Proteomic approach to the analysis of DNA-binding proteins using mass spectrometry Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/8p58pg84n

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  • In proteomic studies, separate experimental protocols have been necessary to identify proteins, determine their function, and predict their three-dimensional structure. In this study, a function-based separation of proteins was conceived to fractionate proteins prior to enzymatic digestion. In the initial demonstration of this technique, a DNA substrate was used to separate the DNA-binding proteins from the rest of the proteins in a lysate in order to identify protein function and to simplify the complex mixture of proteins. A total of 232 putative DNA-binding proteins and over 540 proteins in all were identified from E. coli. Hypothetical or unknown proteins were found, some of which bind to DNA. As a part of this demonstration, changes in protein expression caused by different environmental conditions (aerobic and anaerobic atmospheres) were observed. In a second demonstration, aimed at determining the three-dimensional structure of the DNA binding proteins, binding sites were blocked with oligonucleotides, and the modified proteins were purified, enzymatically digested, and subjected to tandem mass spectrometry. The amino acids in the DNA-binding domains of three proteins were determined. In a final application of function-based separation, DNA-binding proteins were digested with trypsin and the resulting peptides were separated using HPLC and subsequently analyzed using MALDI TOF/TOF and ESI Q-TOF instruments to study the complementary nature of the two ionization techniques, taking into account the differences between the mass analyzers. Based on the analysis of a large data set containing hundreds of peptides and thousands of individual amino acids, some of the currently held notions regarding the ionization processes were confirmed. ESI tends to favor the analysis of hydrophobic amino acids and peptides while MALDI is disposed toward mainly basic and aromatic species. These tendencies in ionization account in large part for the complementary nature of the peptides and proteins identified by the ESI and MALDI instruments and make it necessary to employ both types of instruments to gain the most information out of a given sample in a proteomics study.
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