Correlation of Structure and Function of Zinc Metalloproteins Via a Combined NMR/Molecular Theory Approach
EMSL Project ID
20894
Abstract
The critical nature of zinc in biology requires a detailed understanding of the chemistry, structure, and bondings of these zinc complexes and how, in turn, these manifestations alter the chemistry at the metal binding site. In zinc metalloproteins, the role of zinc can either be structural or catalytic. The structural role of zinc is dictated by its propensity to occupy tetrahedral sites rather than octahedral or pentacoordinate sites in metalloproteins. The catalytic properties often take advantage of the fact that the Zn2+ ion has an intermediate value of hardness or softness. This intermediate hardness introduces an element of flexibility into the Lewis acidity of the Zn2+ ion. Several reviews on this aspect of zinc chemistry have been published. A qualitative understanding is not sufficient, and a direct probe of zinc is required. Historically, the only reliable method for such a characterization of a zinc site has been through X-ray crystallography. X-ray crystallography has been the dominant method because of the unfavorable spectroscopic properties associated with Zn2+. With a stable 3d10 electron configuration, the Zn2+ ion is not amenable to investigation by either UV/Vis or EPR spectroscopy. Recently, a methodology has been implemented to measure the solid-state 67Zn NMR spectrum of zinc metalloproteins. As zinc is quadrupolar with a nuclear spin of 5/2, the dominant interaction in the NMR spectroscopy is the electric field gradient (EFG) at the nucleus in question. The principal observable in a 67Zn NMR experiment will be the quadrupole coupling constant, Cq. Analysis of the lineshape leads to the determination of Cq, which is directly proportional to the EFG at the Zn2+ ion. This relationship results in the Cq being sensitive to changes in structure and bonding as the EFG originates from the nature of the bonding (i.e. amount of ionic character) of the Zn2+ to its ligands. Therefore, the interpretation of this data is highly dependent on the quality of the model developed for the metal center and its surrounding environment. A comprehensive computational approach will be utilized to gain a molecular level understanding of the structural and functional properties of the active sites in zinc metalloproteins. The computational work proposed in this project will be primarily based the combined quantum mechanics molecular mechanics (QM/MM) methodology. In this approach the system is divided into two regions - chemically important region treated with quantum mechanical level of theory (QM region) and surrounding region (MM region) described using molecular mechanics. In our case the QM region will consist of a zinc binding site that include the metal ion(s) and functional groups that constitute the first coordination shell. Depending on a particular situation (i.e. hydrogen bonding) some fragments of the second coordination shell may also be included. We estimate that a typical size of the QM region will be on the order of 100-200 atoms. The rest of protein will be described at the molecular mechanics level using Amber-type force field. Given large size of the QM region and the need to employ high quality basis sets for accurate property calculations the proposed work will require a substantial computational resources. Large scale simulations of that scope are becoming a reality but they do require state-of-the-art computational software that can take advantage of massively parallel architectures. In our project we will rely heavily on QM/MM implementation in NWChem - comprehensive suite of computational chemistry and classical molecular dynamics methods which are specifically designed to run large scale simulations on high-performance parallel supercomputers.
Project Details
Project type
Capability Research
Start Date
2006-10-01
End Date
2009-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Gu W, and VH Helms. 2007. "Different Protonation Equilibria of 4-Methylimidazole and Acetic Acid." Chemphyschem 8(17):2445-2451. doi:10.1002/cphc.200700442
Lipton AS, and PD Ellis. 2007. "Modeling the Metal Center of Cys4 Zinc Proteins." Journal of the American Chemical Society 129(29):9192-9200.
Lipton AS, RW Heck, GR Staeheli, M Valiev, WA De Jong, and PD Ellis. 2008. "A QM/MM Approach to Interpreting 67Zn 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.