What is so special about protein sequence and structure analysis?
The short answer: The protein sequence dictates its potential structure, and the structure of a protein dictates its function.
If you can begin to unravel the details about a protein or a group of proteins you are well on your way to making solid predictions and hypotheses, designing more informative experiments. On the pharmaceutical front, understanding protein structures allows for rational drug design. The first step however is finding your proteins of interest. You want to identify the specific protein or family of proteins that will fit your need. Read the book chapter "Proteins" from Protein Bioinformatics. Assignment 3.1 directs you to complete exercises 1 (there are multiple ways to complete this exercise), 7, 9, and 10 at the end of the chapter. Compile your answers in a word document and submit your asignment via Blackboard.
Assignment 3.2 Guide
In Assignment 3.2 you will select a topic from the list below. As in Unit 2 select a paper that describes a protein of interest. The article and protein identifier are to be submitted to the instructor for approval.
List of topics:
- Cancer drug targets
- Genetically modified food
- Bioremediation
- Metabolic Regulation
- Vaccine Development
- Spider Silk
Some Potential Journals to direct your article search (In addition to search PubMed):
Use your Blackboard username and password to sign in if a login page pops up.
You have the skills learned in Unit 2 to guide you in completing Assignment 3.2 - Phylogentic Analysis. Once your article and protein of interest are approved by the instructor you will perform a BLAST search and create a FASTA file containing the top hits from at least 20 unique species. This file will be used to prepare a multiple alignment, as done in Unit 2. If you have explored the buttons in the Clustal Omega format you already know a quick method for creating a basic phylogenetic tree. Once your alignment is made using Clustal Omega simply click the "Phylogenetic Tree" button, shown below and indicated with the purple arrow. Alternatively you can click the "Send to ClustalsW2_Phylogeny" button and submit your alignment for tree-building on this interface. Both return virtually identical trees. This tree is a graphical view of the relatedness or implied evolutionary relationships among the proteins you identified. This is a realtively simple method for obtaining a phylogenetic tree. Read the article "Phylogenetics: principles and practice" for a more complete assessment of this method. In this article the basic theory behind creating a tree is described. Additionally, several programs are described, along with their strengths and weaknesses.
Once you have your tree output from Clustal Omega, you can format the tree for the best display. In the screen shot below, boxed in blue, is the instruction for modifying the image of your tree. There are several options, inculding changing the font, background color, line color and style of tree (Cladogram is illustrated in the screen shot below). Depending on your presentation style for publication, lab meeting, or conference you may need to alter the appearance of the tree. After you have formatted your tree to your satisfaction (leaving it as originally displayed is acceptable), be sure to take a screenshot of the tree using Jing or any other screen capture application.
Alternative programs for creating a basic tree based on the 21 proteins in your FASTA file include but are not limited to:
- BIONJ (Found on the ExPASy site in the phylogeny/evolution catagory)
- Upload your alignment file
- Select the Jons-Taylor-Thorton matrix (protein) as the substitution model
- Click submit
- Take a screenshot of the output tree or click "Visualize your tree with ATV" below the tree for a more professional image you can capture
- PhyML 3.0
- Use the same instructions detailed for BIONJ
A link (Created through Jing or Voice Thread) to your image with a comment from you describing the composition and basic interpreatation of your tree will be posted to the discussion board. You are then required to view and comment on your peer's phylogenetic trees.
In addition to determining the the evolutionary relationship between your proteins and similar proteins from other organisms you can dive deeper into the characteristics of your protein of interest by studying its primary, secondary, and tertiary structure. These levels of organization are critical in determining the function of a protein and understanding how proteins can be engineered or positioned for a purpose. Additionally, identifying the subtle differences among proteins helps explain why some drugs work for only subsets of the world's populations. Read the article "Pharmacogenetics, Personalized Medicine, and Race" from Nature Education and "Pharmacogenetics, Pharmacogenomics, and Individualized Medicine" from Pharmacological Reviews for a specific examples.
