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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 amino acid 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).

Materials & Methods

Computer Modeling Strategies

o Chimera: allowed visualization of the protein; was used to compare conformation, identity, and conservation of amino acid side chains; was used instead of Dali (Dali didn’t analyze side chains); visualized results from SPRITE in a different way.

o SPRITE: evaluated local alignments- only a small part of the protein; identified active sites; was used to search for configurations of amino acid side chains that have a similar structure to those of known enzyme active sites.

o Dali: aligned the entire 3D protein (global alignment), matched structurally similar proteins rather than sequence similarities like BLAST. Dali is more limited than BLAST since it can only work with protein structures as a whole (there are fewer known structures than known sequences); only had matches based on the backbone of the protein, did not involve amino acid side chains or side chains that would show functionality of the enzyme.

o BLAST: sequence searching that only matched similar amino acid sequences rather than the whole protein; Looked at the sequence in sections, found matching overlaps with sequences in the database, scored the matches based on similarity, and provided a list of matches.

o InterPro: matched similar sequences rather than the whole protein; matched the unknown protein to a family which gave clues about its function, where it is, and general information about qualities that it might share with other proteins in that family.

o SwissDock: computationally predicted how substrates would interact and bind with the active site or allosteric sites; Tested various ligands and provided binding energies.

Key Information about Chemicals, Equipment, & Instrumentation

o E. Coli strain

o Buffers (Sodium Phosphate buffer, Tris-HCl, Re-Suspension Buffer, Cell Lysis Buffer, 1X Wash Buffer, 1X Elution Buffer, 10X SDS-PAGE Buffer, Coomassie Blue Stain, and Destain) were prepared by classmates with appropriate techniques and all materials were stored at necessary temperatures.

o Equipment used: computer modeling systems, Bradford Assay, PAGE, sonication, centrifuge, UV-vis, freezer (Glacier, -86°C, ULTRALOW TEMPERATURE FREEZER)

o Protein samples were kept on ice to avoid denaturing due to temperature changes.

o Glassware was cleaned, all equipment was properly prepared prior to the start of the lab, and contamination was reduced through the use of disposable cuvettes and pipette tips.

o

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.