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#VMD MEASURE MEAN SQUARE DISPLACEMENT FREE#

īudding and assembly of the viral particle takes place at specific locations on the plasma membrane (PM). During the late-stages of the life cycle, assembly of the virion inside the host-cell takes place at the plasma membrane directed by specific lipid-protein interactions. Initially, the virion enters the host cell by direct fusion with the plasma membrane, facilitated by viral membrane proteins. The human immunodeficiency viruses type 1 (HIV-1) is an enveloped retrovirus that infects immune system cells, specifically CD4 +T cells and macrophages. Thus, the composition of the bilayer depends on the complex constitution of lipids from the host-cell’s organelle(s) where assembly and/or budding of the viral particle occurs.

The lipid bilayer itself is derived from the host cell during viral replication. The lipid envelope and membrane proteins act as a container for all the components necessary to fulfill the virus life cycle, adopting morphologies ranging from spheres to tubes. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist.Įnveloped viruses are molecular pathogens enclosed in a lipid bilayer acquired from the host cell during viral assembly and egress. Computational resources were also provided by a LANL institutional computing grant on the Grizzly Supercomputer (2019-2020) (T.R.), and a Great Lakes Consortium for Petascale Computation grant for the NCSA Blue Waters supercomputer (2018-2019) (J.R.P. This work used XSEDE Bridges and Stampede2 at the Pittsburgh Super Computing Center and Texas Advanced Computing Center, respectively, through allocation MCB170096 (JRP). This work used the Extreme Science and Engineering Discovery Environment, which is supported by the National Science Foundation (Grant ACI-1548562) (JRP). Frontera is made possible by NSF award OAC-1818253 (JRP). This research is part of the Frontera computing project at the Texas Advanced Computing Center. Methodology development for the present work was provided by the National Science Foundation award MCB-2027096(JRP), funded in part by Delaware Established Program to Stimulate Competitive Research (EPSCoR). The work is made available under the Creative Commons CC0 public domain dedication.ĭata Availability: All relevant data are within the manuscript and its Supporting information files.įunding: The authors acknowledge funding from the US National Institutes of Health award P50AI1504817 (JRP) and P20GM104316(JRP).

#VMD MEASURE MEAN SQUARE DISPLACEMENT FREE#

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. Received: ApAccepted: DecemPublished: January 18, 2022 Icahn School of Medicine at Mount Sinai, UNITED STATES

#VMD MEASURE MEAN SQUARE DISPLACEMENT FULL#

Overall, our simulations reveal complex relationships between the rich lipid composition of the HIV-1 liposome and its structural, mechanical and dynamical properties with critical consequences to different stages of HIV-1’s life cycle.Ĭitation: Bryer AJ, Reddy T, Lyman E, Perilla JR (2022) Full scale structural, mechanical and dynamical properties of HIV-1 liposomes. Finally, dynamical properties of the lipid molecules reveal important relationships between their 3D diffusion, the location of lipid-rafts and the asymmetrical composition of the envelope. Moreover, full-scale mechanical analyses are employed to derive the global bending rigidity of HIV-1 liposomes.

Analysis of the structural properties reveal the distribution of thicknesses of the bilayers over the entire liposome as well as its global fluctuations. Here, molecular dynamics (MD) simulations of authentic, asymmetric HIV-1 liposomes are used to derive a unique level of resolution of its full-scale structure, mechanics and dynamics. The envelope is derived from the host cell during viral replication. Viral envelopes are lipid bilayers that adopt morphologies ranging from spheres to tubes. Enveloped viruses are enclosed by a lipid membrane inside of which are all of the components necessary for the virus life cycle viral proteins, the viral genome and metabolites.

Vmd measure mean square displacement