Publication Date


Document Type


First Advisor

Zheng, Chong (Professor of chemistry)

Degree Name

M.S. (Master of Science)

Legacy Department

Department of Chemistry




Three different studies have been earned out to investigate protein-structure function relationships. The HIV-1 protease cleavage sites were analyzed using neural networks. Sixty four octamers known to cleave were used to train (find a solution) neural networks using the backpropagation algorithm. The network input consisted of different amino acid characteristics such as hydrophobicity. The weights from these trainings were then used to predict if certain sequences could cleave. The networks were also applied to probe the subsite interactions. On average the networks predicted 80% of the sequences correctly. The second study included a molecular dynamics and energetic analysis of the four a-helix bundle motifs. The simulation results as well as the x-ray data show that the atomic RMS fluctuation is larger at the loop region for four representative proteins: methemerythrin, cytochrome b-562, cytochrome c', and bovine somatotropin. The loop-loop, helix-helix and loop-helix interactions are computed for the unfolded and folded proteins. In the folded and solvated protein structures the loop-helix interaction is stronger than the helix-helix interaction, especially in the electrostatic component The stabilization due to the protein-solvent interaction is greater in the helix region than in the loop region. The percentage of hydrophilic solvent accessible area for the four proteins was calculated with the method of Eisenberg and McLachlan. A Poisson- Boltzmann calculation shows that the potential from the loops acting on a helix is generally more negative than that from other helices. Finally, expression of a mutant of cytochrome c peroxidase was accomplished using the T7 expression system. The system was constructed to accommodate any primers to yield different mutations through PCR. Rabbit antibodies were produced to confirm protein production. The protein was produced in higher quantities than previous expression systems but it still requires high yields for practical applications.


Includes bibliographical references (pages [116]-121)


ix, 141 pages




Northern Illinois University

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