(C) CE McKenna, Ph.D. USC, Chemistry Dept.,
2003
LABORATORY SCHEDULE
Professor Charles E. McKenna
Department of Chemistry
Last updated October 3, 2003
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Week of October 6: Intro to Protein Data Bases
Due date: Your lab date plus one week
Instructions to use the Brookhaven Protein Data Base web site (Adobe acrobat pdf format)
We learned in class that the HIV virus is an assembly of both proteins (viral enzymes, matrix and envelope proteins) and RNA genes. The viral enzymes, and possibly the genes themselves, are targets for drug design. In this lab, we will study the 3D structure of some HIV proteins and nucleic acid (RNA) and examine how they might be utilized for rational drug design. Each structure you will retrieve from Web sources is identified by a unique four-letter code (e.g. 1UBV). You must give this code for each structure that you retrieve.
Submit your work as a single Word document.
I. HIV-1 Protease (10 points).
a) Using the Web as your resource, find an HIV-1 protease crystal structure
i. Display the enzyme in a ribbon representation, color each chain differently using Chime and copy it into your Word document.
ii. Examine the structure. Is protease a monomer (1 chain), a dimer (2 chains), a trimer (3 chains)…?
iii. What is the dominant secondary structure of protease?
b) Find the crystal structure of an HIV protease, labeled “Structural Basis for Specificity of Retroviral Protease”
i. Select the C chain (peptide inhibitor), display in stick format (Chime) and paste it into your Word document.
ii. Use the identify function of Chime to read the amino acid sequence of the peptide (chain C) and enter it into your Word document (three letter code).
iii. Identify each of the following interactions between the peptide inhibitor and the protease:
o Hydrogen bonding (identify interacting amino acids in both peptide and protease).
o Ionic interaction (identify interacting amino acids in both peptide and protease).
o Hydrophobic interaction (identify interacting amino acids in both peptide and protease).
II. HIV-1 Reverse Transcriptase (10 points).
a) Find an HIV-1 reverse transcriptase crystal structure.
i. Display the enzyme in a ribbon representation, color each chain differently and copy it into your Word document.
ii. Examine the structure. Is reverse transcriptase a monomer, a dimer, a trimer…?
iii. What is the dominant secondary structure of reverse transcriptase?
b) Find a crystal structure of HIV-1 reverse transcriptase complexed with an RNA/DNA duplex and a monoclonal antibody. (The antibody, “fab”, co-crystallizes with the RT and RNA/DNA.)
Display, color each chain differently, and paste into your Word document. Using the Word drawing tools, label:
i. The RNA/DNA duplex
ii. The HIV-1 reverse transcriptase
iii. The monoclonal antibody
Link to Brookhaven Protein Data Bank.
(C) CE McKenna, Ph.D. USC, Chemistry Dept.,
2003