scholarly journals Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Melanie Koehler ◽  
Ankita Ray ◽  
Rodrigo A. Moreira ◽  
Blinera Juniku ◽  
Adolfo B. Poma ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Atomic Force Microscopy ◽  
Complex Stability ◽  
Force Microscopy ◽  
Atomic Force ◽  
Binding Energetics ◽  
Almost All ◽  
The Impact ◽  
Induced Immunity ◽  
Insight Into

AbstractDespite an unprecedented global gain in knowledge since the emergence of SARS-CoV-2, almost all mechanistic knowledge related to the molecular and cellular details of viral replication, pathology and virulence has been generated using early prototypic isolates of SARS-CoV-2. Here, using atomic force microscopy and molecular dynamics, we investigated how these mutations quantitatively affected the kinetic, thermodynamic and structural properties of RBD—ACE2 complex formation. We observed for several variants of concern a significant increase in the RBD—ACE2 complex stability. While the N501Y and E484Q mutations are particularly important for the greater stability, the N501Y mutation is unlikely to significantly affect antibody neutralization. This work provides unprecedented atomistic detail on the binding of SARS-CoV-2 variants and provides insight into the impact of viral mutations on infection-induced immunity.

scholarly journals Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants

2021 ◽  
Author(s):  
Melanie Koehler ◽  
Ankita Ray ◽  
Rodrigo Azevedo Moreira da Silva ◽  
Blinera Juniku ◽  
Adolfo Poma ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Complex Stability ◽  
Direct Link ◽  
Force Microscopy ◽  
Atomic Force ◽  
Binding Energetics ◽  
Almost All ◽  
The Impact ◽  
Induced Immunity ◽  
Insight Into

Abstract Despite an unprecedented global gain in knowledge since the emergence of SARS-CoV-2, almost all mechanistic knowledge related to the molecular and cellular details of viral replication, pathology and virulence has been generated using early prototypic isolates of SARS-CoV-2. Here, using atomic force microscopy and molecular dynamics, we investigated how these mutations quantitatively affected the kinetic, thermodynamic and structural properties of RBD—ACE2 complex formation. We observe a direct link between increased RBD—ACE2 complex stability and the greater transmissibility observed for the variants of concern. While the N501Y and E484Q mutations are particularly important for the greater stability, the N501Y mutation is unlikely to significantly affect antibody neutralization. This work provides unprecedented atomistic detail on the binding of SARS-CoV-2 variants and provides insight into the impact of viral mutations on infection-induced immunity.

scholarly journals Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy

2021 ◽  
Author(s):  
Hiroki Koide ◽  
Noriyuki Kodera ◽  
Shveta Bisht ◽  
Shoji Takada ◽  
Tsuyoshi Terakawa
Keyword(s):  
Molecular Dynamics ◽  
Atomic Force Microscopy ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Force Microscopy ◽  
Atomic Force ◽  
Dna Loop ◽  
Dynamics Simulations ◽  
Dsdna Binding ◽  
Hinge Domain

The condensin protein complex compacts chromatin during mitosis using its DNA-loop extrusion activity. Previous studies proposed scrunching and loop-capture models as molecular mechanisms for the loop extrusion process, both of which assume the binding of double-strand (ds) DNA to the so-called hinge domain formed at the interface of the condensin subunits Smc2 and Smc4. However, how the hinge domain contacts dsDNA has remained unknown, potentially due to its conformational plasticity. Here, we conducted atomic force microscopy imaging of the budding yeast condensin holo-complex and used this data as basis for coarse-grained molecular dynamics simulations to model the hinge structure in a transient open conformation. We then simulated the dsDNA binding to open and closed hinge conformations, predicting that dsDNA binds to the outside surface when closed and to the outside and inside surfaces when open. Our simulations also suggested that the hinge can close around dsDNA bound to the inside surface. The conformational change of the hinge domain might be essential for the dsDNA binding regulation and play important roles in condensin-mediated DNA-loop extrusion.

Protective Coating Based on Organic Silicon Polymer of Ladder Structure Nanostructured with Alkoxysilane

2020 ◽  
Vol 992 ◽  
pp. 580-584
Author(s):  
V.Yu. Chukhlanov ◽  
O.G. Selivanov ◽  
N.V. Chukhlanova
Keyword(s):  
Atomic Force Microscopy ◽  
Physical Properties ◽  
Protective Coating ◽  
Silicon Oxide ◽  
Polymer Composition ◽  
Orthosilicic Acid ◽  
Force Microscopy ◽  
Atomic Force ◽  
Destruction Kinetics ◽  
The Impact

New materials based on oligooxidridsilmethylensiloxysilane nanostructured with ethyl ester of orthosilicic acid – tetraethoxysilane have been studied in the research. Tetraethoxysilane introduction into the composition is supposed to cause its decomposition up to nanoparticles of silicon oxide. The alkoxysilane hydrolytic destruction kinetics and the impact of the composition and nature of the polymer composition components on the physical properties have been studied. Atomic force microscopy was used to study the structurization kinetics of the polymer composition. The composition hydrophobicity was determined by the edge wetting angle. To study the adhesion characteristics of the obtained material, the method of disc separation from the substrate has been used. The relative rigidity has been determined by a pendulum device M3. Atomic force microscopy revealed the presence of nanoscale neoplasms (at average of one hundred twenty per one square micrometer) in diameter from two to five nanometers in the surface structure of the composition, modified with tetraethoxysilane. Herewith the physical properties of the material change: rigidity increases, the edge angle of wetting increases as well. The studied nanostructured compositions can also be applied. For example – they can be used as a protective coating with a set of special properties, such as high hydrophobicity.

scholarly journals Quantitative atomic force microscopy provides new insight into matrix vesicle mineralization

2019 ◽  
Vol 667 ◽  
pp. 14-21 ◽  
Author(s):  
Justin S. Plaut ◽  
Agnieszka Strzelecka-Kiliszek ◽  
Lukasz Bozycki ◽  
Slawomir Pikula ◽  
René Buchet ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Matrix Vesicle ◽  
Force Microscopy ◽  
Atomic Force ◽  
Insight Into

scholarly journals Characterisation of InGaN by Photoconductive Atomic Force Microscopy

Materials ◽  
2018 ◽  
Vol 11 (10) ◽  
pp. 1794 ◽  
Author(s):  
Thomas Weatherley ◽  
Fabien Massabuau ◽  
Menno Kappers ◽  
Rachel Oliver
Keyword(s):  
Atomic Force Microscopy ◽  
Cross Sections ◽  
Indium Content ◽  
Light Emitting ◽  
Force Microscopy ◽  
Turn On ◽  
Atomic Force ◽  
Voltage Curve ◽  
Current Voltage Curve ◽  
The Impact

Nanoscale structure has a large effect on the optoelectronic properties of InGaN, a material vital for energy saving technologies such as light emitting diodes. Photoconductive atomic force microscopy (PC-AFM) provides a new way to investigate this effect. In this study, PC-AFM was used to characterise four thick (∼130 nm) In x Ga 1 − x N films with x = 5%, 9%, 12%, and 15%. Lower photocurrent was observed on elevated ridges around defects (such as V-pits) in the films with x ≤ 12 %. Current-voltage curve analysis using the PC-AFM setup showed that this was due to a higher turn-on voltage on these ridges compared to surrounding material. To further understand this phenomenon, V-pit cross sections from the 9% and 15% films were characterised using transmission electron microscopy in combination with energy dispersive X-ray spectroscopy. This identified a subsurface indium-deficient region surrounding the V-pit in the lower indium content film, which was not present in the 15% sample. Although this cannot directly explain the impact of ridges on turn-on voltage, it is likely to be related. Overall, the data presented here demonstrate the potential of PC-AFM in the field of III-nitride semiconductors.

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