LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 33

Search options

  1. Article ; Online: Lipid-protein interactions modulate the conformational equilibrium of a potassium channel

    Ruo-Xu Gu / Bert L. de Groot

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 10

    Abstract: Potassium (K+) channels, such as MthK, are essentional for many biological processes, but how lipid-protein interactions regulate ion permeation of K+ channels remained unclear. Here authors conducted molecular dynamics simulations of MthK and observed ... ...

    Abstract Potassium (K+) channels, such as MthK, are essentional for many biological processes, but how lipid-protein interactions regulate ion permeation of K+ channels remained unclear. Here authors conducted molecular dynamics simulations of MthK and observed different ion permeation rates of MthK in membranes with different properties.
    Keywords Science ; Q
    Language English
    Publishing date 2020-05-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: Lipid-protein interactions modulate the conformational equilibrium of a potassium channel

    Ruo-Xu Gu / Bert L. de Groot

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 10

    Abstract: Potassium (K+) channels, such as MthK, are essentional for many biological processes, but how lipid-protein interactions regulate ion permeation of K+ channels remained unclear. Here authors conducted molecular dynamics simulations of MthK and observed ... ...

    Abstract Potassium (K+) channels, such as MthK, are essentional for many biological processes, but how lipid-protein interactions regulate ion permeation of K+ channels remained unclear. Here authors conducted molecular dynamics simulations of MthK and observed different ion permeation rates of MthK in membranes with different properties.
    Keywords Science ; Q
    Language English
    Publishing date 2020-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size

    Vytautas Gapsys / Bert L de Groot

    eLife, Vol

    2020  Volume 9

    Abstract: Computational simulations, akin to wetlab experimentation, are subject to statistical fluctuations. Assessing the magnitude of these fluctuations, that is, assigning uncertainties to the computed results, is of critical importance to drawing ... ...

    Abstract Computational simulations, akin to wetlab experimentation, are subject to statistical fluctuations. Assessing the magnitude of these fluctuations, that is, assigning uncertainties to the computed results, is of critical importance to drawing statistically reliable conclusions. Here, we use a simulation box size as an independent variable, to demonstrate how crucial it is to gather sufficient amounts of data before drawing any conclusions about the potential thermodynamic and kinetic effects. In various systems, ranging from solvation free energies to protein conformational transition rates, we showcase how the proposed simulation box size effect disappears with increased sampling. This indicates that, if at all, the simulation box size only minimally affects both the thermodynamics and kinetics of the type of biomolecular systems presented in this work.
    Keywords molecular dynamics ; simulation ; statistics ; thermodynamics ; kinetics ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: Predicting Kinase Inhibitor Resistance

    Matteo Aldeghi / Vytautas Gapsys / Bert L. de Groot

    ACS Central Science, Vol 5, Iss 8, Pp 1468-

    Physics-Based and Data-Driven Approaches

    2019  Volume 1474

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2019-08-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

    Vytautas Gapsys / Bert L de Groot

    eLife, Vol

    2019  Volume 8

    Abstract: A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage ... ...

    Abstract A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage et al., 2018). Here, we express three main concerns about that study. In addition, we find that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.
    Keywords molecular dynamics ; thermodynamics ; kinetics ; box size ; hemoglobin ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2019-06-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Article ; Online: Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation

    Matteo Aldeghi / Vytautas Gapsys / Bert L. de Groot

    ACS Central Science, Vol 4, Iss 12, Pp 1708-

    2018  Volume 1718

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2018-12-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling

    Wojciech Kopec / Brad S. Rothberg / Bert L. de Groot

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 15

    Abstract: Potassium channels such as MthK are presumed to have two allosterically coupled gates, the activation gate and the selectivity filter gate, that control gating transitions. Here authors use X-ray crystallography and molecular dynamics simulations on MthK ...

    Abstract Potassium channels such as MthK are presumed to have two allosterically coupled gates, the activation gate and the selectivity filter gate, that control gating transitions. Here authors use X-ray crystallography and molecular dynamics simulations on MthK and observe crosstalk between the gates.
    Keywords Science ; Q
    Language English
    Publishing date 2019-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  8. Article ; Online: Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling

    Wojciech Kopec / Brad S. Rothberg / Bert L. de Groot

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 15

    Abstract: Potassium channels such as MthK are presumed to have two allosterically coupled gates, the activation gate and the selectivity filter gate, that control gating transitions. Here authors use X-ray crystallography and molecular dynamics simulations on MthK ...

    Abstract Potassium channels such as MthK are presumed to have two allosterically coupled gates, the activation gate and the selectivity filter gate, that control gating transitions. Here authors use X-ray crystallography and molecular dynamics simulations on MthK and observe crosstalk between the gates.
    Keywords Science ; Q
    Language English
    Publishing date 2019-11-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  9. Article ; Online: Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches

    Vytautas Gapsys / Ahmet Yildirim / Matteo Aldeghi / Yuriy Khalak / David van der Spoel / Bert L. de Groot

    Communications Chemistry, Vol 4, Iss 1, Pp 1-

    2021  Volume 13

    Abstract: Molecular dynamics-based approaches to calculate absolute protein–ligand binding free energy often rely on equilibrium free energy perturbation (FEP) protocols. Here, the authors study ligands binding to bromodomains and T4 lysozyme and find that both ... ...

    Abstract Molecular dynamics-based approaches to calculate absolute protein–ligand binding free energy often rely on equilibrium free energy perturbation (FEP) protocols. Here, the authors study ligands binding to bromodomains and T4 lysozyme and find that both equilibrium and non-equilibrium approaches converge to the same results with the non-equilibrium method converging faster than FEP.
    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  10. Article ; Online: The 3D structure of lipidic fibrils of α-synuclein

    Benedikt Frieg / Leif Antonschmidt / Christian Dienemann / James A. Geraets / Eszter E. Najbauer / Dirk Matthes / Bert L. de Groot / Loren B. Andreas / Stefan Becker / Christian Griesinger / Gunnar F. Schröder

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 10

    Abstract: Interactions between α-synuclein fibrils and lipids have been associated with the development of Parkinson’s disease. This cryo-EM study reveals structural details of these interactions and suggests a mechanism for fibril-induced lipid extraction. ...

    Abstract Interactions between α-synuclein fibrils and lipids have been associated with the development of Parkinson’s disease. This cryo-EM study reveals structural details of these interactions and suggests a mechanism for fibril-induced lipid extraction.
    Keywords Science ; Q
    Language English
    Publishing date 2022-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top