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Human Immunodeficiency Virus Reverse Transcriptase pp 77–95Cite as

Conformational Dynamics of Reverse Transcription

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Abstract

Synthesis of double-stranded DNA from the retrovirus (+)-strand RNA genome is a multi-step process catalyzed by the virus-coded reverse transcriptase (RT), using a combination of synthetic (RNA- and DNA-dependent DNA synthesis) and degradative activities (ribonuclease H, or RNase H). For human immunodeficiency virus type 1 (HIV-1) RT, the two-subunit p66/p51 heterodimer must accommodate a variety of conformationally distinct nucleic acid substrates, including duplex RNA, RNA/DNA hybrids duplex DNA, and RNA-DNA chimeras to complete this process (Telesnitsky and Goff 1997). Despite a wealth of structural and biochemical studies, the mechanism whereby RT adopts different orientations to coordinate its DNA polymerase and RNase H activities has remained elusive. The lower processivity of HIV-1 RT (Bibillo and Eickbush 2002) also raises the issue of polymerization site targeting when the enzyme re-engages its nucleic acid substrate distal from the primer terminus. Although X-ray crystallography has contributed significantly to our understanding of reverse transcription complexes and resistance to antiviral drugs, it provides a static picture, revealing few details regarding motion of the enzyme on its substrate. In contrast, single-molecule spectroscopy has proven an invaluable tool capable of resolving static and dynamic heterogeneity of an ensemble (Lu et al. 1998; Moerner and Orrit 1999; Weiss 2000). In an early study, (Rothwell et al. 2003) used a fluorescence resonance energy transfer (FRET) approach to distinguish three structurally distinct HIV-1 RT species, including one form where nucleic acid was positioned to permit nucleotide incorporation and a second corresponding to a nucleoprotein complex formed following nucleotide addition but prior to translocation. However, since this seminal study, little progress has been made in dissection of the conformational dynamics of reverse transcription. Progress in these areas and the implications for investigational and established inhibitors that interfere with HIV-1 RT function will be reviewed here.

Conflict of interest statement: None declared

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Abbreviations

Cy3:

Cyanine 3

Cy5:

Cyanine 5

ddNTP:

Dideoxynucleoside triphosphate

dNTP:

Deoxynucleoside triphosphate

FRET:

Fluorescence resonance energy transfer

HIV:

Human immunodeficiency virus

LTR:

Long terminal repeat

MLV:

Murine leukemia virus

NC:

Nucleocapsid protein

NNRTI:

Nonnucleoside RT inhibitor

PPT:

Polypurine tract

RSV:

Rous sarcoma virus

RT:

Reverse transcriptase

UTR:

Untranslated region

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Authors and Affiliations

  1. HIV Drug Resistance Program, National Laboratory for Cancer Research, Building 535, Room 312, Frederick, MD, 21702, USA

    Stuart F. J. LeGrice

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  1. Stuart F. J. LeGrice
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Correspondence to Stuart F. J. LeGrice .

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  1. , HIV Drug Resistance Program, National Cancer Institute, Frederick, 21702, Maryland, USA

    Stuart LeGrice

  2. McGill University, 3775 University Street 3755, Montreal, H3T 1E2, Québec, Canada

    Matthias Gotte

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LeGrice, S.F.J. (2013). Conformational Dynamics of Reverse Transcription. In: LeGrice, S., Gotte, M. (eds) Human Immunodeficiency Virus Reverse Transcriptase. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7291-9_4

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