Arginine side-chain dynamics in the HIV-1 rev-RRE complex.
The binding of human immunodeficiency virus type 1 (HIV-1) Rev protein to its 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 virus. To identify important features that influence the binding affinity and specificity of this Rev-RRE interaction, we have characterized the arginine side-chain dynamics of the Rev arginine-rich motif (ARM) while bound to a 34 nt RNA oligomer that corresponds to SLIIB. As the specificity of the Rev-RRE interaction varies with salt concentration, arginine side-chain dynamics were characterized at two different salt conditions. Following NMR measurements of (15)N spin relaxation parameters for the arginine (15)N(epsilon) nuclei, the dynamics of the corresponding N(epsilon)-H(epsilon) bond vectors were interpreted in terms of Lipari-Szabo model-free parameters using anisotropic expressions for the spectral density functions. Results from these analyses indicate that a number of arginine side-chains display a surprising degree of conformational freedom when bound to RNA, and that arginine residues having known importance for specific RRE recognition show striking differences in side-chain mobility. The (15)N relaxation measurements at different salt conditions suggest that the previously reported increase in Rev-RRE specificity at elevated salt concentrations is likely due to reduced affinity of non-specific Rev-RNA interactions. The observed dynamical behavior of the arginine side-chains at this protein-RNA interface likely plays an important role in the specificity and affinity of Rev-SLIIB complex formation.
Wilkinson
T A
TA
Division of Immunology, Beckman Research Institute of the City of Hope National Medical Center, Duarte, CA, 91010, USA.
Botuyan
M V
MV
Kaplan
B E
BE
Rossi
J J
JJ
Chen
Y
Y
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D016880:Anisotropy; D001120:Arginine / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D001692:Biological Transport; D004058:Diffusion; D015694:Gene Products, rev / Q000737:chemistry / Q000378:metabolism*; D015497:HIV-1 / Q000235:genetics*; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding / Q000187:drug effects; D011487:Protein Conformation; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012492:Salts / Q000494:pharmacology; D013379:Substrate Specificity; D054321:rev Gene Products, Human Immunodeficiency Virus
D015694:Gene Products, rev; D009843:Oligoribonucleotides; D010446:Peptide Fragments; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D012492:Salts; D054321:rev Gene Products, Human Immunodeficiency Virus; D001120:Arginine