scholarly journals Aquaporins: More Than Functional Monomers in a Tetrameric Arrangement

Cells ◽  
2018 ◽  
Vol 7 (11) ◽  
pp. 209 ◽  
Author(s):  
Marcelo Ozu ◽  
Luciano Galizia ◽  
Cynthia Acuña ◽  
Gabriela Amodeo
Keyword(s):  
Conformational Changes ◽  
Regulatory Mechanisms ◽  
Water Molecules ◽  
Complex Structures ◽  
Functional Monomers ◽  
Water Permeation ◽  
Protein Conformational Changes ◽  
Experimental Approaches ◽  
Dynamics Simulations ◽  
Pore Lining

Aquaporins (AQPs) function as tetrameric structures in which each monomer has its own permeable pathway. The combination of structural biology, molecular dynamics simulations, and experimental approaches has contributed to improve our knowledge of how protein conformational changes can challenge its transport capacity, rapidly altering the membrane permeability. This review is focused on evidence that highlights the functional relationship between the monomers and the tetramer. In this sense, we address AQP permeation capacity as well as regulatory mechanisms that affect the monomer, the tetramer, or tetramers combined in complex structures. We therefore explore: (i) water permeation and recent evidence on ion permeation, including the permeation pathway controversy—each monomer versus the central pore of the tetramer—and (ii) regulatory mechanisms that cannot be attributed to independent monomers. In particular, we discuss channel gating and AQPs that sense membrane tension. For the latter we propose a possible mechanism that includes the monomer (slight changes of pore shape, the number of possible H-bonds between water molecules and pore-lining residues) and the tetramer (interactions among monomers and a positive cooperative effect).

scholarly journals Hydrogen bonding changes of internal water molecules in rhodopsin during metarhodopsin I and metarhodopsin II formation

1998 ◽  
Vol 329 (3) ◽  
pp. 713-717 ◽  
Author(s):  
Parshuram RATH ◽  
Frank DELANGE ◽  
J. Willem DEGRIP ◽  
J. Kenneth ROTHSCHILD
Keyword(s):  
Hydrogen Bonding ◽  
Conformational Changes ◽  
Structural Changes ◽  
Integral Membrane Protein ◽  
Water Molecules ◽  
Rod Outer Segments ◽  
Oh Groups ◽  
Protein Conformational Changes ◽  
Hydrogen Deuterium ◽  
Fourier Transform Ir

Rhodopsin is a 7-helix, integral membrane protein found in the rod outer segments, which serves as the light receptor in vision. Light absorption by the retinylidene chromophore of rhodopsin triggers an 11-cis → all-trans isomerization, followed by a series of protein conformational changes, which culminate in the binding and activation of the G-protein transducin by the metarhodopsin II (Meta II) intermediate. Fourier transform IR difference spectroscopy has been used to investigate the structural changes that water, as well as other OH- and NH-containing groups, undergo during the formation of the metarhodopsin I (Meta I) and Meta II intermediates. Bands associated with the OH stretch modes of water are identified by characteristic downshifts upon substitution of H218O for H2O. Compared with earlier work, several negative bands associated with water molecules in unphotolysed rhodopsin were detected, which shift to lower frequencies upon formation of the Meta I and Meta II intermediates. These data indicate that at least one water molecule undergoes an increase in hydrogen bonding upon formation of the Meta I intermediate, while at least one other increases its hydrogen bonding during Meta II formation. Amino acid residue Asp-83, which undergoes a change in its hydrogen bonding during Meta II formation, does not appear to interact with any of the structurally active water molecules. Several NH and/or OH groups, which are inaccessible to hydrogen/deuterium exchange, also undergo alterations during Meta I and Meta II formation.

Fast phase transition of water molecules in a defective carbon nanotube under an electric field

2016 ◽  
Vol 30 (06) ◽  
pp. 1650019 ◽  
Author(s):  
Xianwen Meng ◽  
Jiping Huang
Keyword(s):  
Phase Transition ◽  
Carbon Nanotube ◽  
Electric Field ◽  
Water Molecules ◽  
Single Walled Carbon Nanotube ◽  
Water Permeation ◽  
Single Walled Carbon ◽  
Fast Phase ◽  
Dynamics Simulations ◽  
Insight Into

We utilize molecular dynamics simulations to study the effect of an electric field on the permeation of water molecules through a defective single-walled carbon nanotube (DSWCNT). Compared with a perfect single-walled carbon nanotube (PSWCNT), the behaviors of water molecules respond more quickly under the same electric field in a DSWCNT. Wet–dry phase transition of water molecules occurs when the electric field reaches 0.32 V/nm, which is much lower than the case of the PSWCNT. Besides, the critical electric field is affected by the number of defects. These results pave a way for designing fast wet–dry transition devices and provide a new insight into water permeation through a defective nanochannel.

scholarly journals Mechanism of dehydration in a non-porous variable hydrate

2014 ◽  
Vol 70 (a1) ◽  
pp. C1000-C1000
Author(s):  
Laszlo Fabian
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Chloride Ions ◽  
Smooth Transition ◽  
Water Molecules ◽  
Present Contribution ◽  
Gated Channel ◽  
Mechanism Of Dehydration ◽  
Paroxetine Hydrochloride ◽  
Dynamics Simulations

Paroxetine hydrochloride form II (PHCl-II) is a variable hydrate with a peculiar behaviour [1]. It changes its water content in response to changes in relative humidity with remarkable speed and in a completely reversible fashion. This is commonly observed for channel hydrates, but no continuous channels exist in the PHCl-II structure [2]. Powder diffraction results showed that loss of water produces an isostructural anhydrate, suggesting a simple, non-destructive mechanism of dehydration. The aim of the present contribution is to explain this unusual behaviour at a molecular level by using molecular dynamics simulations. Models of both the hydrated and anhydrous state could be created from the experimental hydrate structure by simple energy minimisation, which is in accordance with the experimentally observed smooth transition. A partially dehydrated supercell model was used to study the mechanism which allows water molecules to cross the steric barrier between adjacent solvent cavities. Since such transitions are rare on the simulation timescale (µs to ms), a steered molecular dynamics approach was applied. The results show that the passage of water molecules is facilitated by conformational changes, in which a ring system acts as a gate between cavities. When passing through the 'gate', water molecules are relayed between two chloride ions: as one Cl...HOH hydrogen bond is broken, another HOH...Cl one is formed. The progress of water molecules along the gated channel is not continuous, they spend a significant amount of time in each cavity between consecutive passages.

Molecular dynamics simulations of water permeation across a combined nanochannel

2018 ◽  
Vol 32 (25) ◽  
pp. 1850278 ◽  
Author(s):  
Xianwen Meng
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Water Transfer ◽  
Water Molecules ◽  
Enhancement Ratio ◽  
Water Permeation ◽  
A Value ◽  
Combined Structure ◽  
Simulation Results ◽  
Dynamics Simulations

The effect of a combined nanochannel structure on the permeation of water molecules across a nanochannel is studied by molecular dynamics simulations. The simulation results show that a combined structure has an effect on enhancing water permeation ability. We obtain a maximal enhancement ratio which can reach a value of 4.381 without changing the entrance radius of the nanochannel. First, we find that the enhancement behavior of water molecules across a combined nanochannel is related to the radius ratio and the radius of the entrance pore. These simulation results will be beneficial for understanding the effect of a combined nanochannel structure on water transfer ability.

Protein Conformational Changes Under Applied Forces

1999 ◽  
Author(s):  
Yangqing Xu ◽  
Gang Bao
Keyword(s):  
Conformational Changes ◽  
Coupling Mechanism ◽  
Mechanical Forces ◽  
Compression Pressure ◽  
Biochemical Responses ◽  
Protein Conformational Changes ◽  
Biochemical Assays ◽  
Chemical Coupling ◽  
Applied Forces ◽  
Dynamics Simulations

Abstract Recent studies confirm that stresses, including that due to gravity, tension, compression, pressure, and shear influence cell growth, differentiation, secretion, movement, signal transduction, and gene expression. Yet, little is known about how cells sense the mechanical stresses or deformations, and convert these mechanical signals into biological or biochemical responses. A possible mechno-chemical coupling mechanism involves protein conformational changes under mechanical forces. Our hypothesis is that mechanical forces can cause large changes of the conformation of proteins, which in turn can influence receptor-ligand binding. To test this hypothesis, molecular dynamics simulations and biochemical assays are performed.

Molecular Basis of Glucose Transport Mechanism in Plants

2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Conformational Dynamics ◽  
Site Directed Mutagenesis ◽  
Free Energy Barrier ◽  
Transport Cycle ◽  
Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

scholarly journals Protein conformational changes and myelin solubilization by anion-detergent solutions

FEBS Letters ◽  
1992 ◽  
Vol 309 (3) ◽  
pp. 376-380 ◽  
Author(s):  
Jaime Monreal ◽  
Pedro Carmona ◽  
Pilar Regueiro ◽  
Ricardo S. Diaz
Keyword(s):  
Conformational Changes ◽  
Protein Conformational Changes ◽  
Detergent Solutions

scholarly journals Electrical Breakdown Mechanism of Transformer Oil with Water Impurity: Molecular Dynamics Simulations and First-Principles Calculations

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 123
Author(s):  
Bin Cao ◽  
Ji-Wei Dong ◽  
Ming-He Chi
Keyword(s):  
Molecular Dynamics ◽  
Thermal Diffusion ◽  
First Principles ◽  
Electrical Breakdown ◽  
Transformer Oil ◽  
Water Molecules ◽  
Conducting Channel ◽  
Breakdown Mechanism ◽  
Water Impurity ◽  
Dynamics Simulations

Water impurity is the essential factor of reducing the insulation performance of transformer oil, which directly determines the operating safety and life of a transformer. Molecular dynamics simulations and first-principles electronic-structure calculations are employed to study the diffusion behavior of water molecules and the electrical breakdown mechanism of transformer oil containing water impurities. The molecular dynamics of an oil-water micro-system model demonstrates that the increase of aging acid concentration will exponentially expedite thermal diffusion of water molecules. Density of states (DOS) for a local region model of transformer oil containing water molecules indicates that water molecules can introduce unoccupied localized electron-states with energy levels close to the conduction band minimum of transformer oil, which makes water molecules capable of capturing electrons and transforming them into water ions during thermal diffusion. Subsequently, under a high electric field, water ions collide and impact on oil molecules to break the molecular chain of transformer oil, engendering carbonized components that introduce a conduction electronic-band in the band-gap of oil molecules as a manifestation of forming a conductive region in transformer oil. The conduction channel composed of carbonized components will be eventually formed, connecting two electrodes, with the carbonized components developing rapidly under the impact of water ions, based on which a large number of electron carriers will be produced similar to “avalanche” discharge, leading to an electrical breakdown of transformer oil insulation. The water impurity in oil, as the key factor for forming the carbonized conducting channel, initiates the electric breakdown process of transformer oil, which is dominated by thermal diffusion of water molecules. The increase of aging acid concentration will significantly promote the thermal diffusion of water impurities and the formation of an initial conducting channel, accounting for the degradation in dielectric strength of insulating oil containing water impurities after long-term operation of the transformer.

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