BCH210H: Physiological Role of the Protein and Ligands - Psychology Assignment Help

Assignment Task :

Assignment Requirements: 

Include the following information in your assignment using the following headings.  Consult the associated references or additional primary literature in order to provide  clear and concise answers using full sentences. For each of the 4 sections, there is a  maximum of 1 page of text + images. The complete assignment should be no more than  4 pages + 1 page of references, submitted in pdf format. 

1. Physiological Role of ‘the Protein and Ligands’ (replace ‘the Protein and Ligands’  with specific details about your assigned protein) 

As an introduction, summarize the physiological role and function of the protein in its  endogenously-expressed cell line or organism, which is summarized as its classification on the RCSB website. Explain what kind of protein it is (membrane, receptor,  transporter, enzyme, structural protein, signalling etc.) and what its role is in the specific  tissue or cell type, as well as its the subcellular location. 

Describe the role (structure/catalysis, etc.) of all of the ligands that can be seen in the  structure, and indicate which ligand is the largest based on molecular weight. This will  be the ligand you will be analyzing in subsequent sections. If the ligands differ from  what is required by the protein in a cell, discuss why they are present in the structure  despite not being physiologically relevant. 

2. Purification of ‘PDB#’ (replace ‘PDB#’ with the name of your protein) 

Explain how the protein was purified in order to obtain the structure. Provide details on  which cells were used and why (are they different from where it is found  physiologically?), and discuss the various purification techniques used. Provide a  summary of the experimental conditions (types of chromatography columns,  purification tags and buffers used) and explain the role of each, as well as the chosen pH  for the purification procedure. Note- a ‘summary’ does not mean re-writing the  experimental procedure stated in the article(s), it means rationalizing why the various  techniques were used and in the particular order, drawing on what you have learned  from the BCH210H lectures. Discuss how the identity and purity of the protein was  confirmed and what experimental technique(s) was used to determine the structure and  why. If multiple techniques were used to determine the structure, provide details on  why each one was used.

3. Structure of ‘PDB#’ (replace ‘PDB#’ with the name of the protein) 

There are many different programs that can be used to generate figures of proteins.  Instructions are provided below in order to generate figures of your protein in the  different programs. In your assignment, provide two side-by-side figures (ie. A&B, no  more than 1/3 page in size) of the protein. The first image (A) should be an electrostatic surface potential representation of the entire protein showing the ligand-binding site  (rotate your protein so that a stick structure of the ligand is visible). This representation  is the blue/white/red colour protein structure that was shown in lecture and will give  you an idea about cavities and projections that are found in the overall protein structure (if there is more than one chain, show both in this image). The second image (B) should  be a cartoon of the chain in ‘chainbow’ format, similar to what you will see when you  initially access your structure on the RCSB website. The structure of your polypeptide  chain must include the secondary structure and the specific interactions with the largest  ligand (if there is more than 1 binding site or chain, only show one structure). Show the  side chains for the major amino acids involved in ligand binding (~5-10 amino acids), and  label each using the associated number and 1-letter-code (ie. A196). Label the N and C terminal amino acids as well. Provide a detailed figure title for your side-by-side images  (A & B) indicating which program was used. 

The PyMOL window is split into 3 sections, the External GUI (Graphical User Interface)  along the top, where commands can be entered following ‘PyMOL>’, the main Viewer  window and the Internal GUI on the right. 

1. In the External GUI command prompt line, type: fetch PDB# (where PDB# = PDB file #  alpha code from above) and press enter to load the structure for vts1. Your structure  should have loaded as a cartoon of secondary structure. 

2. In the External GUI command prompt line, type: bg_colour white and press enter to set  the background to white. 

3. On the Internal GUI, click on H=Hide the waters from the structure. 

4. In the bottom right-hand corner click on S. A banner will appear at the top that displays  the amino acid sequence and ligands in your structure. Select your ligand (either in the  banner or in the structure itself). The internal GUI will show (sele) highlighted. Click the  background to deselect. From the menu of (sele), click on S=Show As sticks to display  your ligand as a stick model. You can also change the colour of the (sele) using the  C=color tab. It may also be useful to colour your ligand by element by clicking C=color  by element HNOS. 

5. To generate an electrostatic potential map, you must use the APBS plugin. In the menu  bar go to Plugin -> APBS Electrostatics and click run.

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