Structure of HIV-1 RRE stem-loop II identifies two conformational states of the high-affinity Rev binding site

Area of Science:

• Molecular Biology
• Structural Biology
• Virology

Background:

• HIV-1 infection requires nuclear export of unspliced viral RNA.
• The Rev response element (RRE) and Rev protein mediate this essential export pathway.
• Understanding RRE-Rev interaction is key to targeting HIV replication.

Purpose of the Study:

• To elucidate the structural basis of Rev protein binding to the RRE stem-loop II.
• To characterize the conformational dynamics of RRE stem-loop II.
• To propose a model for sequential Rev binding to RRE.

Main Methods:

• X-ray crystallography to determine RRE stem-loop II structures.
• Rev binding assays to quantify protein-RNA interactions.
• Structural analysis of distinct RRE conformations.

Main Results:

• Crystal structures reveal RRE stem-loop II in closed and open conformations.
• The high-affinity Rev-binding site is located in the three-way junction, not stem IIB.
• Distinct non-canonical interactions define the closed and open conformers, with the open form facilitating Rev binding.

Conclusions:

• The open RRE stem-loop II conformation presents a widened major groove for initial Rev protein interaction.
• RRE stem-loop II possesses both high- and low-affinity binding sites for Rev dimers.
• A model of sequential binding site formation through Rev-induced structural rearrangements is proposed.