Fold predictions of HIV-1 p1 RNA from therapy-naive and -experienced patients suggest contribution to drug resistance

Poster number: 11

J. Verheyen (1), U. Schuldenzucker (2), E. Litau (1), M. Däumer (1), M. Oette (3), G. Fätkenhäuer (4), J. Rockstroh (5), R. Kaiser (1), D. Hoffmann (2)

  1. Institute for Virology, University of Cologne
  2. Research group Functional Peptides, Stiftung caesar
  3. Clinic for Gastroenterology, Hepatology and Infectious Diseses,University Clinic Düsseldorf
  4. Clinic I for Internal Medicine, University of Cologne
  5. Clinic for Internal Medicine, University of Bonn


HIV-1, as all retroviruses, exploits a frameshift event during ribosomal translation to generate its enzymes protease, reverse transcriptase, and integrase. The frameshift is regulated by a specific motif in the p1 region of the mRNA: a slippery site followed by a hairpin-structure. There are indications that mutations in this region compensate for the decreased enzymatic function due to drug resistance mutations. Currently, the exact mode of action of the compensatory mutations is discussed intensively. We hypothesize that these mutations can change the structure of the hairpin-loop in the p1 region. This structural change may then influence e.g. the frequency of the frameshift.

Patients and Methods:

We compared p1 sequences from two different patient groups infected with HIV-1, subtype B: (1) therapy-naive patients (N group), and (2) therapy-experienced patients (E group) after treatment failure and detection of primary resistance mutations in the HIV protease. The N group comprised 287 sequences, the E group 230 sequences. RNA fold predictions were performed for all sequences using RNAfold from the Vienna package ([1]). For sequences with ambiguous nucleotide assignments all of the possible nucleotide sequences were considered combinatorially.


For RNAs of the E group one long stable hairpin structure was predicted significantly more frequently than for the N group. This structure consists of an upper hairpin of eleven base pairs and a lower helix of eight base pairs. The lower helix is separated on the 3` side from the upper helix by a bulge of three bases. Except for the closing base pair in the lower helix this structure has been proposed [2] and recently confirmed by NMR spectroscopy [3]. In most cases the predicted energies of this structure are close to the minimum predicted free energies, exceeding the latter by at most 0.7 kcal/mol. The energy distribution of the RNA folds of this structure differed between N and E group with the E group having relatively more structures of high or low energies, whereas the N group had more structures of intermediate energies.


Our findings suggest that partial loss of function of HIV protease due to resistance mutations may be correlated with a structural change in the p1 region. This change could tune the number of frameshift events and thus up-regulate the translation of HIV protease and in this way compensate for its partial loss of function.