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Transcript
Hands-on Exercise: Locating Protein Information January 13, 2010 Literature Informatics: Which proteins are related to Alzheimer’s disease? Where/who are the leading centers and scientists for Alzheimer’s research? Protein-centric Information: Identify the human protein containing this short peptide sequence: GPDGMPVIYHGHTLTTKIKFSDVLHTIKE o What is its function? o What is its calculated PI and molecular wt? o Which region of this protein is most hydrophobic? o Locate five experimentally verified Ser/Thr/Tyr phosphorylation sites in this protein. o Find the homologous mouse and fruit fly orthologs of this human protein and report the % protein shared identity. o How many protein domains are reported to be present in this human protein? o Find the location of its largest domain. Structure: View the crystal structure of Chronophin (PDB entry: 2P69). o A variant of this protein with mutations in its amino acid sequence has been isolated (see link http://www.hsls.pitt.edu/guides/genetics/tutorials). o Can you predict any effect the mutations may have on its function? o Hint: Identify the amino acid residues which are in close contact (3.5 A) with PYRIDOXAL-5'-PHOSPHATE (PLP). Bioinformatics Resources: Locate database(s) on G protein coupled receptors Find a suitable protocol for the expression of GST fusion proteins