Book of Abstracts: Albany 2011
June 14-18 2011
©Adenine Press (2010)
Hypothetical Mechanism of the Kissing to Extended Dimer Conversion for the HIV-1 Stem-Loop 1 RNA
Two homologous copies of genomic RNA are packaged as a dimer into the HIV-1 virions (reviewed in (1-3)). The initiation of the dimer formation, which is believed to occur in the cytoplasm of infected cells, has been mapped to a stem-loop SL1 with a palindromic apical loop within the 5’-untranslated region of the HIV-1 RNA. SL1 RNA, its structural features and sequence are strongly conserved among HIV-1 isolates; deletion of SL1 significantly impairs packaging of RNA into the virions. RNA extracted from immature HIV-1 virions is thermally unstable as a dimer; the dimer stability increases with virus maturation, which is a complex process associated with the viral protease activity (4,5). In vitro, SL1 RNA can form either a metastable kissing dimer (KD), which is kept together by a 6-bp duplex formed by the palindromic loops, or a stable extended dimer (ED). KD SL1 RNA can be converted into ED by the viral nucleocapsid protein NCp7 (6), a proteolytic fragment of the Gag polyprotein. This conversion can occur without disruption of the kissing interaction between the palindromic loops (7), which is present in both KD and ED forms. While it is generally accepted that RNA chaperone properties of NCp7 are responsible for the KD-to-ED conversion, the detailed mechanism of the conversion is not known. Indeed, NCp7 destabilizes duplexes only moderately (8), however, 12 base pairs in each SL1 stem need to be broken and re-arranged during the conversion; further, only two NCp7 molecules per SL1 dimer are sufficient for the complete conversion (7). Here, we propose a mechanism for the KD-to-ED conversion that does not require simultaneous dissociation of all base pairs in SL1 stems. This hypothetical mechanism involves formation of an RNA analog of the Holliday junction intermediate between the two stems of the SL1 dimer and a following branch migration towards the palindromic duplex. According to this model, the torsional stress accumulated due to the stem rotation caused by the branch migration is absorbed by the single-stranded purines flanking the palindromic sequence. The NCp7 role is to bring the two stems together by neutralizing the charges on the phosphate groups and to facilitate formation of the initial cross-over, possibly at the level of the G-rich internal loop. We will present the models of the intermediate structures calculated with the miniCarlo program (9).
This research is supported in part by the California HIV/AIDS Research Program award ID09-SF-030.
References and Footnotes
Nikolai B. Ulyanov*
Department of Pharmaceutical Chemistry
University of California, San Francisco, CA 94158-2517, U.S.A.