Determining the Function of the Protein of Interest 2QRU Using Bioinformatic Tools and Wet-Lab Experiments
Abstract
Proteins are complex macromolecules that play a vital role in the facilitation of biological processes. Protein research and documentation are crucial for future advancements. They aid in developing medications, disease diagnosis and treatment, and the understanding of structural biology. Thousands of proteins have been stored in the Protein Data Bank (PDB) since 1971. Although their structures are known, many of their functions have yet to be determined.
This study was conducted in order to shed light on the biological role of a previously uncharacterized protein of interest (POI) with the PDB ID: 2QRU. A two-pronged approach involving both bioinformatics and targeted wet-lab investigations within the framework of the CURE model and BASIL experiments was utilized. Such bioinformatic tools included Chimera, BLAST, SPRITE, DALI, and InterPRO to determine the active site. It was concluded that the active site consisted of the catalytic triad: ASP 219, HIS 247, and SER 102. In depth use of SwissDock was employed to find the most efficient substrate binding and interactions with the active site. Laboratory experiments included cell lysis, affinity chromatography for protein purification, Bradford assay to determine the POI concentration, and SDS-PAGE to assess the purification and size of the POI.
Through these procedures, 2QRU was found to most likely be a carboxylesterase in the alpha/beta hydrolase superfamily, specifically known for their ability to hydrolyze carboxylic acid esters into alcohol and carboxylic acid components. Further research is required to conclude the exact function of 2QRU, including ligand synthesis and enzyme activity assay.
Faculty Sponsors
Dr. Arthur Sikora
Project Type
Event
Location
Alvin Sherman Library
Start Date
4-3-2024 12:30 PM
End Date
4-4-2024 1:30 PM
Determining the Function of the Protein of Interest 2QRU Using Bioinformatic Tools and Wet-Lab Experiments
Alvin Sherman Library
Proteins are complex macromolecules that play a vital role in the facilitation of biological processes. Protein research and documentation are crucial for future advancements. They aid in developing medications, disease diagnosis and treatment, and the understanding of structural biology. Thousands of proteins have been stored in the Protein Data Bank (PDB) since 1971. Although their structures are known, many of their functions have yet to be determined.
This study was conducted in order to shed light on the biological role of a previously uncharacterized protein of interest (POI) with the PDB ID: 2QRU. A two-pronged approach involving both bioinformatics and targeted wet-lab investigations within the framework of the CURE model and BASIL experiments was utilized. Such bioinformatic tools included Chimera, BLAST, SPRITE, DALI, and InterPRO to determine the active site. It was concluded that the active site consisted of the catalytic triad: ASP 219, HIS 247, and SER 102. In depth use of SwissDock was employed to find the most efficient substrate binding and interactions with the active site. Laboratory experiments included cell lysis, affinity chromatography for protein purification, Bradford assay to determine the POI concentration, and SDS-PAGE to assess the purification and size of the POI.
Through these procedures, 2QRU was found to most likely be a carboxylesterase in the alpha/beta hydrolase superfamily, specifically known for their ability to hydrolyze carboxylic acid esters into alcohol and carboxylic acid components. Further research is required to conclude the exact function of 2QRU, including ligand synthesis and enzyme activity assay.
