Date of Award

January 2012

Document Type

Thesis

Degree Name

Master of Science (MS)

Department

Chemistry

First Advisor

Kathryn A. Thomasson

Abstract

The need to understand protein structure and interaction is ever-growing and this has led to scientist and investigators utilizing numerous different techniques in order to obtain substantial insights and explanation to these structures and their interactions. Circular dichroism (CD), which is one of these techniques, is a powerful structural biology technique used to study protein and nucleic acid structures and their dynamics. This technique is important because it identifies the secondary, tertiary and even quaternary structures in proteins and can be used to study folding patterns in proteins. Theoretical and experimental methods are used to better understand and teach the phenomenon of circular dichroism. First, molecular mechanics allows for the energy calculations of different conformations in large molecules like peptides and proteins. Theoretical CD via the dipole interaction model (DInaMo) is used to relate the structural nature of peptides and proteins to the experimental CD observed. Minimization was done on lysozyme, myoglobin and collagen, using the molecular modeling software package, Insight®II to obtain minimum energy structures suitable for CD calculations. Molecular dynamics simulations were performed in water at 300K to create an ensemble of conformations. The program CDCALC was used to predict the CD spectrum of the proteins for comparison with experiment. The output from CDCALC was analyzed using OriginPro Version 7.5 and the analyzed data reported as plots with data from synchrotron radiation circular dichroism (SRCD). Theoretical CD plots showed agreement with SRCD for location, sign, and bandwidths of the peaks. Experimental CD spectra of horse heart myoglobin and pea lectin were measured on a JASCO spectropolarimeter and compared to that obtained from the Protein Circular Dichroism Data Bank (PCDDB) in the development of a physical chemistry laboratory exercise to teach secondary structure analysis.

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