This project was prepared as part of a BioQUEST faculty development workshop entitled Investigating Interdisciplinary Interactions: The Annual BioQUEST Summer Workshop at Beloit College in June 2005. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

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How does Antiretroviral Therapy Affect HIV Mutation?
Authors          Audiences          Overview           Materials          Resources           Future Directions



Devin Iimoto
Whittier College


Possible Audiences:

Non-biology majors
Biology majors (lower and upper division courses)



Brief Overview:

How does Antiretroviral Therapy Affect HIV Mutation?

AIDS is a disease that struck fear in the hearts on many Americans in the early 1980s because not much was known about the disease. However, as scientific research has uncovered the structure of the virus, the mechanism by which the virus replicates inside the host cell, and the structure of the viral proteins needed for replication, new drugs have been developed to inhibit viral replication and help lengthen the lives of people infected with HIV. As with most treatments for infectious diseases, resistant strains of HIV have evolved rendering some of the treatments less effective.

You are a physician who works with people who are infected with HIV. In addition, you have agreed to allow undergraduate students to shadow you in your work. You want your students to learn as much as possible about the work that you do. On the first day that several undergraduate student have come to see your work, a patient comes to you with a CD4 cell count around 350 cells/�l of blood, which indicates that he/she might want to consider taking anti-retroviral drugs. Before giving your patient a particular regimen of drugs, you want to know if your patient has any strains of HIV that might be resistant to some of the available anti-retroviral drugs. You draw a sample of your patient’s blood and send it out for analysis. You ask the lab to determine nucleotide and amino acid sequence for HIV-1 protease and reverse transcriptase to determine which anti-retroviral drugs might be effective and which drugs might be ineffective.

After the patient leaves, the students bombard you with a list of the following questions.

  • How do you determine if a patient needs to be treated?
  • Why are you analyzing the patient's blood before giving him/her a set of drugs?
  • What will the results of these tests on the patient's blood tell you?
  • How do the drugs work?
  • How does HIV become resistant to the drugs?
  • Can a person be infected with multiple strains of HIV?
You are a very busy individual and you do not have the time to give a complete explanation to the students. Instead of giving superficial answers to the questions and being the deeply caring person that you are, you decide that the students would learn more by investigating the answers to their own questions.

  • First you ask the students what they understand about AIDS.
  • Next you ask the students what more they need to understand about AIDS to answer their own questions.
  • Then, you provide them with resources and exercises.

Within the activities you will find some suggestions on these topics.



Project Materials:

Protein Sequences (Cabana Protein Sequences)
Nucleotides Sequences (CabanaN file)
Exercises for the analysis of the sequences



Resources and References:

Web links

Basic information on DNA

Bioinformatics resources –Project Bedrock Stanford HIV Database

Animation on enzyme action

Animation on enzymes kinetics

General information on structure of HIV protease

Power point presentation on HIV protease function, structure and drug design

Video on HIV protease (available for purchase)

Inhibitors of HIV Protease: An Introduction to Carbonyl Chemistry

Protease Inhibitors

HIV Structural Database and Chem-BLAST

Basic information on enzymes


HIV-1 Protease
Molecular modeling of the HIV-1 protease and its substrate binding site.
Science. 1989 Feb 17;243(4893):928-31. PMID: 2537531

Human Immunodeficiency Virus Type 1 Protease Cleavage Site Mutations Associated with Protease Inhibitor Cross-Resistance Selected by Indinavir, Ritonavir, and/or Saquinavir.
Brumme ZL, Harrigan PR. J Virol. 2001 Jan; 75(2): 589-594. PMCID: 113954

Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance. Wang W, Kollman PA. Proc Natl Acad Sci U S A. 2001 Dec 18; 98(26): 14937-14942. PMCID: 64962

High Degree of Interlaboratory Reproducibility of Human Immunodeficiency Virus Type 1 Protease and Reverse Transcriptase Sequencing of Plasma Samples from Heavily Treated Patients. Shafer RW, Hertogs K, Zolopa AR, Warford A, Bloor S, Betts BJ, Merigan TC, Harrigan R, Larder BA. J Clin Microbiol. 2001 Apr; 39(4): 1522-1529. PMCID: 87964

A genetic screen for the isolation and characterization of site-specific proteases.
Sices HJ, Kristie TM. Proc Natl Acad Sci U S A. 1998 Mar 17; 95(6): 2828-2833.
PMCID: 19654

Coevolutionary analysis of resistance-evading peptidomimetic inhibitors of HIV-1 protease.
Rosin CD, Belew RK, Morris GM, Olson AJ, Goodsell DS. Proc Natl Acad Sci U S A. 1999 Feb 16; 96(4): 1369-1374. PMCID: 15469



Future Directions:

  1. Modeling protease mutation rate using Evolve
  2. Modeling of prevalence rates affected by incidence and death using STELLA.
  3. Modeling enzyme action on chemical reations using STELLA.
  4. Determine the spreading of HIV using Epidemiology (imput education prevention and treatment.
  5. Apply the techniques used in this exercise to the analysis of reverse transcription sequences.