6xh2
From Proteopedia
Co-crystal structure of HIV-1 TAR RNA in complex with lab-evolved RRM 6.6
Structural highlights
FunctionSNRPA_HUMAN Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.[1] Publication Abstract from PubMedRNA-protein interfaces control key replication events during the HIV-1 life cycle. The viral trans-activator of transcription (Tat) protein uses an archetypal arginine-rich motif (ARM) to recruit the host positive transcription elongation factor b (pTEFb) complex onto the viral trans-activation response (TAR) RNA, leading to activation of HIV transcription. Efforts to block this interaction have stimulated production of biologics designed to disrupt this essential RNA-protein interface. Here, we present four co-crystal structures of lab-evolved TAR-binding proteins (TBPs) in complex with HIV-1 TAR. Our results reveal that high-affinity binding requires a distinct sequence and spacing of arginines within a specific beta2-beta3 hairpin loop that arose during selection. Although loops with as many as five arginines were analyzed, only three arginines could bind simultaneously with major-groove guanines. Amino acids that promote backbone interactions within the beta2-beta3 loop were also observed to be important for high-affinity interactions. Based on structural and affinity analyses, we designed two cyclic peptide mimics of the TAR-binding beta2-beta3 loop sequences present in two high-affinity TBPs (K(D) values of 4.2 +/- 0.3 and 3.0 +/- 0.3 nm). Our efforts yielded low-molecular weight compounds that bind TAR with low micromolar affinity (K(D) values ranging from 3.6 to 22 mum). Significantly, one cyclic compound within this series blocked binding of the Tat-ARM peptide to TAR in solution assays, whereas its linear counterpart did not. Overall, this work provides insight into protein-mediated TAR recognition and lays the ground for the development of cyclic peptide inhibitors of a vital HIV-1 RNA-protein interaction. Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors.,Chavali SS, Mali SM, Jenkins JL, Fasan R, Wedekind JE J Biol Chem. 2020 Dec 4;295(49):16470-16486. doi: 10.1074/jbc.RA120.015444. Epub , 2020 Oct 13. PMID:33051202[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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