Biophysical Chemistry
Chemistry 537   Biochemistry 5537   Biomaps 501



Course Summary

Student Information

Syllabus and Notes


Project Information



Project Information
Last Updated: November 16, 2006

Studying the structures of enzymes, proteins and nucleic acids at an atomic level can provide a clear understanding of how these molecules function. For each molecule assigned to you, read the primary citation that describes it and make a deposition at the mapdev site ( that describes the following aspects:

  1. What is the rationale for the study described in the primary citation of this entry? What do you think the authors set out to study and what did they find out?

  2. How was the structure determined? Describe the materials and methods used.

  3. Describe the conformation of the protein/enzyme/nucleic acid.

  4. Describe and discuss the interaction(s) of the protein/enzyme/nucleic acid with its ligand/substrate/receptor/binding protein etc. (if any) at a structural level.

  5. Explain how the structure of the protein/enzyme/nucleic acid helps with its function.

  6. Compare the structure in the assigned ID with at least 2 other related PDB entries. Justify your comparison.

  7. For the enzyme depositions, write a description of the mechanism of its action. Start with an accurate description of the chemical or binding reaction catalyzed by the enzyme. Include biochemical, structural, kinetic experiments used to determine the pathway of the enzymatic reaction. Include discussions of the binding interactions of the substrate/ligand from the structure. E.g., what amino acids are involved in binding and catalysis and what types of interactions are involved in binding? From the literature studies of the enzyme, describe what is known about the mechanism of the enzyme and what is not known. Describe briefly the experiments used to determine the substrate binding constants, kcat, Km, reaction pathway etc. involved in the enzyme mechanism. Your report should be like a review article with proper headings and subheadings.

Make original images using Chimera to explain or highlight the structural aspects of the points discussed in your deposition. A list of all references (journal or text books), and PDB IDs that you used for making the deposition, must be included.

Project Due Dates

Oct. 31: The Cytokine and Nucleic acid depositions are due in mapdev.

Nov. 16: Order of Final oral presentations on the Enzyme/Protein complexes decided. The presentations will be held on Nov. 21, Nov. 28, Nov. 30, Dec. 5, Dec. 7 and Dec. 12

Nov. 30: The Enzyme/protein complex deposition due in mapdev. Final corrections to the deposition can be made until Dec. 12.

The final presentations should each be 15 minutes long, followed by 5 minutes for questions or discussions. Please prepare accordingly.
All powerpoints for the presentations should be transferred to the class presentation laptop before the start of the class on the day of the presentation.

Protein/Enzyme complexes | final presentations
Date PDB ID Name of protein Student
11/21 1AVD Avidin Han, Hua
11/21 1S66 Oxygen sensor Wang, Jin
11/21 2AIA Peptide deformylase He, Xianglan
11/21 1EYG SSB Yildirim, Evrim
11/28 4SKN Uracil DNA glycosylase Zang, Qingda
11/28 1AJV HIV protease Delgado-Rivera, Roberto L.
11/28 1HMY DNA methyl transferase Singh, Abhishek
11/28 1A1V HCV NS3 helicase Chen, Yu-Jen
11/30 1GER Glutathione reductase Mao, Lili
11/30 1IZI HIV protease Schneider, Bill
11/30 1Q21 Ras protein Paratkar, Swaroopa
11/30 1ZIN Adenylate kinase Ertekin, Asli
12/05 1LDG Lactate dehydrogenase Lapelosa, Mauro
12/05 2BMD Rab4A Ras-related protein Nguyen, Tung
12/05 1A0I ATP-dependent DNA ligase Landers, John M.
12/05 1DHF Dihydrofolate reductase Jung, Jongjin
12/07 1NP4 Nitrophorin Tao, Yuan
12/07 1BC5 Chemotaxis receptor methyltransferase Zheng, Guohui
12/07 1RVE EcoRV endonuclease Goel, Shivani
12/07 1DR1 Dihydrofolate reductase Hua, Xia
12/12 1A1R HCV NS3 protease Chen, Hsin-Yi
12/12 2A47 GFP like protein Ho, Sau Chum (Eric)
12/12 1F3O ABC transporter Haq, Omar
12/12 2BPF DNA polymerase beta Annavarapu, Srinivas

PDB ID Name of protein Student
1RHG Granulocyte colony-stimulating factor Annavarapu, Srinivas
1AU1 Interferon-beta Chen, Hsin-Yi
1FYH Interferon-gamma Chen, Yu-Jen
1JPY Interleukin-17F Delgado-Rivera, Roberto L.
2ILA Interleukin-1 alpha Ertekin, Asli
1U5X A Proliferation-inducing Ligand, APRIL Goel, Shivani
9ILB Interleukin-1 beta Han, Hua
1ILK Interleukin-10 Haq, Omar
1IJZ Interleukin-13 He, Xianglan
1I16 Interleukin-16 Ho, Sau Chum (Eric)
1J0S Interleukin-18 Hua, Xia
1GCZ Macrophage Migration Inhibitory Factor (MIF) Landers, John M.
1N1F Interleukin-19 Lapelosa, Mauro
1M4C Interleukin-2 Mao, Lili
1M4R Interleukin-22 Jung, Jongjin
1JLI Interleukin-3 Nguyen, Tung
2B8U Interleukin-4 Paratkar, Swaroopa
1HUL Interleukin-5 Schneider, Bill
1ALU Interleukin-6 Singh, Abhishek
3IL8 Interleukin-8 Tao, Yuan
1PVH Leukemia inhibitory factor Wang, Jin
1V7M Thrombopoietin Yildirim, Evrim
1KTZ Transforming growth factor beta 3 Zang, Qingda
4TSV Tumor necrosis factor-alpha Zheng, Guohui

Nucleic acid structures
PDB ID Name of protein Student
2GOZ Hammerhead ribozyme Annavarapu, Srinivas
1NYI Hammerhead ribozyme Chen, Hsin-Yi
1Q29 Hammerhead ribozyme Chen, Yu-Jen
1HMH Hammerhead ribozyme Delgado-Rivera, Roberto L.
1JPQ Quadruplex DNA Ertekin, Asli
3BNA B-DNA Goel, Shivani
1JRN Quadruplex DNA Han, Hua
1KF1 Quadruplex DNA Haq, Omar
1L1H Quadruplex DNA-Drug Complex He, Xianglan
1ZF1 A-DNA Ho, Sau Chum (Eric)
1ZEX A-DNA Hua, Xia
279D Z-DNA Landers, John M.
1ZEY A-DNA Lapelosa, Mauro
1ZFC B-DNA Mao, Lili
1ZFM B-DNA Jung, Jongjin
1ZEW B-DNA Nguyen, Tung
400D Z-DNA Paratkar, Swaroopa
1I0T Z-DNA Schneider, Bill
1DCG Z-DNA Singh, Abhishek
446D B-DNA Tao, Yuan
1YFG Yeast initiator t-RNA Wang, Jin
1EVV Phe t-RNA Yildirim, Evrim
1EHZ Phe t-RNA Zang, Qingda
1I9V Phe t-RNA Neomycin Zheng, Guohui