Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus RNA

Clever, Jared L.; Wong, Mei Lie; Parslow, Tristram G.

doi:10.1128/jvi.70.9.5902-5908.1996

Cited by 184 publications

(105 citation statements)

References 23 publications

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“…The 9–nucleotide loop contains a self‐complementary hexameric sequence GCGCGC (Lai isolate) or GUGCAC (Mal isolate) flanked by two adenines (Lai) or by an adenine and a guanine (Mal) on its 5′side and one adenine on its 3′ side. The dimeric structure seems to be essential for infectivity,1 and the role of the self‐complementary hexameric sequence and of the three flanking purines is crucial 2. It has been shown that the dimerization process is involved at different steps of the replication cycle of the virus such as recombination during reverse transcription,3–6 gag gene translation,7–9 and selective encapsidation of the genome in the viral particles 10.…”

Section: Introductionmentioning

confidence: 99%

On the stability of different experimental dimeric structures of the SL1 sequence from the genomic RNA of HIV‐1 in solution: A molecular dynamics simulation and electrophoresis study

et al. 2004

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SL1 is a stem-loop RNA sequence from the genome of HIV-1 thought to be the initiation site for the dimerization of the retroviral genomic RNA. The aim of this study is to check the stability in solution of different experimental dimeric structures available in the literature. Two kinds of dimer have been evidenced: an extended duplex looking like a double helix with two internal bulges and a kissing complex in which the monomers with a stem/loop conformation are linked by intermolecular loop-loop interactions. Two divergent experimental structures of the kissing complex from the Lai isolate are reported in the literature, one obtained from NMR (Mujeeb et al., Nature Structural Biology, 1998, Vol. 5, pp. 432-436) and the other one from x-ray crystallography (Ennifar et al., Nature Structural Biology, 2001, Vol. 8, pp. 1064-1068). A crystallographic structure of the Mal isolate was also reported (Ennifar et al., Nature Structure Biology, 2001, Vol. 8, pp. 1064-1068). Concerning the extended duplex, a NMR structure is available for Lai (Girard et al., Journal of Biomolecular Structure and Dynamics, 1999, Vol. 16, pp. 1145-1157) and a crystallographic structure for Mal (Ennifar et al., Structure, 1999, Vol. 7, pp. 1439-1449). Using a molecular dynamics technique, all these experimental structures have been simulated in solution with explicit water and counterions. We show that both extended duplex structures are stable. On the contrary, the crystallographic structures of the Lai and Mal kissing complexes are rapidly destabilized in aqueous environment. Finally, the NMR structure of the Lai loop-loop kissing complex remains globally stable over a 20 ns MD simulation, although large rearrangements occur at the level of the stem/loop junctions that are flexible, as shown from free energy calculations. These results are compared to electrophoresis experiments on dimer formation.

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Section: Introductionmentioning

confidence: 99%

On the stability of different experimental dimeric structures of the SL1 sequence from the genomic RNA of HIV‐1 in solution: A molecular dynamics simulation and electrophoresis study

et al. 2004

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“…Ostensibly, dimer formation would occur through a kissing hairpin mechanism by which the two RNAs would form an initial loop-loop contact based on complementary antiparallel base pairing followed by the generation of a stable intermolecular structure composed of hydrogen-bonded nucleotides in the stem regions of the hairpin (29,38,41,44). In support of this model, disruption of the palindromic sequence in the hairpin abrogates in vitro dimerization (12,20,29,38,41,44).…”

mentioning

confidence: 95%

“…Short synthetic retroviral RNAs can spontaneously dimerize in vitro under certain conditions (4,6,8,11,12,14,15,20,27,29,34,41,(43)(44)(45), and the efficiency of dimerization can be enhanced by the viral nucleocapsid (NC) protein (14)(15)(16). Based on studies of in vitro dimer formation with deletion and substitution mutations, the presumptive primary DLS of human immunodeficiency virus type 1 (HIV-1) has been mapped to a region near the major splice donor, which is located just proximal to the beginning of the gag gene (4,34,45).…”

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confidence: 99%

Human immunodeficiency virus type 1 RNA outside the primary encapsidation and dimer linkage region affects RNA dimer stability in vivo

Sakuragi

Panganiban

1997

J Virol

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To characterize the cis-acting determinants that function in RNA dimer formation and maintenance, we examined the stability of RNA dimers isolated from virus particles containing mutations in the encapsidation region of human immunodeficiency virus type 1 (HIV-1). The genomic RNAs of all mutants containing lesions in elements required for in vitro dimerization exhibited thermal stability similar to that of wild-type (WT) HIV-1. These data indicate that the eventual formation of stable dimeric RNA in vivo is not absolutely dependent on the elements that promote dimer formation in vitro. Surprisingly, mutants that lacked a large segment of the middle portion of the genome, outside the likely primary dimer linkage region, formed RNA dimers that were measurably more stable than WT. In addition, the insertion of one or multiple copies of a foreign gene, which resulted in a series of vectors that approached RNA length similar to that of WT RNA, still exhibited augmented dimer stability. These results suggest that there are regions in the HIV-1 genome outside the primary dimer initiation and dimer linkage regions that can negatively affect dimer stability.

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“…The dimer linkage site is located near the 5′‐terminus sequence in the main packaging domain, which has been predicted to contain four stem‐loops SL1, SL2, SL3, and SL4 involved in packaging of the unspliced transcript viral RNA 10–16. SL1 is the largest one (35 nt) and is thought to contain the dimer initiation site (DIS), which corresponds to a 6 nucleotide (nt) palindrome sequence located in a 9 nt apical loop 17–19. This loop is complemented with two and one purine on the 5′ and 3′ sides of DIS, respectively, flanking the palindrome (Figure 1).…”

Section: Introductionmentioning

confidence: 99%

Insight into the intrinsic flexibility of the SL1 stem‐loop from genomic RNA of HIV‐1 as probed by molecular dynamics simulation

Mazier¹,

Genest²

2007

Biopolymers

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The SL1 stem-loop is the dimerization initiation site for linking the two copies of the RNA forming the HIV-1 genome. The 26 nucleotides stem contains a defect consisting on a highly conserved G-rich 1-3 asymmetrical internal loop, which is a major site for nucleocapsid protein binding. Several NMR attempts were undertaken to determine the internal loop structure in the SL1 monomer. However, the RNA constructs used in the different studies were largely mutated, in particular with replacement of the nine nucleotides apical loop by a tetraloop, and divergent results were obtained ranging from a rigid structure to a particularly large flexibility. To investigate the reasons for such discrepancies, we used molecular dynamics simulation of the SL1 monomer to probe the effect of mutations on the conformational stability of the internal loop and of the whole stem. It is found that in the wild-type sequence, the internal loop displays conformational variability originating mainly from the nine nucleotides apical loop flexibility that causes large conformational fluctuations (without changing the average structure) in the 7 bp duplex linking the apical and internal loops. The large amplitude atomic motions in the duplex are transmitted to the internal loop in which they induce conformational changes characterized by a labile hydrogen bond network such as G5 successively H-bonded to A29 and G30. On the contrary, with a four nucleotides apical loop, conformational fluctuations in the duplex are reduced by a factor of 2 and are not sufficiently energizing for promoting changes in the internal loop structure at the time scale of the simulations.

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Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus RNA

Cited by 184 publications

References 23 publications

On the stability of different experimental dimeric structures of the SL1 sequence from the genomic RNA of HIV‐1 in solution: A molecular dynamics simulation and electrophoresis study

On the stability of different experimental dimeric structures of the SL1 sequence from the genomic RNA of HIV‐1 in solution: A molecular dynamics simulation and electrophoresis study

Human immunodeficiency virus type 1 RNA outside the primary encapsidation and dimer linkage region affects RNA dimer stability in vivo

Insight into the intrinsic flexibility of the SL1 stem‐loop from genomic RNA of HIV‐1 as probed by molecular dynamics simulation

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