Quantitative Analysis of Multiplex H-Bonds

Brielle, Esther S.; Arkin, Isaiah T.

doi:10.1021/jacs.0c04357

Cited by 31 publications

(22 citation statements)

References 52 publications

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“…PSiUr3 and PSiUr4 show two peaks of the amino group within 3500 to 3300 cm −1 , that is due to the crystallization effect which is further clarified by X‐rays data (XRD) in Figure 3f. [ 43,44,45 ] It can be seen in Figure 3f that the crystallization degree of all PSiUr samples is very different. The crystallization is mainly caused by the conjugation of the benzene ring on the diaminodiphenyl disulfide.…”

Section: Resultsmentioning

confidence: 99%

Novel Intrinsic Self‐Healing Poly‐Silicone‐Urea with Super‐Low Ice Adhesion Strength

Chen

Luo

et al. 2022

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Accumulation of snow and ice often causes problems and even dangerous situations for both industry and the general population. Passive de‐icing technologies, e.g., hydrophobic, liquid‐infused bionic surfaces, have attracted more and more attention compared with active de‐icing technologies, e.g., electric heating, hot air heating, due to the passive de‐icing technology's lower energy consumption and sustainability footprint. Using passive de‐icing coatings seems to be one of the most promising solutions. However, the previously reported de‐icing coatings suffer from high ice adhesion strength or short service life caused by wear. An intrinsic self‐healing material based on poly‐silicone‐urea is developed in this work to address these problems. The material is prepared by introducing dynamic disulfide bonds into the hard phase of the polymer. Experimental results indicate that this poly‐silicone‐urea has a self‐healing efficiency of close to 99%. More interestingly, it is found that the coating prepared from this poly‐silicone‐urea has a super low ice adhesion force, only 7 ± 1 kPa, which is almost the lowest value compared with previous intrinsic self‐healing de‐/anti‐icing reports. This material can maintain low ice adhesion strength after healing. This intrinsic self‐healing poly‐silicone‐urea can meet several practical applications, opening the door for future sustainable anti‐/de‐icing technologies.

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Section: Resultsmentioning

confidence: 99%

Novel Intrinsic Self‐Healing Poly‐Silicone‐Urea with Super‐Low Ice Adhesion Strength

Chen

Luo

et al. 2022

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“…However, here a bare cholesterol molecule is docked to a bare protein molecule surrounded by two bare bilayer interfaces, all in a hydrophobic environment, so that docking energies will include hydrogen bonding between cholesterol and protein and between cholesterol and the interfacial region of the lipid bilayer. It has been suggested that a multiplex hydrogen bond in which a single hydrogen bond acceptor interacts with multiple hydrogen bond donors is ca 60% stronger than a single, canonical hydrogen bond (Feldblum and Arkin 2014 ; Brielle and Arkin 2020 ) and the hydrogen bond detector in Chimera (Pettersen et al 2004 ) suggests that multiplex hydrogen bonds are formed between a cholesterol –OH and the bilayer interface. Concentrations of cholesterol in a membrane are best expressed in mole fraction units and the standard free energy for formation of a canonical hydrogen bond in a hydrophobic environment in mole fraction units is – 6.5 kcals mol −1 (Ben-Tal et al 1997 ; Feldblum and Arkin 2014 ) giving an energy for a multiplex hydrogen bond between cholesterol and the bilayer interface of ca – 10.4 kcals mol −1 ; this was the value used to interpret binding energies for cholesterol with GABA A receptors (Lee 2021 ).…”

Section: Resultsmentioning

confidence: 99%

The role of cholesterol binding in the control of cholesterol by the Scap–Insig system

Lee

2022

Eur Biophys J

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Scap and Insig, two proteins embedded in the membrane of the endoplasmic reticulum (ER), regulate the synthesis of cholesterol in animal cells by forming a dimer in the presence of high concentrations of cholesterol. Cryo-electron microscopic structures for the Scap–Insig dimer show a sterol-binding site at the dimer interface, but none of the structures include cholesterol itself. Here, a molecular docking approach developed to characterise cholesterol binding to the transmembrane (TM) regions of membrane proteins is used to characterise cholesterol binding to sites on the TM surface of the dimer and to the interfacial binding site. Binding of cholesterol is also observed at sites on the extra-membranous luminal domains of Scap, but the properties of these sites suggest that they will be unoccupied in vivo. Comparing the structure of Scap in the dimer with that predicted by AlphaFold for monomeric Scap suggests that dimer formation could result in relocation of TM helix 7 of Scap and of the loop between TM6 and 7, and that this could be the key change on Scap that signals that there is a high concentration of cholesterol in the ER.

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“…[29] Root-mean-square fluctuations (RMSF) measurements were performed for protein Cα atoms. Hydrogen bonds analysis between ACE2 and S1-RBD was performed at a cut-off distance of 3.5 Å and a cut-off A-D-H angle of 20° using the “Hydrogen Bonds” analysis extension in VMD [31, 32]. Interfacial residues were determined from the available ACE2-S1-RBD complex (PDB ID: 6m0j) at a cut-off distance of 5 Å using PyMOL.…”

Section: Methodsmentioning

confidence: 99%

Decreased Interfacial Dynamics Caused by the N501Y Mutation in the SARS-CoV-2 S1 Spike:ACE2 Complex

Ahmed

Philip

Biswas

2021

Preprint

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COVID-19 caused by SARS-CoV-2 has caused a massive health crisis across the world, and genetic variants such as the D614G gaining enhanced infectivity and competitive fitness have significantly aggravated the global concern. In this regard, the latest SARS-CoV-2 variant, B.1.1.7 lineage, reported from the United Kingdom (UK) is of great significance, in that it contains several mutations that increases its infection and transmission rates as evidenced by the increased number of clinical reports. Specifically, the N501Y mutation in the SARS-CoV-2 S1 receptor binding domain (RBD) domain has been shown to possess increased affinity for ACE2, although the basis for this not yet clear. Here, we dissect the mechanism underlying the increased affinity using molecular dynamics (MD) simulations of the available ACE2-S1-RBD complex structure (6M0J) and show a prolonged and stable interaction of the Y501 residue in the N501Y mutant S1-RBD with interfacial residues, Y41 and K353, in ACE2 as compared to the wild type S1-RBD. Additionally, we find that the N501Y mutant S1-RBD displays altered dynamics that likely aids in its enhanced interaction with ACE2. By elucidating a mechanistic basis for the increased affinity of the N501Y mutation in S1-RBD for ACE2, we believe that the results presented here will aid in developing therapeutic strategies against SARS-CoV-2 including designing drugs targeting the ACE2-S1-RBD interaction.

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Quantitative Analysis of Multiplex H-Bonds

Cited by 31 publications

References 52 publications

Novel Intrinsic Self‐Healing Poly‐Silicone‐Urea with Super‐Low Ice Adhesion Strength

Novel Intrinsic Self‐Healing Poly‐Silicone‐Urea with Super‐Low Ice Adhesion Strength

The role of cholesterol binding in the control of cholesterol by the Scap–Insig system

Decreased Interfacial Dynamics Caused by the N501Y Mutation in the SARS-CoV-2 S1 Spike:ACE2 Complex

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