CSUMB Bio 310L - Protein Structure and Natural Selection - Myoglobin Case Study
Bio 310 Logo The objectives of this second lab are to:
  • Increase familiarity with the National Center for Biotechnology Information (NCBI).
  • Use Blast, Cn3D and Clustal W to examine natural selection in proteins.
  • Use the human myoglobin protein sequence to retrieve related bird, reptile, and mammal proteins.
  • Use clustal to align myoglobin sequences from air-breathing diving vertebrates.
  • Post a word document containing an analysis of myoglobin sequences from air breathing divers compared to non-divers.
   
     
Natural Selection and Sequence Variation
  • Using the NCBI website find and retrieve the FASTA format of sperm whale (Physeter) myoglobin 1VXH_A. Save it to your desktop as a notepad (text) file.
  • Again, using NCBI, find, retrieve, and save the FASTA format of pig (Sus) myoglobin NP_999401.
  • Prepare an alignment using ClustalW of these two sequences. Copy and paste the alignment to this worksheet and begin to answer the questions.
  • Using the Cn3D structure of sperm whale myoglobin, identify each of the amino acids that is different from the pig using the yellow highlighting function. Export the image as a png. Insert into your worksheet and in the caption describe which difference you think might be an adaptation for diving and why.
  • Next, follow instructions in class to use BLAST and NP_005359 to search the database for bird, reptile, and mammal myoglobin sequences.
  • Prepare a multiple alignment using ClustalW of myoglobin sequences from at least two diving representatives from each of these groups.
  • Can you identify any residues that seem to change when an animal needs to bind oxygen more tightly?

Natural Selection and Sequence Conservation.

  • Using this fish sequence (AAG16646) prepare a multiple alignment containing sperm whale and horse, two birds, and two reptiles. Add the alignment to your worksheet.
  • Using the sperm whale crystal structure, identify patches of four or more contiguous amino acids that are exactly the same in all eight species, and highlight them using Cn3D.
  • Edit your campus index.html to include a link to wksht_myo_diver.doc