate this challenge. The first involves the activation of water. What is the pKa of water bound to Zn2+ in a protein and how is the pKa modulated by the protein structure? This is an unanswered question. The reason is that x-ray scattering methods cannot address this issue due to the essential role of protons in answering the question and the uncertainty in a given Zn-O bond distance. Protein examples reflective of these chemical questions are human carbonic anhydrase (CAII), UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) and alkaline phosphatase (AP). The second example involves the structural influence when Zn2+ is found in a cysteine rich environment. Depending on the structure of the protein, Zn2+ tetrahedrally coordinated by cysteinyl ligands can be either a structural site or it can promote the nucleophilicity of the one of the cysteinyl ligands to catalyze an alkyl transfer reaction. Proteins illustrating this conundrum are two DNA repair proteins: human xeroderma pigmentosum complement A (XPA - structural site) and E. coli. Adaptive response to alkylation (Ada - catalytic site). The key to addressing these issues is through a collaboration of a spectroscopic technique, which is critically sensitive to the electrostatics at the metal center, and molecular theory. The spectroscopic technique is the solid-state 67Zn NMR of the metalloproteins in question. Molecular theory in this case involves a hybrid QM/MM approach to develop a model for role the metal plays in these systems.We feel this problem fits well with the EMSL Biological Interactions Science theme. We have brought together a team of experimentalists (biochemists and spectroscopists) in collaboration with molecular theorists to develop the methods that can address their experimental results. The methodologies utilized to solve these questions will directly enable future work in the determination of structure/function relationships in proteins. This work can also have implications for bioremediation, heavy-metal trafficking within microbial communities, understanding the effects of radiation damage in the sense of DNA repair proteins, and bioterrorism (the lethal factor of anthrax is a zinc metalloprotein). All of which are relevant to needs of the DOE and the nation. The NIH through individual peer reviewed grants funds all of the proposed work.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2006-10-01
End Date
2009-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Lipton AS, MM Morlok, G Parkin, and PD Ellis. 2008. "67Zn Solid-State NMR Spectroscopy of {[TpBut,Me]Zn(OH2)}[HOB(C6F5)3]. The Importance of the Anion [HOB(C6F5)3]-." Inorganic Chemistry 47(12):5184-5189. doi:10.1021/ic800009b
Lipton AS, PD Ellis, and TE Polenova. 2009. "Quadrupolar Metal Nuclides in Bioinorganic Chemistry: Solid-State NMR Studies." In Encyclopedia of Magnetic Resonance. John Wiley & Sons, Ltd., Hoboken, NJ.
Lipton AS, RW Heck, GR Staeheli, M Valiev, WA De Jong, and PD Ellis. 2008. "A QM/MM Approach to Interpreting Zn-67 Solid-State NMR data in Zinc Proteins." Journal of the American Chemical Society 130(19):6224-6230.
Lipton AS, RW Heck, M Hernick, CA Fierke, and PD Ellis. 2008. "Residue Ionization in LpxC Directly Observed by 67Zn NMR Spectroscopy." Journal of the American Chemical Society 130(38):12671-12679.