Arginine side-chain dynamics in the HIV-1ReV-RRE complex

The binding of human immunodeficiency virus type 1 (HIV-1) Rev protein to i ts viral RNA target, stem-loop IIB (SLIIB) within the Rev Response element (RRE), mediates the export of singly-spliced and unspliced viral mRNA from the nucleus to the cytoplasm of infected cells; this Rev-mediated transport of viral RNA is absolutely required for the replication of infectious viru s. To identify important features that influence the binding affinity and s pecificity of this Rev-RRE interaction, we have characterized the arginine side-chain dynamics of the Rev arginine-rich motif (ARM) while bound to a 3 4 nt RNA oligomer that corresponds to SLIIB. As the specificity of the ReV- RRE interaction varies with salt concentration, arginine side-chain dynamic s were characterized at two different salt conditions. Following NMR measur ements of N-15 spin relaxation parameters for the arginine N-15(epsilon) nu clei, the dynamics of the corresponding N-epsilon-H-epsilon bond vectors we re interpreted in terms of Lipari-Szabo model-free parameters using anisotr opic expressions for the spectral density functions. Results from these ana lyses indicate that a number of arginine side-chains display a surprising d egree of conformational freedom when bound to RNA, and that arginine residu es having known importance for specific RRE recognition show striking diffe rences in side-chain mobility. The N-15 relaxation measurements at differen t salt conditions suggest that the previously reported increase in Rev-RRE specificity at elevated salt concentrations is Likely due to reduced affini ty of non-specific Rev-RNA interactions. The observed dynamical behavior of the arginine side-chains at this protein-RNA interface likely plays an imp ortant role in the specificity and affinity of Rev-SLIIB complex formation. (C) 2000 Academic Press.