Title

Transfer of Cu(I) between Metal Binding Sites and the Development of Cu(I) Force Field Parameters Using Charmm

Defense Date

6-8-2007

Graduation Date

Summer 1-1-2007

Availability

Restricted

Submission Type

dissertation

Degree Name

PhD

Department

Chemistry and Biochemistry

School

Bayer School of Natural and Environmental Sciences

Committee Chair

Charles T. Dameron

Committee Member

Jeffrey D. Evanseck

Committee Member

Mitchell E. Johnson

Committee Member

Steven M. Firestine

Keywords

Enterococcus hirae, E. hirae, Cu(I) ATPase, Cu(I) Parameters, Cu(I) proteins, metalloproteins, CHARMM Cu(I) parameters

Abstract

Binding and transfer of Cu(I) between three key proteins in the bacterium Enterococcus hirae has been studied. CopA, an ATPase protein, was truncated, and its metal binding domain (AMBD) was expressed as a fusion with maltose binding protein (abbreviated as MALA). MALA binds 1 mol equivalent of Cu(I) and transfers its Cu(I) to the repressor protein CopY. AMBD performs the same Cu(I) transfer role as the chaperone CopZ. The results suggest that AMBD has a higher Cu(I) binding affinity than CopZ. Within E. hirae, Cu(I) is transferred from CopZ to AMBD, suggesting its role as an import/export Cu(I) pump.

CHARMM force field topology and parameters for Cu(I) binding in proteins have been developed for both linear and trigonal planar coordination geometries. Model compounds containing these coordination geometries were selected. Parameterization strategy involved exploring four different methods: B3LYP, S-VWN, MPW1K and MP2 to determine the most accurate results when compared to crystal structures. Two models were implemented: the MPW1K method with the 6-311+G(p, d) basis set for the linear model and 6-31G(3d) basis set for the trigonal planar model. The error between CHARMM and MPW1K/ 6-311+G(d, p) for the linear model is 0.003 ± 0.002 Å for the Cu-S bond distances and 6 ± 4° for the S-Cu-S bond angle. The resulting error for the optimized CHARMM and MPW1K/6-31G(3d) level of theory for the trigonal planar model compound is 0.022 ± 0.015 Å for the Cu-S bond distances and 4 ± 3 ° for angles. Parameters were developed and tested for CHARMM using the Cu(I) chaperone for Superoxide dismutase, containing a linear coordination, and the Cu(I) human chaperone Hah1, containing a trigional planar coordination. The resulting heavy-atom RMSD values for the linear and trigonal planar test cases are 2.38 ± 0.46 Å and 1.20 ± 0.9 Å, respectively. The Cu-S distances measured from test cases provided excellent results when compared to experiment.

Format

PDF

Language

English

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