All of these lesson plans require that your students have access to computers where they can use Protein Explorer or other Chime-based tutorials. If not, in some of the plans below, you could project the molecular images while having students complete worksheets. Of course, that requires that you have a projector and at least one computer.

If you have emphasized a single particular molecule in your class, and you don't have the time for Protein Explorer, here is a good lesson plan.

1. Choose an appropriate on-line Chime-based tutorial dedicated to your single molecule by visiting the World Index of Molecular Visualization Resources, www.molvisindex.org.
2. Hand out a worksheet of questions on paper, and direct your class to answer the questions by exploring the on-line tutorial you specify.
3. Optional: Have groups/students exchange their answers and check each others' work. Or have students form groups and compare their answers in group discussions. (Disputes or issues they aren't sure about should be referred to the teacher.)
4. Optional adaptation: A modified form of this plan is to assign different molecules (hence different on-line tutorials) to different groups in the class. Then you can have each group report their results to the class orally (optionally, with projected computer graphics as illustration).

1. The number and difficulty of questions can be tailored to your class and the time available.
2. The questions can be answered by small groups, or individual students.
3. The questions give each group/student concrete goals, benchmarks for their progress, and a clear gage for completion. Without the questions, regardless of how excellent the on-line tutorial, these features are usually missing (since few on-line Chime-based tutorials provide questions).
4. The questions can be generic (suitable for all molecules, see example below), or specific to the particular molecule. Obviously, the latter case requires at least partially different sets of questions for each molecule.
5. If you do not have fast and reliable Internet access, some tutorials can be downloaded for off-line use. If downloading is not offered by the tutorial in question, email the authors and ask them to send you a copy for off-line use along with instructions for installation.
6. A few tutorials are available in both English and Spanish (or other languages), and the number is growing. Check the Non-English section of the World Index of Molecular Visualization Resources.

• Antibody (www.umass.edu/microbio/chime/antibody). List of questions is provided. Downloadable for off-line use.
• Major histocompatibility complex (www.umass.edu/microbio/chime/mhc). List of questions is provided. Downloadable for off-line use.

Each lesson plan for Protein Explorer (www.proteinexplorer.org) has two parts.

1. Have your students do the QuickTour to learn how to use Protein Explorer. The QuickTour takes at least one hour; two hours is better. It is best if you can lead them through the QuickTour in a computer lab, but if a lab is not available, you can assign them to do it individually. (There is a prominent link to the QuickTour at the FrontDoor page of Protein Explorer at proteinexplorer.org. A printed copy of the QuickTour is very helpful.)
2. Have each group/student pick a molecule from a pre-selected list (or assign one). A starter list is below.
3. Apply Protein Explorer to a problem. The problem can be handed out on paper. Below are suggested problems.

  Pre-selected molecules.

The following molecules are relatively simple. The have been selected to avoid complications (such as being NMR ensembles, lacking sidechains, having a nonstandard file format, having many alternative sidechain conformations, etc.). At the FrontDoor of Protein Explorer (www.proteinexplorer.org), enter the PDB identification code into the slot.

1. Lysozyme, human, complexed to inhibitor, 1LZR.
2. Trypsin (porcine pancreatic) complexed to soybean trypsin inhibitor, 1AVX.
3. Carboxypeptidase A complexed with inhibitor, 1CBX.
4. Myoglobin, oxy, 1MBO.
5. Hemoglobin, deoxy, 1HGA
6. Green fluorescent protein, 1EMB.
7. Calmodulin (with calcium), 1OSA.
8. Potassium channel, 1BL8.
9. HIV protease with inhibitory drug, 1HSH.

10. Transfer RNA (Phe), 1TRA.
11. DNA polymerase complexed with DNA, 7ICG.
12. Lambda repressor complexed to DNA, 1LMB.
13. Zinc finger (Zif268) complexed to DNA, 1AAY.
14. TATA-box binding protein, human, complexed to DNA, 1CDW.
15. EcoRV endonuclease complexed to DNA, 1RVA.

16. Complete IgG antibody, 1IGT.
17. Fab fragment of antibody bound to lysozyme antigen, 1FDL.
18. Major histocompatibility complex, class I, with viral peptide, 2VAB.

18. Sickle cell hemoglobin (dimer of tetramers bound via mutant valine), 1HBS. See hemoglobin tours at molvisindex.org.
19. Succinyl Co-A synthetase. Is this tetramer the functional soluble form of the enzyme? 1SCU.
20. Photosynthetic reaction center with bacteriochlorophyll a, ubiquinone and iron, 1PSS.
21. Gramicidin channel in hydrated lipid bilayer, theoretical model. At the FrontDoor, click under the PDB ID slot on the link Comparator, URL, then copy the example URL ending bilagram.pdb and paste it into the slot, and click on the Go button. Be sure to try SELECT Solvent, DISPLAY Only. Find a tutorial on this structure at molvisindex.org (also in Spanish).
22. Calcium pumping ATPase, with cytoplasmic and transmembrane domains, 1EUL.
23. Calmodulin, with calcium, NMR ensemble showing flexibility of linker, 1CFC.
24. Calmodulin, with calcium, complexed to fragment of myosin light chain kinase, NMR ensemble, 2BBN.
25. Nucleosome with DNA, 1AOI.
26. Ribosome, 70S, with 3 tRNA's and mRNA. This is too large to fit in one PDB file, so it is published in 2 (1GIX, 1GIY). A combined model with the sidechains missing is available at http://molvis.sdsc.edu/pdb/1gix1giy.pdb. Copy this URL and paste it into the long slot on the FrontDoor. Find tours of the ribosome at molvisindex.org.

  Application to Problems: Lists of Questions for Worksheets.

Here is a generic list of questions suitable for any molecule. Answers are not provided here, and must be worked out by the teacher for the subset of molecules assigned to the students. There is a separate page of hints on how to use Protein Explorer to answer each question. Whether you provide the hints to your students is optional.

If you write questions for your class to use with Protein Explorer, specific to a particular molecule, we would very much like to put your questions on the web and link the questions to the PDB ID code (at molvisindex.org). If you are willing to have your questions "published" on-line in this way (crediting your authorship of course!), please send the questions by email to Eric Martz (emartz@microbio.umass.edu).

An alternative to the generic questions above is the Form for Recording Observations linked at the bottom of the FirstView page. It has a short version and a more advanced version.

Finally, there is the Tutorial linked at the FrontDoor (under About Protein Explorer). This is an extensive tutorial designed for college students. Completion of the entire tutorial, including the study questions, requires over twelve hours of work.

  Student Assessment of Learning Gains from Protein Explorer

If you use Protein Explorer in your course, please consider using the free, customizable Student Assessment of Learning Gains (SALGains) website for on-line feedback from your students. Alternatively, you can hand out a set of questions on paper. For details, see Student Assessment of Learning Gains from Protein Explorer. Assessment results from you and your students will help determine development priorities and future funding for Protein Explorer!

Send lesson plan feedback to Eric Martz.