Project Information

Mid-Term assignment - Due date Oct. 16, 2008

Studying the structures of proteins and nucleic acids at an atomic level can provide a clear understanding of how these molecules function. For each protein molecule assigned to you, read the primary citation that describes it and make a deposition in the class site ( Your depositions should cover 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 molecule(s) in the structure.
4. Describe and discuss the interaction(s) of the protein with its ligand/substrate/receptor/binding protein etc. (if any) at a structural level.
5. Explain how the structure of the molecule helps with its function.
6. Compare the structure in the assigned ID with at least 2 other related PDB entries (structures with alternate conformations, complexes with ligands or other proteins etc.). Justify your comparisons.

Protein name PDB IDs Student name
coagulation factor IX 1edm Rebecca Allison
coagulation factor V 1czt John Harrold
coagulation factor VII 1kli Daniel Heller -dropped
coagulation factor VIII 1d7p Eileen Hwang
coagulation factor X 1c5m Hungoo Lee
coagulation factor XI 1xx9 Huabing Li
Fibrinogen 1fzg Soma Mandal
Fibrinogen gamma 1fid Binchen Mao
Kallikrein 2anw Peter Mazari
Thrombin 1thr Anand Ramanathan
plasminogen 1ddj Ramya Rao
plasminogen activator inhibitor 1dvn Tamjeed Saleh
platelet factor 4 1rhp Peter Stivers
Annexin A5 1g5n Qumiao Xu
Tissue factor pathway inhibitor 1tfx TianYi Yu
tissue factor pathway inhibitor 2 1zr0 Zhuoxin Yu
Elafin 1fle Paramita Sarkar-dropped
von Willebrand factor 1atz *Yu-Chen Tsai*

Note: All depositions should include a title, original text, labeled figures, and a list of citations used. The text should include attributions (references).

Final assignments - presentations starting Oct. 30, 2008

Each student is assigned a research article that uses a biophysical method. Study the assigned research article. In addition to a critical analysis of the original research, obtain background information about the biophysical method/s used in that paper from additional review articles. Prepare a 20 min presentation of the paper with about 15 slides. One of your tasks is to educate the class on the principles of the biophysical method/s used in the assigned paper. Your presentation should cover the following aspects:
1. Background: Introduction to the biological problem and methods used. (What do you think the authors set out to study?) Describe and discuss the biophysical method/s used. Why is it that the preferred method over other methods for solving the problem in hand?
2. Experimental section: Pick the important experiments to present (you have limited time). In each slide, start with the question, then describe the experimental design, then the results, and finally the conclusions from that experiment.
3. Conclusions and future directions: Discuss what was learned from the study. What are the future directions of the project?

Grading: In addition to being graded on each of the above aspects, you will be graded on presentation, keeping on time, using effective slides, cartoons, etc where necessary, answering questions appropriately, and demonstrating a good grasp of the assigned paper.


Name Paper Presentation Date pdfs
The Energetics of Consensus
Promoter Opening by T7 RNA Polymerase
Oct. 30, 2008 Energetics of Consensus Promoter Opening.pdf
Use of 2-aminopurine as a
fluorescent tool for characterizing antibiotic recognition of the bacterial
rRNA A-site
Oct. 30, 2008 2-aminopurine as a fluorescent tool.pdf
Visualizing RNA Extrusion and
DNA Wrapping in Transcription Elongation Complexes of Bacterial and
Eukaryotic RNA Polymerases
Oct. 30, 2008 AFM transcription.pdf
Incorporation and Replication of
8-Oxo-deoxyguanosine by the Human Mitochondrial DNA Polymerase
Nov. 6, 2008 Replication of 8-Oxo-deoxyguanosine kinetics.pdf
Analysis of Catalytic Residues
in Enzyme Active Sites
Nov. 6, 2008 Analysis of Catalytic Residues.pdf
The Catalytic Power of Uracil
DNA Glycosylase in the Opening of Thymine Base Pairs
Nov. 6, 2008 Catalytic Power of Uracil DNA Glycosylase.pdf
The ATPase Cycle of the
Mitochondrial Hsp90 Analog Trap1
Nov. 13, 2008 ATPase Cycle of.pdf
Structural Basis for Substrate
Binding and the Catalytic Mechanism of Type III Pantothenate Kinase
Nov. 13, 2008 struc and calorimetry.pdf
Helicase from Hepatitis C Virus,
Energetics of DNA Binding
Nov. 13, 2008 Energetics of DNA Binding.pdf
Dynamic binding orientations
direct activity of HIV reverse transcriptase
Nov. 20, 2008 binding orientations FRET.pdf
Structure of the Tertiary
Complex of the RepA Hexameric Helicase of Plasmid RSF1010 with the ssDNA and
Nucleotide Cofactors in Solution
Nov. 20, 2008 RepA Hexameric Helicase FRET.pdf
Observing spontaneous branch
migration of Holliday junctions one step at a time
Nov. 20, 2008 HJ single molecule FRET.pdf
Single-Molecule Studies Reveal
Dynamics of DNA Unwinding by the Ring-Shaped T7 Helicase
Dec. 4, 2008 Single-Molecule Studies.pdf
Intrinsic motions along an
enzymatic reaction trajectory
Dec. 4, 2008 motions along an enzymatic.pdf
A continuous spectrophotometric
assay for inorganic phosphate and for measuring phosphate release kinetics in
biological systems
Dec. 4, 2008

continuous spectrophotometric assay.pdf

Biosensor for Inorganic Phosphate.pdf