Discovery in Protein Explorer
This is the long version. There is also a short version.
Revised Sept. 2004

A protein molecule may be assigned to you by your teacher, or a list of molecules may be provided from which you can pick one. Ask your teacher whether you are responsible for any of the optional questions.

Record your observations and interpretations regarding the questions below on separate sheets of paper. Hints are available to help you!

  1. How many protein chains are in your molecule? Are there any nucleic acid chains?
    1. Optional: Are any of the chains identical in sequence with each other? Are there any gaps in the chains? Are the nucleic acids DNA or RNA?

  2. Does your protein have any disulfide bonds? Are there any disulfide bonds between chains?

  3. Briefly summarize the secondary structure of your protein. Is is all alpha helix, all beta strands, or a mixture of both?
    1. Optional: Does your protein appear to include multiple domains?

  4. Are there any ligands in your protein? If so, what are they?
    1. Optional: Describe their contacts with the protein.

  5. (Skip unless you are doing the optional questions.)
    1. Does your protein have an "active site"?
    2. If so, what secondary structures are included in the active site?

  6. Does your protein exhibit a hydrophobic core?
    1. Is the surface of your protein largely hydrophilic or hydrophobic?
    2. Based on the surface of your protein, do you think it is soluble in water, or is it a transmembrane domain?

  7. Do you think your protein is neutral, or has negative or positive net charge at pH 7? If it has a net charge, how does this support its function?
    1. What is the isoelectric point (pI) of your protein?
    2. What is its quantitative net charge at ph 7?

  8. Is there anything especially interesting, unusual or unexpected about your protein?

  9. What are the important biological functions of your protein? How does its structure support its functions?
    1. Optional: What is the primary literature reference for this structure?

  10. Does your molecule form specific oligomers necessary for function?

  11. What regions of your molecule are most conserved in evolution?

  12. (Skip unless you are doing the optional questions.)
    1. How many PDB file entries that describe your protein are in the Protein Data Bank?
    2. What method was used to obtain the model of your molecule that you have been exploring?
    3. How reliable is this model of your molecule?