Investigation of HIV-1 Conserved Components for Genomic Recognition

Abstract

Genomic recognition for HIV-1 is an intricate process that requires the coordination of distinct intermolecular interactions between the 5'-leader (5'-L) of the viral genome and the RNA-binding nucleocapsid (NC) domain of the Gag polyprotein. Structural and biophysical studies in combination with in vivo packaging experiments identified the minimal packaging unit within the 5'-L, termed the ?CES (core encapsidation signal), which adopts a unique tandem three-way junction structure and is predicted to function as a nucleation site for Gag multimerization. Identification of the initial high affinity binding sites within the lower three-way junction of the ?CES, coined the ?3WJ-1 revealed a potential mechanism of selective RNA packaging. However, these findings, along with the vast majority of HIV-1 structural biology, stem from investigating the widely utilized laboratory strain known as NL4-3. As a means of interpreting the possibility of a structure-function relationship for the conserved 5'- L the present studies investigate another variant of HIV-1, MAL. Sequence alignment of the ?CES region of the two strains indicates a ninety-one percent sequence homology,while additional evaluation of the ?3WJ-1 illustrated higher sequence identity at ninety- five percent. Isothermal titration calorimetry (ITC) experiments identified that the binding isotherms for both strains are similar, indicating the sequence variations between MAL and NL4-3 do not perturb the mechanism of action for NC binding. Through the utilization of solution-state nuclear magnetic resonance (NMR), nucleotide-specific 2H-labeling, and residual dipolar coupling (RDC) measurements the three-dimensional structure of the MAL_?3WJ-1 was characterized, leading to a more comprehensive understanding of the complexities behind selective packaging of the viral genome.