Identification of the minimal conserved structure of HIV-1 protease in the presence and absence of drug pressure.
OBJECTIVE
To define the extent of amino acid protease (PR) conservation in vivo in the absence and presence of pharmacological pressure in a large patient cohort.


METHODS
Plasma-derived complete protein PR sequences from a well-defined cohort of 1096 HIV-1 infected individuals (457 drug-naive and 639 under antiretroviral therapy including PR-inhibitors) were obtained and analysed, and are discussed in a structural context.


RESULTS
In naive patients, the PR sequence showed conservation (< 1% variability) in 68 out of 99 (69%) residues. Five large conserved regions were observed, one (P1-P9) at the N-terminal site, another (E21-V32) comprised the catalytic active-site, a third (P44-V56) contained the flap, a fourth contained the region G78-N88, and another (G94-F99) contained the C-terminal site. In PR-inhibitor treated patients, the appearance of mutations primarily associated with drug resistance determined a decrease of amino acid invariance to 45 out of 99 residues (45% conservation). The overall degree of enzyme conservation, when compared to the PR sequences in drug-naive patients, was preserved at the N- and C-terminal regions, whereas the other large conserved areas decreased to smaller domains containing, respectively, the active-site residues D25-D29, the tip of the flap G49-G52, and the G78-P81 and G86-R87 turns.


CONCLUSIONS
Amino acid conservation in HIV PR can be minimally present in 45 residues out of 99. Identification of these invariable residues, with crucial roles in dimer stability, protein flexibility and catalytic activity, and their mapping on the three-dimensional structure of the enzyme will help guide the design of novel resistance-evading drugs.
Department of Experimental Medicine, University of Rome Tor Vergata, Italy.
Francesca
F
Ceccherini-Silberstein
Fulvio
F
Erba
Federico
F
Gago
Ada
A
Bertoli
Federica
F
Forbici
Maria Concetta
MC
Bellocchi
Caterina
C
Gori
Roberta
R
D'Arrigo
Luisa
L
Marcon
Claudia
C
Balotta
Andrea
A
Antinori
Antonella D'Arminio
AD
Monforte
Carlo-Federico
CF
Perno
D000595:Amino Acid Sequence / Q000235:genetics; D023241:Antiretroviral Therapy, Highly Active / Q000379:methods; D015331:Cohort Studies; D017124:Conserved Sequence; D024882:Drug Resistance, Viral / Q000235:genetics; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy / Q000235:genetics; D016333:HIV Protease / Q000235:genetics*; D017320:HIV Protease Inhibitors / Q000627:therapeutic use; D015497:HIV-1 / Q000235:genetics; D006801:Humans; D008956:Models, Chemical; D008957:Models, Genetic; D009154:Mutation; D011110:Polymorphism, Genetic
D017320:HIV Protease Inhibitors; D016333:HIV Protease