Protein design and simulation. Part I. Protein design. Part II. Protein simulation

Citation

Park, Changmoon (1993) Protein design and simulation. Part I. Protein design. Part II. Protein simulation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/sv6x-9s75. https://resolver.caltech.edu/CaltechTHESIS:11112009-114142428

Abstract

Since specific DNA binding proteins play many important roles in the regulation of cellular reactions including replication, transcription, and translation by the specific interactions of DNA binding proteins with DNA, the design and synthesis of sequence-specific DNA binding proteins is of great interest in modern chemistry and biology. Chapter 1 introduces a strategy by which to design new protein structures recognizing new sequences of DNA. The results of experiments using new protein show that there is cooperation between the monomers in binding to DNA and each monomer recognizes the half-site of the dimer binding site. Chapter 2 describes the advantage of palindromic sites and dimerization in DNA recognition according to the experimental results. The results also show that each monomer in a dimer recognizes one half-site of the dimer binding site irrespective of the relative orientation monomer in the dimer and the dimer binding site depends on the relative orientation of the two monomer in the dimer. Chapter 3 shows that the monomer of DNA binding region of the v-Jun leucine zipper protein recognizes the dimer binding site. Our results support the possibility that two monomers of v-Jun might bind sequentially to the dimer site with dimerization of v-Jun occurring while bound. Chapter 4 describes the design of a new protein recognizing a new 16 by site in DNA. Our results show that there is cooperation between monomers and all three monomers in the new peptide recognize unique half-sites in the proposed trimeric binding site. Chapter 5 describes quantum mechanical calculations on the active site of cytochrome P-450cam to improve force constants for the molecular simulations of cytochrome P-450cam. Our results show that the size of iron ion is a function of its spin and oxidation state and plays a key role in the process of oxygenation.

Thesis Files