I. Theoretical investigations of the sequence-dependent structure and dynamics of oligodeoxyribonucleotides. II. Thermodynamic perturbation Gibbs free energy calculations of the self-association of human insulin analogues

James Thomas Metz, Purdue University

Abstract

In part I, the sequence dependent structure and dynamics of the 12mer oligodeoxyribonucleotide, d(CGCGAATTCGCG)$\sb2$, were investigated using the molecular mechanics program AMBER. Initial structures were obtained from X-ray crystallography and model building and were subjected to potential energy minimization and molecular dynamics calculations. The helical twist angle, roll angle, propeller twist angle, and change in delta backbone torsion angle were calculated using the program NEWHELIX and were compared to predictions from the Calladine rules. The agreement between predictions from the Calladine rules and helical parameters obtained from calculated structures varied widely. A refinement of the NMR solution structure of the 10mer oligodeoxyribonucleotide, d(CCCGATCGGG)$\sb2$, was performed with the programs AMBER and MORASS and a set of 2D NOESY data starting from A- and B-DNA model-built structures. In part II, the relative difference in Gibbs free energies of self-association of five human insulin B-chain analogues, HI B-Lys28Pro29, B-Pro28Pro29, B-Lys28Lys29, B-Pro28Lys29 (human insulin), and B-Asp28Lys29, were calculated using the thermodynamic perturbation window growth approach implemented in AMBER. The calculated relative differences in free energy were compared to the results of sedimentation equilibrium experiments. For comparison to the free energy perturbation method, the potential energies of HI B-Pro28Lys29 and B-Lys29Pro28 monomers and dimers were calculated using molecular dynamics and potential energy minimization. Thermodynamic perturbation Gibbs free energy calculations were found to be more accurate for the purpose of predicting the relative self-association of human insulin analogues than molecular dynamics and potential energy minimization methods.

Degree

Ph.D.

Advisors

Gorenstein, Purdue University.

Subject Area

Biochemistry|Pharmacology|Chemistry

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