scholarly journals Glycerol transport through the aquaglyceroporin GlpF: bridging dynamics and kinetics with atomic simulation

2019 ◽  
Vol 10 (29) ◽  
pp. 6957-6965 ◽  
Author(s):  
Dongdong Wang ◽  
Jingwei Weng ◽  
Wenning Wang
Keyword(s):  
Kinetic Models ◽  
Md Simulations ◽  
Transport Kinetics ◽  
Membrane Channels ◽  
Concentration Gradients ◽  
Atomic Simulation ◽  
Glycerol Transport ◽  
Kinetics Of ◽  
Non Equilibrium

We present a strategy to obtained non-equilibrium transport kinetics of membrane channels through atomistic MD simulations. Using two kinetic models, the permeation fluxes of aquaglyceroporin GlpF under various concentration gradients were calculated.

scholarly journals Solid-State Redox Kinetics of CeO2 in Two-Step Solar CH4 Partial Oxidation and Thermochemical CO2 Conversion

Catalysts ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 723
Author(s):  
Mahesh Muraleedharan Nair ◽  
Stéphane Abanades
Keyword(s):  
Solid State ◽  
Solar Energy ◽  
Kinetic Models ◽  
Oxygen Carrier ◽  
Co2 Conversion ◽  
Oxidation Reactions ◽  
Redox Kinetics ◽  
Concentrated Solar Energy ◽  
Ceria Reduction ◽  
Kinetics Of

The CeO2/CeO2−δ redox system occupies a unique position as an oxygen carrier in chemical looping processes for producing solar fuels, using concentrated solar energy. The two-step thermochemical ceria-based cycle for the production of synthesis gas from methane and solar energy, followed by CO2 splitting, was considered in this work. This topic concerns one of the emerging and most promising processes for the recycling and valorization of anthropogenic greenhouse gas emissions. The development of redox-active catalysts with enhanced efficiency for solar thermochemical fuel production and CO2 conversion is a highly demanding and challenging topic. The determination of redox reaction kinetics is crucial for process design and optimization. In this study, the solid-state redox kinetics of CeO2 in the two-step process with CH4 as the reducing agent and CO2 as the oxidizing agent was investigated in an original prototype solar thermogravimetric reactor equipped with a parabolic dish solar concentrator. In particular, the ceria reduction and re-oxidation reactions were carried out under isothermal conditions. Several solid-state kinetic models based on reaction order, nucleation, shrinking core, and diffusion were utilized for deducing the reaction mechanisms. It was observed that both ceria reduction with CH4 and re-oxidation with CO2 were best represented by a 2D nucleation and nuclei growth model under the applied conditions. The kinetic models exhibiting the best agreement with the experimental reaction data were used to estimate the kinetic parameters. The values of apparent activation energies (~80 kJ·mol−1 for reduction and ~10 kJ·mol−1 for re-oxidation) and pre-exponential factors (~2–9 s−1 for reduction and ~123–253 s−1 for re-oxidation) were obtained from the Arrhenius plots.

scholarly journals Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment

2021 ◽  
Author(s):  
Arghadwip Paul ◽  
Suman Samantray ◽  
Marco Anteghini ◽  
Mohammed Khaled ◽  
Birgit Strodel
Keyword(s):  
Amyloid Β ◽  
Md Simulations ◽  
Amyloid Β Peptide ◽  
Intrinsically Disordered ◽  
Thermodynamics And Kinetics ◽  
Markov State ◽  
Markov State Models ◽  
State Models ◽  
Kinetics Of

The convergence of MD simulations is tested using varying measures for the intrinsically disordered amyloid-β peptide (Aβ). Markov state models show that 20–30 μs of MD is needed to reliably reproduce the thermodynamics and kinetics of Aβ.

Kinetics of the multidrug transporter (P-glycoprotein) and its reversal

1997 ◽  
Vol 77 (2) ◽  
pp. 545-590 ◽  
Author(s):  
W. D. Stein
Keyword(s):  
Final Section ◽  
Transport Kinetics ◽  
Multidrug Transporter ◽  
Chemotherapeutic Drugs ◽  
Multidrug Resistance Proteins ◽  
Binding Properties ◽  
Membrane Pump ◽  
Resistance Proteins ◽  
P Glycoprotein ◽  
Kinetics Of

Most cancer deaths result from the cancer's either being intrinsically resistant to chemotherapeutic drugs or becoming resistant after being initially sensitive. Often, in cells grown in cell culture, drug resistance correlates with the presence of one or more of the so-called P-glycoproteins or multidrug resistance proteins, products of the mdr family of genes. This review is largely concerned with the transport kinetics of the P-glycoproteins. We first present a brief overview of the P-glycoproteins, their properties, and their clinical significance. Later sections of the review expand on this material with special emphasis on the substrates of P-glycoprotein and how they cross the cell membrane, on the transport kinetics of the P-glycoprotein, on reversers of its action, and on its activity as an ATPase. In a final section, we consider the mechanism of action of P-glycoprotein as an actively transporting membrane pump. The characteristic of P-glycoprotein considered the most difficult to explain is its very broad specificity (or lack of specificity), but there are precedents for this property in well-known proteins such as serum albumin, which binds a range of molecular types, including substrates and reversers of P-glycoprotein, seemingly as broad as does P-glycoprotein. Pointing out this analogy does not provide a molecular explanation for the substrate-binding properties of P-glycoprotein but does make those properties more assimilable.

scholarly journals Kinetics of Phenolic Compounds Modification during Maize Flour Fermentation

Molecules ◽  
2021 ◽  
Vol 26 (21) ◽  
pp. 6702
Author(s):  
Oluwafemi Ayodeji Adebo ◽  
Ajibola Bamikole Oyedeji ◽  
Janet Adeyinka Adebiyi ◽  
Chiemela Enyinnaya Chinma ◽  
Samson Adeoye Oyeyinka ◽  
...  
Keyword(s):  
Phenolic Compounds ◽  
Phenolic Acids ◽  
Kinetic Models ◽  
Titratable Acidity ◽  
Second Order ◽  
Soluble Solids ◽  
Maize Flour ◽  
First Order ◽  
Compound Modification ◽  
Kinetics Of

This study aimed to investigate the kinetics of phenolic compound modification during the fermentation of maize flour at different times. Maize was spontaneously fermented into sourdough at varying times (24, 48, 72, 96, and 120 h) and, at each point, the pH, titratable acidity (TTA), total soluble solids (TSS), phenolic compounds (flavonoids such as apigenin, kaempferol, luteolin, quercetin, and taxifolin) and phenolic acids (caffeic, gallic, ferulic, p-coumaric, sinapic, and vanillic acids) were investigated. Three kinetic models (zero-, first-, and second-order equations) were used to determine the kinetics of phenolic modification during the fermentation. Results obtained showed that fermentation significantly reduced pH, with a corresponding increase in TTA and TSS. All the investigated flavonoids were significantly reduced after fermentation, while phenolic acids gradually increased during fermentation. Among the kinetic models adopted, first-order (R2 = 0.45–0.96) and zero-order (R2 = 0.20–0.82) equations best described the time-dependent modifications of free and bound flavonoids, respectively. On the other hand, first-order (R2 = 0.46–0.69) and second-order (R2 = 0.005–0.28) equations were best suited to explain the degradation of bound and free phenolic acids, respectively. This study shows that the modification of phenolic compounds during fermentation is compound-specific and that their rates of change may be largely dependent on their forms of existence in the fermented products.

scholarly journals Unexpected Role of Electronic Coupling between Host Redox Centers in Transport Kinetics of Lithium Ions in Olivine Phosphate Materials

2021 ◽  
Author(s):  
Yu Gao ◽  
Jun Huang ◽  
Yuwen Liu ◽  
Shengli Chen
Keyword(s):  
Activation Energy ◽  
Diffusion Coefficient ◽  
Lithium Ion ◽  
Transport Kinetics ◽  
Electronic Coupling ◽  
Lithium Ions ◽  
Kinetics Of ◽  
Olivine Phosphate ◽  
Redox Centers

The discrepancy between the trend in the diffusion coefficient of lithium ion (DLi+) and that in the activation energy of ion hopping signals hidden factors determining ion transport kinetics in...

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.

scholarly journals Carbon Nanotube Electrodes for Electrochemical Detection of Dopamine

2021 ◽  
Author(s):  
Gaurang Khot ◽  
Frank Platte ◽  
Neil Shirtcliffe ◽  
Tansu Celikel
Keyword(s):  
Electron Transport ◽  
Pyrolytic Carbon ◽  
Transport Kinetics ◽  
Electrochemical Kinetics ◽  
Current Voltage ◽  
Surface Diameter ◽  
Kinetics Of ◽  
The Brain ◽  
Anodic Region ◽  
Basal Concentration

AbstractCarbon nanotubes (CNTs) are suited for neurochemistry because of their biological inertness, ability to withstand biofouling, and superior electron transport kinetics. Dopamine, the canonical monoaminergic neuromodulator, contributes to reward, cognition and attention, however, its detection in real-time is challenging due to its low basal concentration in the brain (100nM L-1). In our present work, we fabricate pyrolytic carbon electrodes and perform a CNT coating to improve the electrochemical kinetics of dopamine. Upon CNTs coating, dopamine shows a sensitivity of 9±18nA/μM for a cylindrical electrode having a mean surface diameter of 8±4μm. Increasing the scan frequency from 10-100 Hz shows that dopamine electron transfer kinetics improves; wherein dopamine is oxidized at 0.35±0.09V and reduced to -0.10±0.05V for 10 Hz. Increasing the frequency results in a shift of oxidation peak towards the anodic region, wherein dopamine oxidizes at 0.08±3V and reduces at -0.1±0.05V for 100 Hz, thus showing that dopamine redox is reversible which can be attributed to the superior electron transport kinetics of CNTs. The sensor was able to distinguish dopamine signals against other neurochemicals like serotonin and foulant 3,4-Dihydroxyphenylacetic acid (DOPAC). The minimum chemical detection that can be performed using these nanopipettes is 50±18nM L-1, which is well below the physiological concentrations of dopamine in the brain.Graphical AbstractA: Pictorial view of background-subtracted voltammetry. The waveform used was -0.4V to 1.3 V and cycled back to -0.4V at 10 Hz. B: The voltammogram was converted as a 2-D representation, into current, voltage, and repetition to understand the dopamine oxidation. C: Background subtracted voltammetry for dopamine using 100 Hz waveform. D: The 2-D representation of current, voltage, and repetition.

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