Identification and structural characterization of novel genetic elements in the HIV-1 V3 loop regulating coreceptor usage.
BACKGROUND
The interaction between HIV-1 gp120 and CCR5 N terminus is critical for R5-virus entry and affects CCR5 antagonists' activity. Knowledge of how different genetic signatures of gp120 V3 domain effect the strength of this interaction is limited.


METHODS
HIV-1 coreceptor usage was assessed in 251 patients using enhanced-sensitivity Trofile assay and V3 sequencing plus tropism prediction by Geno2pheno algorithm. Bayesian partitional model and recursive model selection have been used to define V3 genetic determinants correlated with different coreceptor usage. Gp120 interaction with CCR5 N terminus was evaluated by docking-analysis/molecular-dynamic simulations starting from the model described previously.


RESULTS
Selected V3 genetic determinants (beyond known aminoacidic positions) significantly correlate with CCR5- or CXCR4-usage, and modulate gp120 affinity for CCR5 N terminus. This is the case for N5Y and N7K, absent in CCR5-using viruses and present in 4.5% and 6% of CXCR4-using viruses, respectively, and A19V, occurring in 2.6% of CCR5-using viruses and 22.0% of CXCR4-using viruses (P=10(-2) to 10(-7)). Their presence determines a decreased affinity for CCR5 N terminus even stronger than that observed in the presence of the well-known mutation S11R (N5Y: -6.60 Kcal/mol; N7K: -5.40 Kcal/mol; A19V: -5.60 Kcal/mol; S11R: -6.70 Kcal/mol; WT: -6.90 Kcal/mol). N7K significantly increases the distance between V3 position 7 and sulphotyrosine at CCR5 position 14 (crucial for binding to gp120; from 4.22 Å to 8.30 Å), thus abrogating the interaction between these two important residues.


CONCLUSIONS
Key determinants for tropism within the V3 sequence, confirmed by structure- and by phenotypic-tropism, have been identified. This information can be used for a finer tuning of potential efficacy of CCR5-antagonists in clinical practice, and to provide molecular implications for design of new entry inhibitors.
Department of Experimental Medicine and Biochemical Sciences, University of 'Tor Vergata', Rome, Italy.
Valentina
V
Svicher
Claudia
C
Alteri
Anna
A
Artese
Jing Maria
JM
Zhang
Giosuè
G
Costa
Fabio
F
Mercurio
Roberta
R
D'Arrigo
Stefano
S
Alcaro
Giorgio
G
Palù
Massimo
M
Clementi
Maurizio
M
Zazzi
Massimo
M
Andreoni
Andrea
A
Antinori
Adriano
A
Lazzarin
Francesca
F
Ceccherini-Silberstein
Carlo Federico
CF
Perno
D001483:Base Sequence; D001499:Bayes Theorem; D016000:Cluster Analysis; D015699:HIV Envelope Protein gp120 / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D015497:HIV-1 / Q000235:genetics* / Q000502:physiology; D006801:Humans; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009154:Mutation; D010446:Peptide Fragments / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D019713:Receptors, CCR5 / Q000235:genetics / Q000378:metabolism*; D019718:Receptors, CXCR4 / Q000235:genetics / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D053586:Virus Internalization
C527276:CXCR4 protein, human; D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments; D019713:Receptors, CCR5; D019718:Receptors, CXCR4