Circular dichroism spectroscopy and the conformational analysis of globular proteins in the native and denatured state Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/6w924f423

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  • A simple matrix method for the analysis of protein circular dichroism (CD) spectra is presented and used to compute the secondary structure of globular proteins in their native and denatured states. The method uses singular value decomposition and generalized inverse algorithms, and a basis set of CD spectra for proteins whose secondary structures are known from x-ray crystallography. Inverse CD functions for five major secondary structures are constructed, and the fraction of each structure present in a protein is computed by taking the dot product of the inverse CD function with its CD spectrum. The method is tested by computating secondary structure for proteins in the basis set. Furthermore, the secondary structure of dihydrofolate reductase from T4 bacteriophage, a protein whose x-ray structure is not known, is predicted. CD analysis in conjunction with amino acid sequence information indicates that the T4 enzyme contains both parallel and antiparallel segments of β-sheet. This β-sheet mixture is found in several other proteins, and may represent a new subclass of tertiary folding. Remaining sections are devoted to analyzing the CD of proteins at extreme pH or temperature to determine the structural changes associated with denaturation. Studies of pH denaturation in myoglobin and concanavalin-A indicate that a-helices are affected by acid but not base; whereas, β-sheet is rearranged by base but is unaffected by acid. Thermal denaturation of ribonuclease and papain results in the denaturation of α-helix, without disturbing β-sheet. Analysis of papain indicates that its two separate domains are acting independently during denaturation.
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