BIOMG 1350 – Section 7 Worksheet 1 Name: Section: Introduction to PyMOL, Protein Folding, and Protein Structure/Function Part 1: Start reading at, “There are two files on your computer that contain…” 1. In the diagram at right, label the backbone and the side chain by circling those atoms that are part of the side chain and those atoms that are part of the backbone respectively. Continue reading… 2. Are there alpha helices in this molecule? 3. Are there beta-sheets in this molecule? Are the beta-sheets oriented parallel, anti-parallel, or are there examples of both? Continue reading… 4. Rotate the molecule to visualize this α helix from an end-on view. Do the side chains project into the interior of the α helix or to the exterior? Continue reading… 5. Are these hydrogen bonds oriented perpendicular to the helix or do they run parallel with the helix? Continue reading… 6. Look at the orientation of the glutamic acid side chain. Is it oriented toward or away from the ATP? Do you think it can interact with ATP in this orientation? Finish reading part 1… (DON’T CLOSE ANYTHING!) COLOR CHART 1HCK (unbound) 1FIN (bound) 1HCK (unbound CDK) NA ATP T-Loop Glutamic Acid CDK_2 (bound CDK) NA Cyclin NA O O H H CH2 CH3 CH3C H - + H N CH C CBIOMG 1350 – Section 7 Worksheet 2 Part 2: Start reading at, “Binding of cyclin to CDK causes a conformational change in…” 7. Are there any beta sheets present in cyclin? Continue reading… 8. Look at the glutamic acid residue. Is the glutamic acid side chain pointing towards or away from the ATP molecule? How is this different from where the glutamic acid residue was oriented in the CDK molecule without bound cyclin? Do you think glutamic acid can interact with ATP in this orientation? Continue reading… 9. How does the T-loop move in relation to ATP when cyclin binds CDK? (hide and show the T_loop_1 to get a better idea of exactly how the T-loop has changed position) Continue reading… 10. Rotate the molecule to find the ATP. How has the cleft (e.g. opening) where ATP is located changed? Do you think target proteins can access ATP in this conformation? Continue reading… 11. Describe where the ATP is positioned within the CDK molecule: (e.g. is it sticking out?) 12. When cyclin binds CDK it causes a conformational change, which moves the position of the T-loop. How do you think this affects the ability of proteins to bind CDK and access the ATP molecule? (1 sentence max!) 13. Thinking back to everything you just did…is the movement of the T-loop the only conformational change that occurs in CDK when cyclin binds? If not what other conformational changes did you observe? (1-2 sentences max!) Finish