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Multiscale computer simulation of the immature HIV-1 virion.

ABSTRACT: Multiscale computer simulations, employing a combination of experimental data and coarse-graining methods, are used to explore the structure of the immature HIV-1 virion. A coarse-grained (CG) representation is developed for the virion membrane shell and Gag polypeptides using molecular level information. Building on the results from electron cryotomography experiments, the simulations under certain conditions reveal the existence of an incomplete p6 hexameric lattice formed from hexameric bundles of the Gag CA domains. In particular, the formation and stability of the immature Gag lattice at the CG level requires enhanced interfacial interactions of the CA protein C-terminal domains (CTDs). An exact mapping of the CG representation back to the molecular level then allows for detailed atomistic molecular dynamics studies to confirm the existence of these enhanced CA(CTD) interactions and to probe their possible origin. The multiscale simulations further provide insight into potential CA(CTD) mutations that may disrupt or modify the Gag immature lattice assembly process in the immature HIV-1 virion.

SUBMITTER: Ayton GS

PROVIDER: S-EPMC2966041 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature

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Multiscale computer simulation of the immature HIV-1 virion.

Ayton Gary S GS Voth Gregory A GA

Biophysical journal 20101101 9

Multiscale computer simulations, employing a combination of experimental data and coarse-graining methods, are used to explore the structure of the immature HIV-1 virion. A coarse-grained (CG) representation is developed for the virion membrane shell and Gag polypeptides using molecular level information. Building on the results from electron cryotomography experiments, the simulations under certain conditions reveal the existence of an incomplete p6 hexameric lattice formed from hexameric bundl ...[more]

PMID: 21044572

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Project description:Despite the progress in the Prevention of the Mother-to-Child Transmission of HIV (PMTCT), the paediatric HIV epidemic remains worrying in Cameroon. HIV prevalence rate for the population of pregnant women was 7.6% in 2010 in Cameroon. The extent of the paediatric HIV epidemic is needed to inform policymakers. We developed a stochastic simulation model to estimate the number of new paediatric HIV infections through MTCT based on the observed uptake of services during the different steps of the PMTCT cascade in Cameroon in 2011. Different levels of PMTCT uptake was also assessed.A discrete events computer simulation-based approach with stochastic structure was proposed to generate a cohort of pregnant women followed-up until 6 weeks post-partum, and optionally until complete breastfeeding cessation in both prevalent and incident lactating HIV-infected women. The different parameters of the simulation model were fixed using data sources available from the 2011 national registry surveys, and from external cohorts in Cameroon. Different PMTCT coverages were simulated to assess their impact on MTCT. Available data show a low coverage of PMTCT services in Cameroon in 2011.Based on a simulation approach on a population of 995, 533 pregnant women, the overall residual MTCT rate in 2011 was estimated to be 22.1% (95 % CI: 18.6%-25.2%), the 6-week perinatal MTCT rate among prevalent HIV-infected mothers at delivery is estimated at 12.1% (95% CI: 8.1%-15.1%), with an additional postnatal MTCT rate estimated at 13.3% (95% CI: 9.3%-17.8%). The MTCT rate among children whose mothers seroconverted during breastfeeding was estimated at 20.8% (95% CI: 14.1%-26.9%). Overall, we estimated the number of new HIV infections in children in Cameroon to be 10, 403 (95% CI: 9, 054-13, 345) in 2011. When PMTCT uptake have been fixed at 100%, 90% and 80%, global MTCT rate failed to 0.9% (9% CI: 0.5%-1.7%), 2.0% (95% CI: 0.9%-3.2%) and 4.3% (95% CI: 2.4%-6.7%) respectively.This model is helpful to provide MTCT estimates to guide the national HIV policy in Cameroon. Increasing supply and uptake of PMTCT services among prevalent HIV infected pregnant women, as well as HIV-prevention interventions including the offer and acceptance of HIV testing and counselling in lactating women could reduce significantly the residual HIV MTCT in Cameroon. A public health effort should be made to encourage health care workers and pregnant women to use PMTCT services until complete breastfeeding cessation.

Dataset Information

Multiscale computer simulation of the immature HIV-1 virion.

Publications

Multiscale computer simulation of the immature HIV-1 virion.

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