Lateral proton conduction along a lipid-water interface layer: a molecular mechanism for the role of hydration water molecules

Biochimie ◽  
1989 ◽  
Vol 71 (1) ◽  
pp. 33-36 ◽  
Author(s):  
Michel Prats ◽  
Jean-François Tocanne ◽  
Justin Teissié
Keyword(s):  
Molecular Mechanism ◽  
Interface Layer ◽  
Proton Conduction ◽  
Water Molecules ◽  
Hydration Water ◽  
Water Interface

Study of the molecular array behaviour of laurel alkanolamide at the oil–water interface and the high interfacial activity enhanced by an inherent synergistic effect

RSC Advances ◽  
2014 ◽  
Vol 4 (79) ◽  
pp. 41831-41837 ◽  
Author(s):  
Sen Zhang ◽  
Pengfei Zhu ◽  
Yange Sun ◽  
Yong Yang ◽  
Xulong Cao ◽  
...  
Keyword(s):  
Synergistic Effect ◽  
Interface Layer ◽  
Water Molecules ◽  
Water Interface ◽  
Interfacial Activity ◽  
Oil Water

Intricate H-bonds network existed between alkanolamide and water molecules in oil–water interface layer, which laid the foundation for the high interfacial density and high interfacial efficiency of alkanolamide at the oil–water interface.

scholarly journals The role of the protein–water interface in dictating proton conduction across protein-based biopolymers

2021 ◽  
Vol 2 (5) ◽  
pp. 1739-1746
Author(s):  
Yuval Agam ◽  
Ramesh Nandi ◽  
Tatiana Bulava ◽  
Nadav Amdursky
Keyword(s):  
Proton Transport ◽  
Proton Conduction ◽  
Water Interface

The role of different water states and their interface with a protein microstructure in mediating protons has been investigated using several approaches, concluding on the importance of the protein/water interface in proton transport.

scholarly journals Structure, dynamics and reactions of protein hydration water

2004 ◽  
Vol 359 (1448) ◽  
pp. 1181-1190 ◽  
Author(s):  
Jeremy C. Smith ◽  
Franci Merzel ◽  
Ana-Nicoleta Bondar ◽  
Alexander Tournier ◽  
Stefan Fischer
Keyword(s):  
Water Molecule ◽  
Transfer Reactions ◽  
Protein Hydration ◽  
Water Molecules ◽  
Hydration Water ◽  
Protein Motions ◽  
Wide Range ◽  
Recent Computer ◽  
Proton Transfer Reactions

The apparent simplicity of the water molecule belies the wide range of fascinating protein phenomena in which it participates. We review recent computer simulation work on buried, internal water molecules, discussing the thermodynamics of water molecule binding and the participation of water in proton transfer reactions. Surface water molecules are also considered, with emphasis on the modification of average solvent structure on a protein surface, the role of water in the protein dynamical ‘glass’ transition and a simplified description of the protein motions thereby activated.

scholarly journals Brillouin Neutron Spectroscopy as a Probe to Investigate Collective Density Fluctuations in Biomolecules Hydration Water

2012 ◽  
Vol 27 ◽  
pp. 293-305 ◽  
Author(s):  
D. Russo ◽  
A. Orecchini ◽  
A. De Francesco ◽  
F. Formisano ◽  
A. Laloni ◽  
...  
Keyword(s):  
Diffusion Processes ◽  
Terahertz Spectroscopy ◽  
Bulk Water ◽  
Density Fluctuations ◽  
Water Molecules ◽  
Relaxation Processes ◽  
Hydration Water ◽  
Solvent Interaction ◽  
Biological Functionality

The role of water in the behaviour of biomolecules is well recognized. The coupling of motions between water and biomolecules has been studied in a wide time scale for theselfpart whilecollectivedynamics is still quite unexplored.Self-dynamics provides information about the diffusion processes of water molecules and relaxation processes of the protein structure.Collectivedensity fluctuations might provide important insight on the transmission of information possibly correlated to biological functionality. The idea that hydration water layers surrounding a biological molecule show aself-dynamical signature that differs appreciably from that of bulk water, in analogy with glass-former systems, is quite accepted. In the same picture Brillouin terahertz spectroscopy has been used to directly probecollectivedynamics of hydration water molecules around biosystems, showing a weaker coupling and a more bulklike behaviour. We will discuss results of collective modes of hydration water, arising from neutron Brillouin spectroscopy, in the context of biomolecules-solvent interaction.

Temperature Dependence of the Air/Water Interface Revealed by Polarization Sensitive Sum-Frequency Generation Spectroscopy

2018 ◽  
Author(s):  
Daniel R. Moberg ◽  
Shelby C. Straight ◽  
Francesco Paesani
Keyword(s):  
Temperature Dependence ◽  
Low Frequency ◽  
Potential Energy Function ◽  
Md Simulations ◽  
Sum Frequency Generation ◽  
Water Molecules ◽  
Water Interface ◽  
Sum Frequency ◽  
Air Water Interface ◽  
Frequency Generation

<div> <div> <div> <p>The temperature dependence of the vibrational sum-frequency generation (vSFG) spectra of the the air/water interface is investigated using many-body molecular dynamics (MB-MD) simulations performed with the MB-pol potential energy function. The total vSFG spectra calculated for different polarization combinations are then analyzed in terms of molecular auto-correlation and cross-correlation contributions. To provide molecular-level insights into interfacial hydrogen-bonding topologies, which give rise to specific spectroscopic features, the vSFG spectra are further investigated by separating contributions associated with water molecules donating 0, 1, or 2 hydrogen bonds to neighboring water molecules. This analysis suggests that the low frequency shoulder of the free OH peak which appears at ∼3600 cm−1 is primarily due to intermolecular couplings between both singly and doubly hydrogen-bonded molecules. </p> </div> </div> </div>

QM/MM Simulations of Organic Phosphorus Adsorption at the Diaspore-Water Interface

2019 ◽  
Author(s):  
Prasanth Babu Ganta ◽  
Oliver Kühn ◽  
Ashour Ahmed
Keyword(s):  
Interaction Energy ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Water Interface ◽  
Mineral Surfaces ◽  
Soil Mineral ◽  
Phosphorus Adsorption ◽  
Covalent Bonds ◽  
Binding Mechanisms

The phosphorus (P) immobilization and thus its availability for plants are mainly affected by the strong interaction of phosphates with soil components especially soil mineral surfaces. Related reactions have been studied extensively via sorption experiments especially by carrying out adsorption of ortho-phosphate onto Fe-oxide surfaces. But a molecular-level understanding for the P-binding mechanisms at the mineral-water interface is still lacking, especially for forest eco-systems. Therefore, the current contribution provides an investigation of the molecular binding mechanisms for two abundant phosphates in forest soils, inositol hexaphosphate (IHP) and glycerolphosphate (GP), at the diaspore mineral surface. Here a hybrid electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) based molecular dynamics simulation has been applied to explore the diaspore-IHP/GP-water interactions. The results provide evidence for the formation of different P-diaspore binding motifs involving monodentate (M) and bidentate (B) for GP and two (2M) as well as three (3M) monodentate for IHP. The interaction energy results indicated the abundance of the GP B motif compared to the M one. The IHP 3M motif has a higher total interaction energy compared to its 2M motif, but exhibits a lower interaction energy per bond. Compared to GP, IHP exhibited stronger interaction with the surface as well as with water. Water was found to play an important role in controlling these diaspore-IHP/GP-water interactions. The interfacial water molecules form moderately strong H-bonds (HBs) with GP and IHP as well as with the diaspore surface. For all the diaspore-IHP/GP-water complexes, the interaction of water with diaspore exceeds that with the studied phosphates. Furthermore, some water molecules form covalent bonds with diaspore Al atoms while others dissociate at the surface to protons and hydroxyl groups leading to proton transfer processes. Finally, the current results confirm previous experimental conclusions indicating the importance of the number of phosphate groups, HBs, and proton transfers in controlling the P-binding at soil mineral surfaces.

The role of (bio)surfactant sorption in promoting the bioavailability of nutrients localized at the solid-water interface

1999 ◽  
Vol 39 (7) ◽  
pp. 91-98 ◽  
Author(s):  
Ryan N. Jordan ◽  
Eric P. Nichols ◽  
Alfred B. Cunningham
Keyword(s):  
Mass Transfer ◽  
Cell Membrane ◽  
Substrate Concentration ◽  
Water Interface ◽  
Industrial Systems ◽  
Solid Liquid Interface ◽  
Solid Liquid ◽  
Surfactant Sorption

Bioavailability is herein defined as the accessibility of a substrate by a microorganism. Further, bioavailability is governed by (1) the substrate concentration that the cell membrane “sees,” (i.e., the “directly bioavailable” pool) as well as (2) the rate of mass transfer from potentially bioavailable (e.g., nonaqueous) phases to the directly bioavailable (e.g., aqueous) phase. Mechanisms by which sorbed (bio)surfactants influence these two processes are discussed. We propose the hypothesis that the sorption of (bio)surfactants at the solid-liquid interface is partially responsible for the increased bioavailability of surface-bound nutrients, and offer this as a basis for suggesting the development of engineered in-situ bioremediation technologies that take advantage of low (bio)surfactant concentrations. In addition, other industrial systems where bioavailability phenomena should be considered are addressed.

Artificial RNA Editing with ADAR for Gene Therapy

2020 ◽  
Vol 20 (1) ◽  
pp. 44-54 ◽  
Author(s):  
Sonali Bhakta ◽  
Toshifumi Tsukahara
Keyword(s):  
Gene Therapy ◽  
Genetic Code ◽  
Molecular Mechanism ◽  
Rna Editing ◽  
Comparative Studies ◽  
Genetic Diseases ◽  
Adenosine Deaminases ◽  
Family Protein ◽  
Hydrolytic Deamination

Editing mutated genes is a potential way for the treatment of genetic diseases. G-to-A mutations are common in mammals and can be treated by adenosine-to-inosine (A-to-I) editing, a type of substitutional RNA editing. The molecular mechanism of A-to-I editing involves the hydrolytic deamination of adenosine to an inosine base; this reaction is mediated by RNA-specific deaminases, adenosine deaminases acting on RNA (ADARs), family protein. Here, we review recent findings regarding the application of ADARs to restoring the genetic code along with different approaches involved in the process of artificial RNA editing by ADAR. We have also addressed comparative studies of various isoforms of ADARs. Therefore, we will try to provide a detailed overview of the artificial RNA editing and the role of ADAR with a focus on the enzymatic site directed A-to-I editing.

Sign in / Sign up

Export Citation Format

Share Document