The Protein Project will consist of 3 parts. If you have not selected your own protein then you will be assigned a protein for completion of the project. Literature references should be included with citations to the source of material.
Part A: Protein Description and History
Identify some of the basic structure and chemical features (AA sequence, MW, pI, etc.) of your protein using the information and tools on NCBI, ExPASy, Protein Data Bank, etc. websites. (See the Resources links below.)
Give an extensive literature based overview of your protein. From journal articles determine more about the history, functions, and possible roles in cellular mechanisms. Also, explore if this protein has been linked to diseases or disorders.
Part B: Understanding the Structure & Function
Develop a set of visuals (tables, charts, images, etc.) to convey the basic information of the protein identified above (MW, pI, hydrophobicity, etc.).
Give the complete amino acid sequence for protein
Give an image of the 3-D structure and identify secondary structural features
How do the elements of the protein structure influence the function of the protein? Are there elements that could be changed and not affect the function? What are the structural elements that are required for proper function?
Part C: Comparisons to Other Proteins and Species
Use the BLAST tool on the protein websites to compare you protein sequence to other proteins and species. If you use NCBI, you can control the species name to get only other proteins within that species or leave it blank to get proteins in all species.
From the BLAST data, create a phylogenetic tree of different proteins with the organism and one relating the same protein in different species.
Use the ClustalW link on one of the websites to develop an amino acid sequence comparison and present this comparison.
Explore the Gene page for the underlying genomic DNA sequence as there is a large amount of basic information on this page relevant to the function and relationship with other proteins.
Identify interactions with other proteins, activities within the cell or biological functions (Gene Onotology, Biosystems, Pathways, etc.).
From the HomoloGene page identify the protein motifs found with in your protein and the level of conservancy of this protein across species.
How does a deeper understanding of primary amino acid sequence and identification of specific sequence motifs help identify the protein structure and function? Expand on the similarity of this protein to other proteins and the level of conservancy across species. How can this knowledge improve our understanding of the function and history of this protein? What can you learn about functions from identifying interactions between this protein and other proteins?
Part D: Conclusion/Discussion of the Protein
Expand on the role of this protein in known cellular and organismal mechanisms. What are some known disorders or diseases caused by abnormal structure and function of this protein? Speculate on some possible changes in protein structure and function that have not been identified or confirmed yet and how that abnormal structure could affect the functions of this protein in some future disease.