3P02 Biochemistry

1.Hypothesize the effect on function of changes in primary amino acid sequence, in the context of disease or in the process of developing novel functions.

2. Modeling of the potential tertiary structure of a protein based on the known structure of similar proteins as for example modeling the structure of an alternative splice variant protein based on the structure of the wild type protein.

3. Analysis of the function of conserved amino acids in a family of homologous proteins.General outline of report:

Your goal in this report to carry out an original analysis on how the protein structure influences and determines its function(s). This will first require a brief introduction to your protein, what it does and how it works. This should not take more than a page. Importantly, we are interested in the link between structure and function, not the “selling” of the reader on how important your protein is to a cell, in a disease state, etc. In other words we are not looking to have a literature review performed nor a long winded discussion on how the chosen protein is involved in various diseases, cellular functions, etc….we are purely concerned with the structure/function relationship, not about the perceived “importance” of the chosen protein. If you are working with a protein that is altered in a disease state then this is fine to indicate, however the length of this background information should be kept quite minimal.

The task of compiling an original analysis on how the protein structure influences and determines its function(s) is the main focus of this report. In the same line that we are not looking for a literature review or sales pitch towards the importance of your protein, this assignment is also not looking to summarize work that has already been done in the field. The Deep View program offers dozens of customizable tools and modifications that can be made to any PDB file and as such nearly anything can be done to the protein of your choice. Rather than show what has been done by others, the goal of this assignment is to get you to use Deep View to carry out your own independent analysis. Think of this as being able to custom modify or build, tweak, distort, etc. your protein of interest. Every change you make will have the capacity to impact the function and structure of your protein. The video lecture on the assignment showed and spoke of a number of things you can do to start. Briefly, tools that are readily available to you on Deep View with little to no practice learning the program are below. These are just a few starting areas you may be interested in looking at…there are dozens more and you are expected to spend some time going through the Deep View program trying out different modifications/tools. You don’t have to use all of these, but the following are good to get you started