Protein Modeling Glen Cochrane Half Hollow Hills

1. Protein Modeling Glen Cochrane Half Hollow Hills CRYSTAL STRUCTURE OF THE COMPLEX OF XIAP-BIR2 AND CASPASE 3 (pdb1i3o)

2. The Protein Modeling event is comprised of three parts: • a pre‐build (40% of the score) • on‐site build (30% of the score) • on‐site exam (30% of the score) • Center for BioMolecular Modeling (CBM) website (http://cbm.msoe.edu/stupro/so/index.html ) • Major resource for protein biochemistry, modeling proteins and about these specific proteins and how they play a role in the regulation of apoptosis and the connection to this rare disease.

3. Objective of this presentation is to assist coaches to prepare their team. • Know the principles of protein biochemistry • Acquire resources and learn the specifics of this year’s protein. • Instructions to build the models. • Practice Jmol software • Extract information from pdb files. • Prepare five double sided pages of notes.

4. Protein Basics: Proteins are macromolecules Amino acids are the basic building blocks of proteins Click

5. Amino Acids are classified by properties: polar, nonpolar, and charged (ionic)

6. Polypeptides are constructed by condensation reactions with amino acids

7. Protein function depends on specific conformation (shape) There are four levels of protein structure. The primary structure is the linear sequence of amino acids. What determines this sequence? Where in the cell are amino acids joined this way?

8. The secondary structure of protein depends on hydrogen bonding between C=O and N-H groups. Alpha Helix and Beta Pleated sheets

9. Tertiary structure is determined by the interactions between the side chains (R groups) List these types of interactions and which ones are weak or strong

10. Quaternary structure is the overall protein structure resulting from combinations of polypeptide subunits

11. Resources and learn the specifics of this year’s protein. Besides the protein basics, this is key to the written exam August 2004 Molecule of the Month by David Goodsell Click Look for additional references in articles and onlline about Caspases

12. 2012 Protein Modeling Event will focus on the XIAP and other proteins involved in the regulation of cell death. Caspases have been termed "executioner" proteins for apoptosis. XIAP is an inhibitor of apoptosis protein that binds to, and inhibits, caspase–3. When XIAP is bound to caspase–3, the protease is not active. Click

13. Pre-Built Model: • Based on chains A and B of the 1i3o.pdb file • Impounded an hour before the competition begins. • Model is built at a scale of 2cm/amino acids. • Chain A is 143 amino acids Mini-Toober is 286cm. • Chain B is 101 amino acids Mini-Toober is 202cm.

14. Creative additions Must demonstrate function: • Interaction with other molecules • Zinc fingers • Ligands • Significant side chains Could be 20% of score Include 3X5 card with team and explain additions

15. Common Mistakes • Blue cap/red cap in wrong position • N-terminus, or the beginning of the protein, is the BLUE cap and C-terminus, or the end of the protein, is the RED cap • Missing secondary structures • Model has 3 helices, and it should have 4 (or vice versa) • Left-handed helices • Tertiary structure is incorrect • Protein should be globular and it is flat • Creative additions on the prebuild are inappropriate • Incorrect sidechains • Too much information (all of the sidechains) • Onsite amino acids are positioned incorrectly • In the wrong spot (position 49 rather than 59) • Amino acids are pointing in the wrong direction (should be pointing to the center of the protein and it is facing outward)

16. Prebuild Kit http://www.3dmoleculardesigns.com/scienceolympiad.asp

17. Instructions to build the models Click Use the CBM website for the video instructions

18. On-Site Build: No on-line resources, file will be loaded on the computer. Bring 10 pages (5 sheets) of info.

19. Jmol Teams are expected to understand the Jmol protein visualization tools. These online tools will be necessary for construction of both the Pre-build and the On-site build. Click Jmol: an open-source Java viewer for chemical structures in 3D

20. http://cbm.msoe.edu/includes/pdf/JmolQuickReferenceSheet.pdf

21. Common Commands: Restrict*A (removes all but chain A) Restrict*A,*B (removes all but A and B) PRACTICE

22. Take a look at the protein using Jmol Go to www.pdb.org Search: 1i3o

23. The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. Obtained by X-ray crystallography or NMR spectroscopy. Submitted by biologists and biochemists from around the world.

24. How to display pdb file from pdb.org Click Click

25. Regionals: Selected region of XIAP (1i3opdb)

26. States: Selected region of PARP (3od8.pdb)

27. The On-Site Exam (30% of a team’s final score) • Combination of multiple choice and short answer questions • Can bring 10 pages of notes (No internet) • Topics include • Basic chemistry questions regarding atoms, bonds, and reactions • Basic protein structure • Structure/function relationship questions • Specific protein questions (related to prebuilt and onsite build proteins) Past Exams: http://cbm.msoe.edu/stupro/so/SONTExamRubric.html

29. Protein Modeling Teams of 3 (only 2 at state competition). Prepare using CBM website. Superior event incorporating the tools used by scientists, on-line resources, communication, cooperation, delegation of responsibilities, …