Effects of the Chemical and Structural Properties of Silane Monolayers on the Organization of Water Molecules and Ions at Interfaces, from Molecular Dynamics Simulations

Lecot, Solène; Lavigne, Antonin; Yang, Zhi-Cheng; Chevolot, Yann; Phaner‐Goutorbe, Magali; Yeromonahos, Christelle

doi:10.1021/acs.langmuir.1c00338

Cited by 14 publications

(13 citation statements)

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“…Regarding the surface, the amorphous SiO 2 layer was taken from the study of Roscioni et al and resized to the simulation box dimensions with a 2 nm thickness by a homemade Python code. Silane monolayers were built following our process adapted from the method proposed by Roscioni et al, as we have previously described. ,, Shortly, hydrolyzed silane molecules were initially randomly positioned on the silica (SiO 2 ) surface without using explicit bonding, allowing for their spontaneous lateral organization. Six different silane monolayers were designed, all with a surface coverage of 3.0 nm –2 .…”

Section: Methodsmentioning

confidence: 99%

“…Silane monolayers were built following our process adapted from the method proposed by Roscioni et al 21 , as we have previously described. 19,22,23 Shortly, hydrolyzed silane molecules were initially randomly positioned on the silica (SiO 2 ) surface without using explicit bonding, allowing their spontaneous lateral organization. Six different silane monolayers were designed, all with a Secondary structure of the ACE2 -S-RBD complex.…”

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confidence: 99%

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Curious Binding Energy Increase between the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein and Angiotensin-Converting Enzyme 2 Adsorbed on a Silane Monolayer from Molecular Dynamics Simulations

et al. 2021

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In the context of the Covid-19 outbreak since December 2019, antigenic tests are widely used, for diagnosis purpose, to detect the SARS-CoV-2 spike protein in nasopharyngeal fluid through its interactions with specific antibodies. However, the SARS-CoV-2 spike protein is subject to rapid mutations yielding more and more variants which might lose their affinity towards the currently used antibodies. The virus entry into the host cell involves interactions between the Angiotensin-Converting Enzyme 2 and the SARS-CoV-2 spike protein receptor binding domain, which should be preserved whatever the mutations to keep the infectious potential of the virus. However, as the enzyme has not evolved to recognize the virus, its affinity with the spike protein receptor binding domain is lower than with the specific antibodies. The present molecular dynamics simulations study suggests that the adsorption of the Angiotensin-Converting Enzyme 2 on specific silane monolayers could increase its affinity towards the spike protein receptor binding domain. Indeed silane monolayer, combining silane molecules with short alkyl chains and positively charged head-groups and silane molecules without charged head-groups, could adsorb the Angiotensin-Converting Enzyme 2 while keeping its bioactivity (orientation compatible with the spike protein trapping, low conformational changes) and increasing its interactions with the spike protein receptor binding domain (number of hydrogen bonds and electrostatic interactions) to lead to an increase by 20% both in the binding free energy and in the enzyme / receptor binding domain rupture force. This work could help to develop biosensing tools efficient towards any variants of the SARS-CoV-2 spike protein. NH 3 +3-aminopropyldimethylethoxy-silane Mix shortMix CH 3 short: NH 3 + (1:1) Mix longMix CH 3 long: NH 3 + (1:1) MethodsThis work is divided into three parts. Firstly, MD simulations of ACE2 on different types of silane monolayers were performed to select the monolayers that could lead to ACE2 adsorption with an orientation compatible with S-RBD trapping. Also, the adsorption-induced conformational changes in ACE2 were characterized. Secondly, three selected silane monolayers and the complex ACE2 -S-RBD were considered. Adsorption-induced conformational changes in ACE2 were characterized, especially at the interface with S-RBD and compared to the structure of the complex in water without surface. Finally, SMD simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) analysis gave insight into the impact of conformational changes on the strength of interactions between ACE2 and the S-RBD. System descriptionMD simulations were performed from the PDB crystal structure 6M0J of the ACE2 -S-RBD complex. 15 Water molecules were kept while the zinc and chloride ions were not considered.Regarding the surface, the amorphous SiO 2 layer was taken from Roscioni et al. 21 and resized to the simulation box dimensions with a 2nm-thickness by a home-made Python code. Silane monolayers were built f...

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

Curious Binding Energy Increase between the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein and Angiotensin-Converting Enzyme 2 Adsorbed on a Silane Monolayer from Molecular Dynamics Simulations

et al. 2021

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“…MMT surface’s high negative charge (−628e) is balanced by the presence of positively charged ions (Na + , Ca 2+ ). The presence of ionic species is known to influence protein–surface interaction. ,, To quantify the extent of ion-surface interaction, we evaluated the contact frequency of ions with the surface. Figure c shows the number of ions and the corresponding percentage of contact frequency with the MMT surface for Na-MMT and Ca-MMT systems.…”

Section: Nature Of Protein–surface Interaction and Influence Of Count...mentioning

confidence: 99%

Structural and Dynamic Insights into SARS-CoV-2 Spike-Protein–Montmorillonite Interactions

et al. 2022

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The spike (S) protein of SARS-CoV-2 has been found to play a decisive role in the cell entry mechanism of the virus and has been the prime target of most vaccine development efforts. Although numerous vaccines are already in use and more than half of the world population has been fully vaccinated, the emergence of new variants of the virus poses a challenge to the existing vaccines. Hence, developing an effective drug therapy is a crucial step in ending the pandemic. Nanoparticles can play a crucial role as a drug or a drug carrier and help tackle the pandemic effectively. Here, we performed explicit all-atom molecular dynamics simulations to probe interactions between S protein and Montmorillonite (MMT) nano clay surface. We built two systems with different counterions (Na + and Ca 2+ ), namely Na-MMT and Ca-MMT, to investigate the effect of different ions on S protein-MMT interaction. Structural modification of S protein was observed in the presence of MMT surface, particularly the loss of helical content of S protein. We revealed that electrostatic and hydrophobic interactions synergistically govern the S protein-MMT interactions. However, hydrophobic interactions were more pronounced in the Na-MMT system than in Ca-MMT. We also revealed residues and glycans of S protein closely interacting with the MMT surface. Interestingly, N165 and N343, which we found to be closely interacting with MMT in our simulations, also have a critical role in cell entry and in thwarting the cell’s immune response in recent studies. Overall, our work provides atomistic insights into S protein-MMT interaction and enriches our understanding of the nanoparticle-S protein interaction mechanism, which will help develop advanced therapeutic techniques in the future.

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“…Despite the common use and the growing interest in SA/biotin technology, the understanding of the parameters that define the stability and orientation of SA on biotinylated surfaces is very limited (Migliorini et al, 2014;Osypova et al, 2015) since the corresponding orientation of SA on the surface can rarely be confirmed by experiments. Several macroscopic parameters such as chain length, charge of the head group of linker molecules are known (Lecot et al, 2020) to impact conformational fluctuations of Streptavidin while immobilizing over the surface and hence affecting biotin binding. Furthermore, a recent AFM and Steered Molecular Dynamics (SMD) study (Sedlak et al, 2020) highlighted the differences in an unbinding pathway with 4-fold different unbinding forces in pulling out biotin molecules from 4 different subunits of Streptavidin; in particular, owing to the tethered geometry of the linker molecule, the conformational changes of the biotin-binding loop of Streptavidin is affected differently for different monomeric units thus leading to potential discrepancy in the escaping mechanism of biotin.…”

Section: Introductionmentioning

confidence: 99%

Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study

Dutta

Gagliardi²,

Bellucci³

et al. 2022

Front. Mol. Biosci.

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A rationally designed gold-functionalized surface capable of capturing a target protein is presented using the biotin–streptavidin pair as a proof-of-concept. We carried out multiscale simulations to shed light on the binding mechanism of streptavidin on four differently biotinylated surfaces. Brownian Dynamics simulations were used to reveal the preferred initial orientation of streptavidin over the surfaces, whereas classical molecular dynamics was used to refine the binding poses and to investigate the fundamental forces involved in binding, and the binding kinetics. We assessed the binding events and the stability of the streptavidin attachment through a quartz crystal microbalance with dissipation monitoring (QCM-D). The sensing element comprises of biotinylated polyethylene glycol chains grafted on the sensor’s gold surface via thiol-Au chemistry. Finally, we compared the results from experiments and simulations. We found that the confined biotin moieties can specifically capture streptavidin from the liquid phase and provide guidelines on how to exploit the microscopic parameters obtained from simulations to guide the design of further biosensors with enhanced sensitivity.

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Effects of the Chemical and Structural Properties of Silane Monolayers on the Organization of Water Molecules and Ions at Interfaces, from Molecular Dynamics Simulations

Cited by 14 publications

References 51 publications

Curious Binding Energy Increase between the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein and Angiotensin-Converting Enzyme 2 Adsorbed on a Silane Monolayer from Molecular Dynamics Simulations

Curious Binding Energy Increase between the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein and Angiotensin-Converting Enzyme 2 Adsorbed on a Silane Monolayer from Molecular Dynamics Simulations

Structural and Dynamic Insights into SARS-CoV-2 Spike-Protein–Montmorillonite Interactions

Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study

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