User:Jennifer Taylor/Sandbox 2
From Proteopedia
Contents |
Introduction
This protein (PDB ID 3h04) is an uncharacterized protein that was structurally solved in 2000 during a Protein Structure Initiative(PSI) by the National Institutes of Health. This initiative lasted fifteen years and scientists determined a large quanitity of structures of proteins. We selected this protein from their collection.While it's structure was solved and known, it's actual function was yet to be revealed. Through in Silico Analysis, Bacterial Transformations, Protein Expression, Protein Purification, Colorimetric Enzyme (Lipase) Assay, we attempt to confirm that 3H04 Is a Lipase. Prior to our research the only information on its characteristics was that it was potentially a hydrolase that could be a alpha/beta found in E.Coli.
Proteins are extremely important to current science and research in all aspects. The function that proteins carry can often be used in ground breaking research for all areas of medical treatments. While many proteins have been structurally solved, they still remain un characterized and therefore their function unknown. The issue with this is that while it is good to have the structural integrity of a protein derived, the function is what determines its applicability in certain fields. In this experiment we attempt aid in the efforts of characterization and characterize 3h04
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Approach
In our efforts to characterize 3h04 we used computer softwares such as PyMOL, ProMol, BLAST, Pfam as well as Dali. After using Blast Pfam and Dali we were able to analyze it's In silico enzymatic characteristics, however to further understand our protein, we utilized PyMol, ProMol, and Pfam. Through these programs we were able to take a closer look at it's active sites and catalytic triad. After loading our protein into these proteins, we were able to compare RMS levels with other similar proteins hoping that finding a protein with a similar structure would reveal similar functions. Through this analysis it revealed that 3h04 showed close similarities with 1AZW and 1YSC with a RMS. While the structure were similar we hoped for a lower RMS. As a result we began analyzing the active sites and Catalytic Triads. Reasoning for this was that the Active site and Catalytic are where the protein generally carries out its function-therefore it would have a more prevalent relationship towards it function. Through this approach it revealed an extremely low RMS with protein 1TAH of 0.016. We then decided to research 1TAH and it revealed that it was a Hydrolase; Esterase; Lipase. After this analysis we decided to run a Lipase Assay.
Function
Disease
Relevance
Structural highlights
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