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Part 1: Document Description
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Citation |
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Title: |
Supplementary Material for 'Entropic barrier of water permeation through single-file channels' |
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Identification Number: |
doi:10.18419/darus-3390 |
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Distributor: |
DaRUS |
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Date of Distribution: |
2023-06-30 |
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Version: |
1 |
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Bibliographic Citation: |
Wachlmayr, Johann; Fläschner, Gotthold; Pluhackova, Kristyna; Sandtner, Walter; Siligan, Christine; Horner, Andreas, 2023, "Supplementary Material for 'Entropic barrier of water permeation through single-file channels'", https://doi.org/10.18419/darus-3390, DaRUS, V1 |
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Citation |
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Title: |
Supplementary Material for 'Entropic barrier of water permeation through single-file channels' |
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Identification Number: |
doi:10.18419/darus-3390 |
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Authoring Entity: |
Wachlmayr, Johann (Johannes Kepler University Linz) |
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Fläschner, Gotthold (ETH Zürich) |
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Pluhackova, Kristyna (Universität Stuttgart) |
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Sandtner, Walter (Medical University of Vienna) |
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Siligan, Christine (Johannes Kepler University Linz) |
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Horner, Andreas (Johannes Kepler University Linz) |
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Software used in Production: |
GROMACS |
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Grant Number: |
P31074 |
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Grant Number: |
358283783 - SFB 1333 |
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Grant Number: |
EXC 2075 - 390740016 |
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Grant Number: |
440719683 |
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Grant Number: |
440719683 |
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Distributor: |
DaRUS |
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Access Authority: |
Pluhackova, Kristyna |
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Depositor: |
Pluhackova, Kristyna |
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Date of Deposit: |
2023-03-27 |
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Holdings Information: |
https://doi.org/10.18419/darus-3390 |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, Physics, Molecular Dynamics Simulation, Entropy, Activation Energy, Single-File Channel, Water Permeation |
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Abstract: |
Facilitated water permeation through narrow biological channels is fundamental for all forms of life. This process involves dehydration of bulk water entering the single-file region and hydrogen bond formation with channel lining amino acid residues. Despite its significance in health and disease as well as for biotechnological applications the energetics of water permeation are still elusive. Whereas the enthalpic contribution to Gibbs free energy is readily accessible via temperature dependent water permeability measurements, estimation of the entropic contribution requires information on the temperature dependence of the rate of water permeation. By means of accurate activation energy measurements of water permeation through AQP1 and by determining the accurate single channel permeability we were, for the first time, able to estimate the entropic barrier of water permeation through a narrow biological channel. This is a first step in understanding the energetic contributions in various biological and artificial channels exhibiting vastly different pore geometries. |
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Notes: |
Files and structures for performing and analysing molecular dynamics simulations of water permeation through AQP1 and AQPZ embedded in a model of E. Coli PLE. If you use E. Coli PLE please also cite <a href="https://doi.org/10.1186/s12915-020-00936-8">doi:10.1186/s12915-020-00936-8</a>.<br/> You can find additional files and scripts for E Coli PLE on my github <a href="https://github.com/KristynaPluhackova/MD_models_Ecoli-PLE">https://github.com/KristynaPluhackova/MD_models_Ecoli-PLE</a> |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Title: |
Wachlmayr, Johann; Fläschner, Gotthold; Pluhackova, Kristyna; Sandtner, Walter, Siliga, Christine; Horner, Andreas, "Entropic barrier of water permeation through single-file channels" Comms. Chem. 2023, |
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Identification Number: |
10.1038/s42004-023-00919-0 |
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Bibliographic Citation: |
Wachlmayr, Johann; Fläschner, Gotthold; Pluhackova, Kristyna; Sandtner, Walter, Siliga, Christine; Horner, Andreas, "Entropic barrier of water permeation through single-file channels" Comms. Chem. 2023, |
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Label: |
AQP1.tar.gz |
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Text: |
Simulation and analysis files of tetrameric AQP1 embedded in E. coli PLE membrane model. All-atom simulation using CHARMM36m force field. Structures after 500ns at 277K, 289K, 296K and 309K are also included. Guides how to run and analyse the simulations are included in the workflow.sh files in the corresponding directories. The workflow is tested for GROMACS 2018, the analysis requires GROMACS 4.5 and the extension g_flux available elsewhere. |
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Notes: |
application/x-gzip |
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Label: |
AQPZ.tar.gz |
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Text: |
Simulation and analysis files of tetrameric AQPZ embedded in E. coli PLE membrane model. All-atom simulation using CHARMM36m force field. Structures after 500ns at 277K, 289K, 296K and 309K are also included. Guides how to run and analyse the simulations are included in the workflow.sh files in the corresponding directories. The workflow is tested for GROMACS 2018, the analysis requires GROMACS 4.5 and the extension g_flux available elsewhere. |
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Notes: |
application/x-gzip |
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charmm36-jul2017.ff.tar.gz |
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Text: |
GROMACS simulation files for CHARMM36m including all special atomtypes from this project (also for CNTs). |
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Notes: |
application/x-gzip |
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CNT.tar.gz |
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Simulation and analysis files of four single layered narrow carbon nanotube porins (16 repetition-long) embedded in a DLPC membrane. All-atom simulation using CHARMM36m force field. Structures after 500ns at 289K, 299K, 309K, and 319K are also included. Guides how to run and analyse the simulations are included in the workflow.sh files in the corresponding directories. The workflow is tested for GROMACS 2018, the analysis requires GROMACS 4.5 and the extension g_flux available elsewhere. |
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Notes: |
application/x-gzip |