User:Jennifer Taylor/Sandbox 6

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Contents 1 Overview 2 Background 3 Structure 4 References

Overview

Throughout the course of this past year, we attempted to determine the function of our protein 2QRU. Protein shape and protein function are really closely related, so if two proteins that look similar are compared, there is a high likelihood that they do the same thing. This was the underlying basis for our project. After initial computer analysis, we found that many of the proteins that had structural similarity to 2QRU were esterases. Thus, our preliminary hypothesis predicted that 2QRU would be a lipase, a subclass of esterases. We performed an esterase assay to prove that 2QRU was an esterase first, and are yet to determine if it can be classified as a lipase.

Background

Proteins are one of four major macromolecules in biology. Present in nearly every living organism, proteins have a diverse set of functions ranging from regulating cell activity to catalyze reactions. Due to the sheer number of proteins in existence, there still remain many to discover and characterize. In 2000, the Protein Structure Initiative began an attempt to solve 3D-structures of proteins with known sequences in order to understand their functions. Though the initiative was successful, they faced financial drawbacks in 2015. There still remain several protein structures with unknown functions in a public database called the Protein Data Bank. In a final PSI summary published in 2017, 6920 structures had been solved in their seventeen years of work. What we tried to do is take one of the protein structures solved by the PSI and characterize its function.

Structure

Here is a visualization of my protein highlighting the This protein is an alpha/beta hydrolase that has one chain. It's 816 base pairs long. This alpha/beta hydrolase is important to note because ______

spinqualitylabelsall models Caption for this structure Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image This is a default text for your page Jennifer Taylor/Sandbox 6. Click above on edit this page to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue. Function Assays In order to determine if our protein was an esterase, we used an assay found in a published paper that sought to characterize 3FAK as an esterase. They performed a colorimetric assay which we modified for our study. Future Directions This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

References

1. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
2. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644