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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.
Introduction
Research Question
What is the function and qualities (location and optimal conditions) of our assigned unknown protein, 2QRU?
Problem Relevance
The function of this protein is not known past the fact that it is in the super family alpha/beta hydrolase. Knowing the function of this protein could be helpful since knowing a protein’s function allows for extensive classification of said protein.
Research Significance
Identifying the structure of the unknown protein would reveal its function which could be used in many different ways. By connecting the protein’s function to symptoms and mechanisms, it could be used as a target for treatment of various diseases.
Hypothesis
Based on the super family classification, protein 2QRU is a type of hydrolase. Running experiments to test the protein under three different pH conditions based on the three most common locations of hydrolases (digestive system, neurons, and muscle cells) will reveal the activity of the protein in these different pH’s and therefore could suggest where the protein is found and consequently its function.
How Experimental Data Will Answer the Hypothesis
o The different computer modeling strategies used such as Chimera, SPRITE, Dali, BLAST, InterPRO, and SwissDock allowed visualization of the protein’s structure as a whole
and at the AA level, showed us different alignments and active sites, compared it to other proteins for function analysis, showed different substrate interactions and much
more which we will dive into in the experimental section.
o PAGE Gel told us whether the purification process worked or not and which sample to use when we tested for enzyme activity based on the strongest band.
o Bradford assay provided a concentration of our samples and determined which sample would be used for further testing.
o UV-Vis provided protein activity in different pH’s (more activity meant more absorbance from color change and therefore possible conclusions that the
enzyme functioned in an area of the body at that pH).
Methods & Materials
Overview of 'this type of enzyme'
The role in the body this would play based on results. Any potential implications of the enzyme if disrupted based on findings and related enzymes.
Proposed Function
The function is to do this. We believe this because of these data - use your computer modeling, research, and lab data here.
Structural highlights
Highlight the data that helped you come to your conclusion here including any relevant figures. Make sure include potential substrates and binding sites.
