Pappalardo L, Kerwood D J, Pelczer I, Borer P N
Department of Chemistry, Syracuse University, Syracuse, NY, 13244-4100, USA.
J Mol Biol. 1998 Oct 2;282(4):801-18. doi: 10.1006/jmbi.1998.2046.
An NMR-based structure is presented for a 20 mer hairpin model of the SL3 stem-loop from the HIV-1 packaging signal. The stem has an A-family structure. However, the GGAG tetraloop appears to be flexible with the second (G10) and fourth (G12) bases extruded from the normal stacking arrangement. The A-base (A11) occupies a cavity large enough for it to jump rapidly between stacking upon G9 (in the loop) and G13 (from the base-pair adjacent to the loop). The H-bonding loci of G10, A11, and G12 are unoccupied in the free RNA structure. The loop should be easily adaptable to binding by the HIV-1 nucleocapsid protein or loop receptors.
本文给出了来自HIV-1包装信号的SL3茎环的20聚体发夹模型的基于核磁共振的结构。该茎具有A家族结构。然而，GGAG四环似乎具有柔性，其第二个（G10）和第四个（G12）碱基从正常堆积排列中挤出。A碱基（A11）占据了一个足够大的空腔，使其能够在与G9（在环中）堆积和与G13（来自与环相邻的碱基对）堆积之间快速跳跃。在游离RNA结构中，G10、A11和G12的氢键位点未被占据。该环应该很容易适应与HIV-1核衣壳蛋白或环受体的结合。
