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Force Field Development for Calbindin D9k

DURHAM, PHILIP R.

Abstract Details

2008, MS, University of Cincinnati, Arts and Sciences : Chemistry.
The potential energy surfaces of both calcium binding sites in calbindin D9k were determined in DFT calculations using the Gaussian031 program. The potential energy surfaces were also determined using the CHARMM2 program; the default force field and a charge modified force field were used in the classical calculations. The potential energy surface was found for the interaction energy between the Ca2+ ion and the ligand oxygens plus limited neighbors. The binding sites are in the form of a pentagonal bipyramid around the calcium where 6 of the ligands are contributed by the protein and one is an oxygen atom from a water molecule. A large and significant difference is seen between the classical and quantum results; this dictates that any classical calculations involving the calcium ion in this and other EF-hand structures need to take this into account. A potential has been calculated using a Metropolis Monte Carlo simulated annealing procedure. Future work will implement this potential into a classical molecular dynamics program.
Thomas L. Beck, PhD (Committee Chair)
Bruce S. Ault, PhD (Committee Member)
William B. Connick, PhD (Committee Member)
46 p.

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Citations

  • DURHAM, P. R. (2008). Force Field Development for Calbindin D9k [Master's thesis, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1218547540

    APA Style (7th edition)

  • DURHAM, PHILIP. Force Field Development for Calbindin D9k. 2008. University of Cincinnati, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1218547540.

    MLA Style (8th edition)

  • DURHAM, PHILIP. "Force Field Development for Calbindin D9k." Master's thesis, University of Cincinnati, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1218547540

    Chicago Manual of Style (17th edition)