Access Type

Open Access Thesis

Date of Award

January 2016

Degree Type


Degree Name



Biochemistry and Molecular Biology

First Advisor

Ladislau Kovari


HIV-1 protease (PR) is a 99 amino acid protein responsible for cleavage of the viral polyprotein. We have identified a novel clinical isolate, MDR/28, which contains a five residue insertion between codons 28 and 29 of a multi-drug resistant (MDR) PR. This clinical isolate displays reduced viral replicative capacity compared to the wild-type. As opposed to drug-resistance mutations, studies on insertions remain largely underrepresented in the literature, and the consequences of such insertions are largely unknown. To understand the mechanism leading to reduced replicative capacity, three PR models were created and subjected to 40ns molecular dynamics simulations: MDR/28, wild type, and MDR PR. In addition, PR inhibitors (PI) atazanavir (ATV), darunavir (DRV), lopinavir (LPV) and saquinavir (SQV), as well as cleavage peptide CA/p2 were docked to the three models. The MDR/28-PI complexes displayed decreased binding affinity when compared to WT complexes, likely due to an increased active site cavity volume and altered secondary structure at residues local to the insertion mutant. Additionally, in the active site of MDR/28 the predicted binding mode of the CA/p2 peptide did not include contact with the catalytic residues, and migrated from that position, a behavior not seen with any tested PIs or with either of the other PR models. These structural changes produced by the insertion suggest a mechanism for reduced replicative capacity of the mutant virus.

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Biochemistry Commons