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Protein functional explorations using mass spectrometry, nuclear magnetic resonance imaging and bioinformatics tools

Jennifer Cheri Copeland, University of Nebraska - Lincoln


Proteins are the workhorses of the cells. The Human Genome Project, completed in 2001, opened the pathway to genomic studies, as the knowledge of so many putative proteins sparked the interest of scientists around the world. Whole and partial genomes are completed continually, and there are nearly 28 million putative proteins predicted from these. A rapid approach for dealing with these involves using bioinformatics with sequence and structural homology, but these only help annotate around 60% of the proteins, leaving a large number of proteins that cannot be approached through computation alone. Biological assays of all of these proteins are cost- and time-consuming and not feasible with this large (and growing) number. High-throughput screening (HTS) techniques have been developed to approach this through a combinatorial approach. These include using highly sensitive analytical detectors like mass spectroscopy (MS) and nuclear magnetic resonance imaging (NMR). This can cut down on the time of analysis, allowing more proteins to be analyzed. Ligands are placed with the protein and interactions are monitored by the detectors. The work in this dissertation attempts to combine the approaches of bioinformatics and analytical chemistry to study protein functional relationships. 1D- 1H NMR spectra are analyzed, and interaction is verified with 2D- 15N HSQC experiments. The compound library used for these analyses is based on biologically-relevant compounds that are typically small and water soluble. This is the Functional Annotation Screening Technology by NMR (FAST-NMR) process that has been developed. The nature of the protein-ligand binding is probed with Comparison of Active-Site Structures (CPASS), a program and database that searches and aligns protein active sites. The compound library is also used in MS studies, and their applicability to an LC-MS library is discussed. CPASS is further discussed, with improvements in calculation and scope being addressed. The potential to use active-site binding information in protein evolutionary studies is also addressed, in relation to common evolutionary determination by sequence and structure alignment.

Subject Area

Chemistry|Analytical chemistry|Biochemistry

Recommended Citation

Copeland, Jennifer Cheri, "Protein functional explorations using mass spectrometry, nuclear magnetic resonance imaging and bioinformatics tools" (2013). ETD collection for University of Nebraska - Lincoln. AAI3558775.