Dataset Information

Investigation of HIV-1 Gag binding with RNAs and lipids using Atomic Force Microscopy.

ABSTRACT: Atomic Force Microscopy was utilized to study the morphology of Gag, ΨRNA, and their binding complexes with lipids in a solution environment with 0.1Å vertical and 1nm lateral resolution. TARpolyA RNA was used as a RNA control. The lipid used was phospha-tidylinositol-(4,5)-bisphosphate (PI(4,5)P2). The morphology of specific complexes Gag-ΨRNA, Gag-TARpolyA RNA, Gag-PI(4,5)P2 and PI(4,5)P2-ΨRNA-Gag were studied. They were imaged on either positively or negatively charged mica substrates depending on the net charges carried. Gag and its complexes consist of monomers, dimers and tetramers, which was confirmed by gel electrophoresis. The addition of specific ΨRNA to Gag is found to increase Gag multimerization. Non-specific TARpolyA RNA was found not to lead to an increase in Gag multimerization. The addition PI(4,5)P2 to Gag increases Gag multimerization, but to a lesser extent than ΨRNA. When both ΨRNA and PI(4,5)P2 are present Gag undergoes comformational changes and an even higher degree of multimerization.

SUBMITTER: Chen S

PROVIDER: S-EPMC6996966 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Investigation of HIV-1 Gag binding with RNAs and lipids using Atomic Force Microscopy.

Chen Shaolong S Xu Jun J Liu Mingyue M Rao A L N ALN Zandi Roya R Gill Sarjeet S SS Mohideen Umar U

PloS one 20200203 2

Atomic Force Microscopy was utilized to study the morphology of Gag, ΨRNA, and their binding complexes with lipids in a solution environment with 0.1Å vertical and 1nm lateral resolution. TARpolyA RNA was used as a RNA control. The lipid used was phospha-tidylinositol-(4,5)-bisphosphate (PI(4,5)P2). The morphology of specific complexes Gag-ΨRNA, Gag-TARpolyA RNA, Gag-PI(4,5)P2 and PI(4,5)P2-ΨRNA-Gag were studied. They were imaged on either positively or negatively charged mica substrates dependi ...[more]

PMID: 32015565

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Project description:We present a magnetic force-based direct drive modulation method to measure local nano-rheological properties of soft materials across a broad frequency range (10 Hz to 2 kHz) using colloid-attached atomic force microscope (AFM) probes in liquid. The direct drive method enables artefact-free measurements over several decades of excitation frequency, and avoids the need to evaluate medium-induced hydrodynamic drag effects. The method was applied to measure the local mechanical properties of polyacrylamide hydrogels. The frequency-dependent storage stiffness, loss stiffness, and loss tangent (tan??) were quantified for hydrogels having high and low crosslinking densities by measuring the amplitude and the phase response of the cantilever while the colloid was in contact with the hydrogel. The frequency bandwidth was further expanded to lower effective frequencies (0.1 Hz to 10 Hz) by obtaining force-displacement (FD) curves. Slow FD measurements showed a recoverable but highly hysteretic response, with the contact mechanical behaviour dependent on the loading direction: approach curves showed Hertzian behaviour while retraction curves fit the JKR contact mechanics model well into the adhesive regime, after which multiple detachment instabilities occurred. Using small amplitude dynamic modulation to explore faster rates, the load dependence of the storage stiffness transitioned from Hertzian to a dynamic punch-type (constant contact area) model, indicating significant influence of material dissipation coupled with adhesion. Using the appropriate contact model across the full frequency range measured, the storage moduli were found to remain nearly constant until an increase began near ?100 Hz. The softer gels' storage modulus increased from 7.9 ± 0.4 to 14.5 ± 2.1 kPa (?85%), and the stiffer gels' storage modulus increased from 16.3 ± 1.1 to 31.7 ± 5.0 kPa (?95%). This increase at high frequencies may be attributed to a contribution from solvent confinement in the hydrogel (poroelasticity). The storage moduli measured by both macro-rheometry and AFM FD curves were comparable to those measured using the modulation method at their overlapping frequencies (10-25 Hz). In all cases, care was taken to ensure the contact mechanics models were applied within the important limit of small relative deformations. This study thus highlights possible transitions in the probe-material contact mechanical behaviour for soft matter, especially when the applied strain rates and the material relaxation rates become comparable. In particular, at low frequencies, the modulus follows Hertzian contact mechanics, while at high frequencies adhesive contact is well represented by punch-like behaviour. More generally, use of the Hertz model on hydrogels at high loading rates, at high strains, or during the retraction portion of FD curves, leads to significant errors in the calculated moduli.

Dataset Information

Investigation of HIV-1 Gag binding with RNAs and lipids using Atomic Force Microscopy.

Publications

Investigation of HIV-1 Gag binding with RNAs and lipids using Atomic Force Microscopy.

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