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Protein structural disorder of the envelope V3 loop contributes to the switch in human immunodeficiency virus type 1 cell tropism. PLoS One 2017; 12:e0185790. [PMID: 29049306 PMCID: PMC5648111 DOI: 10.1371/journal.pone.0185790] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/19/2017] [Indexed: 11/29/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) envelope gp120 is partly an intrinsically disordered (unstructured/disordered) protein as it contains regions that do not fold into well-defined protein structures. These disordered regions play important roles in HIV’s life cycle, particularly, V3 loop-dependent cell entry, which determines how the virus uses two coreceptors on immune cells, the chemokine receptors CCR5 (R5), CXCR4 (X4) or both (R5X4 virus). Most infecting HIV-1 variants utilise CCR5, while a switch to CXCR4-use occurs in the majority of infections. Why does this ‘rewiring’ event occur in HIV-1 infected patients? As changes in the charge of the V3 loop are associated with this receptor switch and it has been suggested that charged residues promote structure disorder, we hypothesise that the intrinsic disorder of the V3 loop is permissive to sequence variation thus contributing to the switch in cell tropism. To test this we use three independent data sets of gp120 to analyse V3 loop disorder. We find that the V3 loop of X4 virus has significantly higher intrinsic disorder tendency than R5 and R5X4 virus, while R5X4 virus has the lowest. These results indicate that structural disorder plays an important role in HIV-1 cell tropism and CXCR4 binding. We discuss the potential evolutionary mechanisms leading to the fixation of disorder promoting mutations and the adaptive potential of protein structural disorder in viral host adaptation.
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Seager I, Travers SA, Leeson MD, Crampin AC, French N, Glynn JR, McCormack GP. Coreceptor usage, diversity, and divergence in drug-naive and drug-exposed individuals from Malawi, infected with HIV-1 subtype C for more than 20 years. AIDS Res Hum Retroviruses 2014; 30:975-83. [PMID: 24925099 DOI: 10.1089/aid.2013.0240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
There are few cohorts of individuals who have survived infection with HIV-1 for more than 20 years, reported and followed in the literature, and even fewer from Africa. Here we present data on a cohort of subtype C-infected individuals from rural northern Malawi. By sequencing multiple clones from long-term survivors at different time points, and using multiple genotyping approaches, we show that 5 of the 11 individuals are predicted as CXCR4 using (by ≥3/5 predictors) but only one individual is predicted as CXCR4 using by all five algorithms. Using any one genotyping approach overestimates the number of predicted CXCR4 sequences. Patterns of diversity and divergence were variable between the HIV-1 long-term survivors with some individuals showing very small amounts of variation and change, and others showing a greater amount; both patterns are consistent with what has been described in the literature.
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Affiliation(s)
- Ishla Seager
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Simon A. Travers
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
- South African National Bioinformatics Institute, SA Medical Research Council Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
| | - Michael D. Leeson
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Amelia C. Crampin
- Karonga Prevention Study, Chilumba, Malawi
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Neil French
- Karonga Prevention Study, Chilumba, Malawi
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Judith R. Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Grace P. McCormack
- Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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