scholarly journals Water and Deuterium Oxide Permeability through Aquaporin 1: MD Predictions and Experimental Verification

2007 ◽  
Vol 130 (1) ◽  
pp. 111-116 ◽  
Author(s):  
Artem B. Mamonov ◽  
Rob D. Coalson ◽  
Mark L. Zeidel ◽  
John C. Mathai
Keyword(s):  
Deuterium Oxide ◽  
Diffusion Constant ◽  
Structural Data ◽  
Md Simulations ◽  
Water Model ◽  
Aquaporin 1 ◽  
Self Diffusion ◽  
Osmotic Permeability ◽  
Protein Channels ◽  
And Diffusion

Determining the mechanisms of flux through protein channels requires a combination of structural data, permeability measurement, and molecular dynamics (MD) simulations. To further clarify the mechanism of flux through aquaporin 1 (AQP1), osmotic pf (cm3/s/pore) and diffusion pd (cm3/s/pore) permeability coefficients per pore of H2O and D2O in AQP1 were calculated using MD simulations. We then compared the simulation results with experimental measurements of the osmotic AQP1 permeabilities of H2O and D2O. In this manner we evaluated the ability of MD simulations to predict actual flux results. For the MD simulations, the force field parameters of the D2O model were reparameterized from the TIP3P water model to reproduce the experimentally observed difference in the bulk self diffusion constants of H2O vs. D2O. Two MD systems (one for each solvent) were constructed, each containing explicit palmitoyl-oleoyl-phosphatidyl-ethanolamine (POPE) phospholipid molecules, solvent, and AQP1. It was found that the calculated value of pf for D2O is ∼15% smaller than for H2O. Bovine AQP1 was reconstituted into palmitoyl-oleoyl-phosphatidylcholine (POPC) liposomes, and it was found that the measured macroscopic osmotic permeability coefficient Pf (cm/s) of D2O is ∼21% lower than for H2O. The combined computational and experimental results suggest that deuterium oxide permeability through AQP1 is similar to that of water. The slightly lower observed osmotic permeability of D2O compared to H2O in AQP1 is most likely due to the lower self diffusion constant of D2O.

scholarly journals Liquid-Liquid Phase Transition in Supercooled H2O and D2O: A Path-Integral Computer Simulation Study

2021 ◽  
Author(s):  
Ali Eltareb ◽  
Gustavo E. Lopez ◽  
Nicolas Giovambattista
Keyword(s):  
Path Integral ◽  
Md Simulations ◽  
Anomalous Behavior ◽  
State Equation ◽  
Water Model ◽  
Substitution Effects ◽  
Computer Simulation Study ◽  
Self Diffusion ◽  
Wide Range ◽  
Nuclear Quantum Effects

Abstract We perform path-integral molecular dynamics (PIMD) and classical MD simulations of H2O and D2O using the q-TIP4P/F water model over a wide range of temperatures and pressures. The density ρ(T), isothermal compressibility κT(T), and self-diffusion coefficients D(T) of H2O and D2O are in excellent agreement with available experimental data; the isobaric heat capacity CP(T) obtained from PIMD and MD simulations agree qualitatively well with the experiments. Some of these thermodynamic properties exhibit anomalous maxima upon isobaric cooling, consistent with recent experiments and with the possibility that H2O and D2O exhibit a liquid-liquid critical point (LLCP) at low temperatures and positive pressures. The data from PIMD/MD for H2O and D2O can be fitted remarkably well using the Two-State-Equation-of-State (TSEOS). Using the TSEOS, we estimate that the LLCP for q-TIP4P/F H2O, from PIMD simulations, is located at Pc = 167±9 MPa, Tc = 159±6 K, and ρc = 1.02±0.01 g/cm3. Isotope substitution effects are important; the LLCP location in q-TIP4P/F D2O is estimated to be Pc = 176 ± 4 MPa, Tc = 177 ± 2 K, and ρc = 1.13±0.01 g/cm3. Interestingly, for the water model studied, differences in the LLCP location from PIMD and MD simulations suggest that nuclear quantum effects (i.e., atoms delocalization) play an important role in the thermodynamics of water around the LLCP (from the MD simulations of q-TIP4P/F water, Pc = 203 ± 4 MPa, Tc = 175 ± 2 K, and ρc = 1.03 ± 0.01 g/cm3). Overall, our results strongly support the LLPT scenario to explain water anomalous behavior, independently of the fundamental differences between classical MD and PIMD techniques. The reported values of Tc for D2O and, particularly, H2O suggest that improved water models are needed for the study of supercooled water.

Permeability in Relation to Viscosity and Structure of Rubber

1942 ◽  
Vol 15 (3) ◽  
pp. 537-544 ◽  
Author(s):  
Richard M. Barrer
Keyword(s):  
Viscous Flow ◽  
Thermal Energy ◽  
Diffusion Constant ◽  
The Self ◽  
Self Diffusion ◽  
Functional Relations ◽  
Diffusion Media ◽  
Entropy Of Activation ◽  
Arrhenius Energy ◽  
And Diffusion

Abstract Some properties of flow of solutes in and through rubbers are outlined. These properties indicate that, due to fluctuations of thermal energy, activated zones exist in certain polymers, of which viscous flow and diffusion are a consequence. A simple statistics of activated zones has been given, and from it equations are obtained for ΣN, D, Ds, and η, denoting respectively the total number of activated zones in rubber, the diffusion constant of simple solutes in the polymer, the self-diffusion constant of rubber, and its viscosity. Functional relations are predicted between log Do, log ηo, or ΔS* (the entropy of activation) and the Arrhenius energy of activation for diffusion or viscous flow. The available data clearly demonstrate this relationship. They also indicate no discontinuity between rubbers and liquids as diffusion media.

Diffusion Constant and Diffusion Coefficient

Science ◽  
1955 ◽  
Vol 121 (3137) ◽  
pp. 215-216 ◽  
Author(s):  
J. VERDUIN
Keyword(s):  
Diffusion Coefficient ◽  
Diffusion Constant ◽  
And Diffusion

Vacancy-Mediated Diffusion and Diffusion-Controlled Processes in Ordered Binary Intermetallics by Kinetic Monte Carlo Simulations

2021 ◽  
Vol 29 ◽  
pp. 95-115
Author(s):  
Rafal Kozubski ◽  
Graeme E. Murch ◽  
Irina V. Belova
Keyword(s):  
Monte Carlo ◽  
Kinetic Monte Carlo ◽  
Simulation Studies ◽  
Self Diffusion ◽  
Monte Carlo Techniques ◽  
Diffusion Controlled ◽  
Kinetic Monte Carlo Simulations ◽  
Kinetic Effects ◽  
Kinetics Of ◽  
And Diffusion

We review the results of our Monte Carlo simulation studies carried out within the past two decades in the area of atomic-migration-controlled phenomena in intermetallic compounds. The review aims at showing the high potential of Monte Carlo methods in modelling both the equilibrium states of the systems and the kinetics of the running processes. We focus on three particular problems: (i) the atomistic origin of the complexity of the ‘order-order’ relaxations in γ’-Ni3Al; (ii) surface-induced ordering phenomena in γ-FePt and (iii) ‘order—order’ kinetics and self-diffusion in the ‘triple-defect’ β-NiAl. The latter investigation demonstrated how diverse Monte Carlo techniques may be used to model the phenomena where equilibrium thermodynamics interplays and competes with kinetic effects.

scholarly journals Biophysical characterization of the SARS-CoV-2 E protein

2021 ◽  
Author(s):  
Aujan Mehregan ◽  
Sergio Perez-Conesa ◽  
Yuxuan Zhuang ◽  
Ahmad Elbahnsi ◽  
Diletta Pasini ◽  
...  
Keyword(s):  
Recombinant Expression ◽  
Structural Data ◽  
Md Simulations ◽  
Full Length ◽  
Coarse Grained ◽  
Biophysical Characterization ◽  
Viral Budding ◽  
Nmr Structures ◽  
E Protein

SARS-CoV-2 is the virus responsible for the COVID-19 pandemic which continues to wreak havoc across the world, over a year and a half after its effects were first reported in the general media. Current fundamental research efforts largely focus on the SARS-CoV-2 Spike protein. Since successful antiviral therapies are likely to target multiple viral components, there is considerable interest in understanding the biophysical role of its other proteins, in particular structural membrane proteins. Here, we have focused our efforts on the characterization of the full-length E protein from SARS-CoV-2, combining experimental and computational approaches. Recombinant expression of the full-length E protein from SARS-CoV-2 reveals that this membrane protein is capable of independent multimerization, possibly as a tetrameric or smaller species. Fluorescence microscopy shows that the protein localizes intracellularly, and coarse-grained MD simulations indicate it causes bending of the surrounding lipid bilayer, corroborating a potential role for the E protein in viral budding. Although we did not find robust electrophysiological evidence of ion-channel activity, cells transfected with the E protein exhibited reduced intracellular Ca2+, which may further promote viral replication. However, our atomistic MD simulations revealed that previous NMR structures are relatively unstable, and result in models incapable of ion conduction. Our study highlights the importance of using high-resolution structural data obtained from a full-length protein to gain detailed molecular insights, and eventually permitting virtual drug screening.

scholarly journals Resolving the Dynamic Non-Covalent Interaction inside Membrane Protein Channel by Single-Molecule Interaction Spectrum

2018 ◽  
Author(s):  
Meng-Yin Li ◽  
Yi-Lun Ying ◽  
Xi-Xin Fu ◽  
Jie Yu ◽  
Shao-Chuang Liu ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Single Molecule ◽  
Ionic Current ◽  
Md Simulations ◽  
Energy Spectra ◽  
Membrane Channels ◽  
Non Covalent Interactions ◽  
Protein Channels ◽  
Covalent Interactions ◽  
Molecule Interaction

Millions of years of evolution have produced membrane protein channels capable of efficiently moving ions across the cell membrane. The underlying fundamental mechanisms that facilitate these actions greatly contribute to the weak non-covalent interactions. However, uncovering these dynamic interactions and its synergic network effects still remains challenging in both experimental techniques and molecule dynamics (MD) simulations. Here, we present a rational strategy that combines MD simulations and frequency-energy spectroscopy to identify and quantify the role of non-covalent interactions in carrier transport through membrane protein channels, as encoded in traditional single channel recording or ionic current. We employed wild-type aerolysin transporting of methylcytosine and cytosine as a model to explore the dynamic ionic signatures with non-stationary and non-linear frequency analysis. Our data illuminate that methylcytosine experiences strong non-covalent interactions with the aerolysin nanopore at Region 1 around R220 than cytosine, which produces characteristic frequency-energy spectra. Furthermore, we experimentally validate the obtained hypothesis from frequency-energy spectra by designing single-site mutation of K238G which creates significantly enhanced non-covalent interactions for the recognition of methylcytosine. The frequency-energy spectrum of ions flowing inside membrane channels constitutes a single-molecule interaction spectrum, which bridges the gap between traditional ionic current recording and the MD simulations, facilitating the qualitative and quantitive description of the non-covalent interactions inside membrane channels.

Chloride Ion Hydration and Diffusion in Supercritical Water Using a Polarizable Water Model

2002 ◽  
Vol 106 (15) ◽  
pp. 3979-3986 ◽  
Author(s):  
Masahito Kubo ◽  
Ronald M. Levy ◽  
Peter J. Rossky ◽  
Nobuyuki Matubayasi ◽  
Masaru Nakahara
Keyword(s):  
Supercritical Water ◽  
Chloride Ion ◽  
Water Model ◽  
Ion Hydration ◽  
And Diffusion

Deformation and Diffusion: Quantitative Relations

1993 ◽  
Author(s):  
Brian Bayly
Keyword(s):  
Normal Stress ◽  
Arc Length ◽  
Self Diffusion ◽  
Quantitative Form ◽  
Stress Components ◽  
And Diffusion ◽  
Pressure Driven

The purpose of this chapter is to put the ideas of Chapter 11 into quantitative form. The first step is to link L0 to N and K; L0 is the arc-length of the imaginary quarter-cylinders in Figure 11. 5b, N is the material's viscosity (Pa-sec), and K is its coefficient for pressure-driven self-diffusion (m2/Pa-sec). The point emphasized in Chapter 11 is that if two migration paths exist, one curved and one straight, but both having the same length and the same variation of normal-stress components along their length, migration will be equally vigorous along the two paths. Further, the shortening rates at the source-ends of the two paths will be equal. The procedure used to find the relation of L0 to (NK)1/2 is to write the two shortening rates and equate them.

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