Exploring three-dimensional structures of the HIV-1 RNA/tRNALys3 initiation complex

Area of Science:

• Molecular Biology
• Virology
• Structural Biology

Background:

• Human immunodeficiency virus type 1 (HIV-1) utilizes host transfer RNA (tRNA) as a primer for reverse transcription.
• The 3' end of human tRNALys3 (18 nucleotides) is known to be complementary to the primer binding site on the HIV-1 RNA.
• A proposed model includes additional base-pairing between tRNALys3 and HIV-1 RNA beyond the primer binding site.

Purpose of the Study:

• To evaluate the proposed secondary structure model of the HIV-1 RNA/tRNALys3 initiation complex.
• To identify potential structural problems with extended tRNA-viral RNA interactions.

Main Methods:

• Attempts to build compatible three-dimensional models of the proposed secondary structure.
• Analysis of topological knotting in the proposed complex.
• Evaluation of all-atom models based on known RNA structures.

Main Results:

• The proposed extended interactions lead to topological knotting, problematic for initiation complex folding and reverse transcription.
• Inability to construct all-atom models consistent with the proposed secondary structure.
• Subsequent biochemical and genetic studies challenge the proposed extended interactions.

Conclusions:

• The proposed secondary structure model for the HIV-1 RNA/tRNALys3 initiation complex presents significant structural challenges.
• The validity of extended tRNA/HIV-1 RNA interactions beyond the primer binding site is questionable based on modeling and experimental data.