How binding of small molecule and peptide ligands to HIV-1 TAR alters the RNA motional landscape.
The HIV-1 TAR RNA represents a well-known paradigm to study the role of dynamics and conformational change in RNA function. This regulatory RNA changes conformation in response to binding of Tat protein and of a variety of peptidic and small molecule ligands, indicating that its conformational flexibility and intrinsic dynamics play important roles in molecular recognition. We have used (13)C NMR relaxation experiments to examine changes in the motional landscape of HIV-1 TAR in the presence of three ligands of different affinity and specificity. The ligands are argininamide, a linear peptide mimic of the Tat basic domain and a cyclic peptide that potently inhibits Tat-dependent activation of transcription. All three molecules induce the same motional characteristics within the three nucleotides bulge that represents the Tat-binding site. However, the cyclic peptide has a unique motional signature in the apical loop, which represents a binding site for the essential host co-factor cyclin T1. These results suggest that all peptidic mimics of Tat induce the same dynamics in TAR within this protein binding site. However, the new cyclic peptide mimic of Tat represents a new class of ligands with a unique effect on the dynamics and the structure of the apical loop.
Bardaro
Michael F
MF
Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA.
Shajani
Zahra
Z
Patora-Komisarska
Krystyna
K
Robinson
John A
JA
Varani
Gabriele
G
D001120:Arginine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000235:genetics*; D008024:Ligands; D008958:Models, Molecular; D009038:Motion; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D010456:Peptides, Cyclic / Q000737:chemistry / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D054322:tat Gene Products, Human Immunodeficiency Virus / Q000737:chemistry
D008024:Ligands; D010456:Peptides, Cyclic; D012367:RNA, Viral; D054322:tat Gene Products, Human Immunodeficiency Virus; C069339:argininamide; D001120:Arginine