A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae
Publication Date
January 27, 2016
Journal
PLOS Computational Biology
Authors
Susanne Gerber, Martina Fröhlich, Hella Lichtenberg Fraté, Sergey Shabala, et al
Volume
12
Issue
1
Pages
e1004703
DOI
https://dx.plos.org/10.1371/journal.pcbi.1004703
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1004703
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/26815455
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729481
Europe PMC
http://europepmc.org/abstract/MED/26815455
Web of Science
000369366100032
Scopus
84956757334
Mendeley
http://www.mendeley.com/research/thermodynamic-model-monovalent-cation-homeostasis-yeast-saccharomyces-cerevisiae-1
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/4286968"], "description"=>"<p>Assignment of phenomenological coefficients to their realizing transporters.</p>", "links"=>[], "tags"=>["Yeast Saccharomyces cerevisiae Cationic", "interplay", "flux", "understanding", "e.g", "intracellular cation concentrations", "ATP", "consumption", "Monovalent Cation Homeostasis", "KCl stimulus", "plasma membrane ion transporters", "model"], "article_id"=>2635297, "categories"=>["Biophysics", "Biochemistry", "Cell Biology", "Chemical Sciences not elsewhere classified", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified"], "users"=>["Susanne Gerber", "Martina Fröhlich", "Hella Lichtenberg-Fraté", "Sergey Shabala", "Lana Shabala", "Edda Klipp"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004703.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Assignment_of_phenomenological_coefficients_to_their_realizing_transporters_/2635297", "title"=>"Assignment of phenomenological coefficients to their realizing transporters.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-01-27 05:25:04"}
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  • {"files"=>["https://ndownloader.figshare.com/files/4286974"], "description"=>"<p>Estimated model parameters for stress with 4 different concentrations of KCl. All other <i>L</i>s could be set to 0 without affecting the goodness of fit.</p>", "links"=>[], "tags"=>["Yeast Saccharomyces cerevisiae Cationic", "interplay", "flux", "understanding", "e.g", "intracellular cation concentrations", "ATP", "consumption", "Monovalent Cation Homeostasis", "KCl stimulus", "plasma membrane ion transporters", "model"], "article_id"=>2635303, "categories"=>["Biophysics", "Biochemistry", "Cell Biology", "Chemical Sciences not elsewhere classified", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified"], "users"=>["Susanne Gerber", "Martina Fröhlich", "Hella Lichtenberg-Fraté", "Sergey Shabala", "Lana Shabala", "Edda Klipp"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004703.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Initial_concentrations_global_quantities_and_volumes_and_estimated_parameters_for_P1_/2635303", "title"=>"Initial concentrations, global quantities and volumes, and estimated parameters for P1.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-01-27 05:25:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/4286911", "https://ndownloader.figshare.com/files/4286914"], "description"=>"<div><p>Cationic and heavy metal toxicity is involved in a substantial number of diseases in mammals and crop plants. Therefore, the understanding of tightly regulated transporter activities, as well as conceiving the interplay of regulatory mechanisms, is of substantial interest. A generalized thermodynamic description is developed for the complex interplay of the plasma membrane ion transporters, membrane potential and the consumption of energy for maintaining and restoring specific intracellular cation concentrations. This concept is applied to the homeostasis of cation concentrations in the yeast cells of <i>S</i>. <i>cerevisiae</i>. The thermodynamic approach allows to model passive ion fluxes driven by the electrochemical potential differences, but also primary or secondary active transport processes driven by the inter- play of different ions (symport, antiport) or by ATP consumption (ATPases). The model—confronted with experimental data—reproduces the experimentally observed potassium and proton fluxes induced by the external stimuli KCl and glucose. The estimated phenomenological constants combine kinetic parameters and transport coefficients. These are in good agreement with the biological understanding of the transporters thus providing a better understanding of the control exerted by the coupled fluxes. The model predicts the flux of additional ion species, like e.g. chloride, as a potential candidate for counterbalancing positive charges. Furthermore, the effect of a second KCl stimulus is simulated, predicting a reduced cellular response for cells that were first exposed to a high KCl stimulus compared to cells pretreated with a mild KCl stimulus. By describing the generalized forces that are responsible for a given flow, the model provides information and suggestions for new experiments. Furthermore, it can be extended to other systems such as e.g. <i>Candida albicans</i>, or selected plant cells.</p></div>", "links"=>[], "tags"=>["Yeast Saccharomyces cerevisiae Cationic", "interplay", "flux", "understanding", "e.g", "intracellular cation concentrations", "ATP", "consumption", "Monovalent Cation Homeostasis", "KCl stimulus", "plasma membrane ion transporters", "model"], "article_id"=>2635243, "categories"=>["Biophysics", "Biochemistry", "Cell Biology", "Chemical Sciences not elsewhere classified", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified"], "users"=>["Susanne Gerber", "Martina Fröhlich", "Hella Lichtenberg-Fraté", "Sergey Shabala", "Lana Shabala", "Edda Klipp"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1004703.s001", "https://dx.doi.org/10.1371/journal.pcbi.1004703.s002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Thermodynamic_Model_of_Monovalent_Cation_Homeostasis_in_the_Yeast_i_Saccharomyces_cerevisiae_i_/2635243", "title"=>"A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast <i>Saccharomyces cerevisiae</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2016-01-27 05:25:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/4286980"], "description"=>"<p>Estimated model parameters for stress with 4 different concentrations of KCl. All other <i>L</i>s could be set to 0 without affecting the goodness of fit.</p>", "links"=>[], "tags"=>["Yeast Saccharomyces cerevisiae Cationic", "interplay", "flux", "understanding", "e.g", "intracellular cation concentrations", "ATP", "consumption", "Monovalent Cation Homeostasis", "KCl stimulus", "plasma membrane ion transporters", "model"], "article_id"=>2635309, "categories"=>["Biophysics", "Biochemistry", "Cell Biology", "Chemical Sciences not elsewhere classified", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified"], "users"=>["Susanne Gerber", "Martina Fröhlich", "Hella Lichtenberg-Fraté", "Sergey Shabala", "Lana Shabala", "Edda Klipp"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004703.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Initial_concentrations_global_quantities_and_volumes_and_estimated_parameters_for_P2a_/2635309", "title"=>"Initial concentrations, global quantities and volumes, and estimated parameters for P2a.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-01-27 05:25:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/4286950"], "description"=>"<p>Separation of <i>J</i><sub>K</sub> into a K<sup>+</sup> (green) and a H<sup>+</sup> (blue) dependent part for simulations with parameter sets a) P2a and b) P2b. c) Separation of <i>J</i><sub>K</sub> into a chemical (green) and an electrical (blue) potential dependent part with parameter set P2a. d) Ratio of the electrical and the chemical potential dependent part of <i>J</i><sub>K</sub> with P2a. Simulation of the membrane potential with parameter sets e) P2a and f) P2b.</p>", "links"=>[], "tags"=>["Yeast Saccharomyces cerevisiae Cationic", "interplay", "flux", "understanding", "e.g", "intracellular cation concentrations", "ATP", "consumption", "Monovalent Cation Homeostasis", "KCl stimulus", "plasma membrane ion transporters", "model"], "article_id"=>2635279, "categories"=>["Biophysics", "Biochemistry", "Cell Biology", "Chemical Sciences not elsewhere classified", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified"], "users"=>["Susanne Gerber", "Martina Fröhlich", "Hella Lichtenberg-Fraté", "Sergey Shabala", "Lana Shabala", "Edda Klipp"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004703.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Analysis_of_individual_forces_/2635279", "title"=>"Analysis of individual forces.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-27 05:25:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/4286983"], "description"=>"<p>Estimated model parameters for stress with 4 different concentrations of KCl. All other <i>L</i>s could be set to 0 without affecting the goodness of fit.</p>", "links"=>[], "tags"=>["Yeast Saccharomyces cerevisiae Cationic", "interplay", "flux", "understanding", "e.g", "intracellular cation concentrations", "ATP", "consumption", "Monovalent Cation Homeostasis", "KCl stimulus", "plasma membrane ion transporters", "model"], "article_id"=>2635312, "categories"=>["Biophysics", "Biochemistry", "Cell Biology", "Chemical Sciences not elsewhere classified", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified"], "users"=>["Susanne Gerber", "Martina Fröhlich", "Hella Lichtenberg-Fraté", "Sergey Shabala", "Lana Shabala", "Edda Klipp"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004703.t005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Initial_concentrations_global_quantities_and_volumes_and_estimated_parameters_for_P2b_/2635312", "title"=>"Initial concentrations, global quantities and volumes, and estimated parameters for P2b.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-01-27 05:25:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/4286923"], "description"=>"<p>Sketch of the system and the model-relevant key elements.</p>", "links"=>[], "tags"=>["Yeast Saccharomyces cerevisiae Cationic", "interplay", "flux", "understanding", "e.g", "intracellular cation concentrations", "ATP", "consumption", "Monovalent Cation Homeostasis", "KCl stimulus", "plasma membrane ion transporters", "model"], "article_id"=>2635252, "categories"=>["Biophysics", "Biochemistry", "Cell Biology", "Chemical Sciences not elsewhere classified", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified"], "users"=>["Susanne Gerber", "Martina Fröhlich", "Hella Lichtenberg-Fraté", "Sergey Shabala", "Lana Shabala", "Edda Klipp"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004703.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Sketch_of_the_system_and_the_model_relevant_key_elements_/2635252", "title"=>"Sketch of the system and the model-relevant key elements.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-27 05:25:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/4286956"], "description"=>"<p>Model M2 with parameter set P2a was used to predict the reaction of the system to a second KCl stimulus following the glucose stimulus. As first stimulus the KCl concentrations 0.01, 0.1, 1 and 10 mM were used, in consistency with the data used for model fitting. The second stimulus was modeled as additional 10 mM KCl in all cases. The K<sup>+</sup> flux is labeled in green, H<sup>+</sup> flux in blue. Darker colors represent higher KCl concentrations used for the first KCl stimulus (applied to the system prior to time point 0). Glucose was added in this experiment at time point 660 s, the second KCl stimulus was at 1000 s.</p>", "links"=>[], "tags"=>["Yeast Saccharomyces cerevisiae Cationic", "interplay", "flux", "understanding", "e.g", "intracellular cation concentrations", "ATP", "consumption", "Monovalent Cation Homeostasis", "KCl stimulus", "plasma membrane ion transporters", "model"], "article_id"=>2635285, "categories"=>["Biophysics", "Biochemistry", "Cell Biology", "Chemical Sciences not elsewhere classified", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified"], "users"=>["Susanne Gerber", "Martina Fröhlich", "Hella Lichtenberg-Fraté", "Sergey Shabala", "Lana Shabala", "Edda Klipp"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004703.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Prediction_of_second_KCl_stimulus_/2635285", "title"=>"Prediction of second KCl stimulus.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-27 05:25:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/4286959"], "description"=>"<p>Overview of transmembrane ion transporters and channels.</p>", "links"=>[], "tags"=>["Yeast Saccharomyces cerevisiae Cationic", "interplay", "flux", "understanding", "e.g", "intracellular cation concentrations", "ATP", "consumption", "Monovalent Cation Homeostasis", "KCl stimulus", "plasma membrane ion transporters", "model"], "article_id"=>2635288, "categories"=>["Biophysics", "Biochemistry", "Cell Biology", "Chemical Sciences not elsewhere classified", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified"], "users"=>["Susanne Gerber", "Martina Fröhlich", "Hella Lichtenberg-Fraté", "Sergey Shabala", "Lana Shabala", "Edda Klipp"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004703.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Overview_of_transmembrane_ion_transporters_and_channels_/2635288", "title"=>"Overview of transmembrane ion transporters and channels.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-01-27 05:25:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/4286929"], "description"=>"<p>Data resulting from microelectrode ion flux measurements (MIFE) of potassium fluxes (green) and proton fluxes (blue) in the <i>S</i>. <i>cerevisiae</i> wild-type strain PLY232 [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004703#pcbi.1004703.ref043\" target=\"_blank\">43</a>] due to four different stimuli with KCl (0.01 mM, 0.1 mM, 1 mM, 10 mM) at time 300 s followed by addition of glucose at time 600 s (<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004703#pcbi.1004703.s002\" target=\"_blank\">S1 Data</a>). Simulations were performed using the model with parameter set P1. a) Presentation of the best fit (solid lines) and the experimental data (squares), b) prediction of the membrane potential.</p>", "links"=>[], "tags"=>["Yeast Saccharomyces cerevisiae Cationic", "interplay", "flux", "understanding", "e.g", "intracellular cation concentrations", "ATP", "consumption", "Monovalent Cation Homeostasis", "KCl stimulus", "plasma membrane ion transporters", "model"], "article_id"=>2635258, "categories"=>["Biophysics", "Biochemistry", "Cell Biology", "Chemical Sciences not elsewhere classified", "Biological Sciences not elsewhere classified", "Information Systems not elsewhere classified"], "users"=>["Susanne Gerber", "Martina Fröhlich", "Hella Lichtenberg-Fraté", "Sergey Shabala", "Lana Shabala", "Edda Klipp"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004703.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Simulations_using_model_M1_with_parameter_set_P1_/2635258", "title"=>"Simulations using model M1 with parameter set P1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-27 05:25:04"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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