Literature DB >> 19486672

Molecular model of a cell plasma membrane with an asymmetric multicomponent composition: water permeation and ion effects.

Robert Vácha1, Max L Berkowitz, Pavel Jungwirth.   

Abstract

We present molecular dynamics simulations of a multicomponent, asymmetric bilayer in mixed aqueous solutions of sodium and potassium chloride. Because of the geometry of the system, there are two aqueous solution regions in our simulations: one mimics the intracellular region, and one mimics the extracellular region. Ion-specific effects are evident at the membrane/aqueous solution interface. Namely, at equal concentrations of sodium and potassium, sodium ions are more strongly adsorbed to carbonyl groups of the lipid headgroups. A significant concentration excess of potassium is needed for this ion to overwhelm the sodium abundance at the membrane. Ion-membrane interactions also lead to concentration-dependent and cation-specific behavior of the electrostatic potential in the intracellular region because of the negative charge on the inner leaflet. In addition, water permeation across the membrane was observed on a timescale of approximately 100 ns. This study represents a step toward the modeling of realistic biological membranes at physiological conditions in intracellular and extracellular environments.

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Year:  2009        PMID: 19486672      PMCID: PMC2711485          DOI: 10.1016/j.bpj.2009.03.010

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  34 in total

1.  Molecular simulation analysis and X-ray absorption measurement of Ca2+, K+ and Cl- ions in solution.

Authors:  Liem X Dang; Gregory K Schenter; Vassiliki-Alexandra Glezakou; John L Fulton
Journal:  J Phys Chem B       Date:  2006-11-30       Impact factor: 2.991

2.  Quantification and rationalization of the higher affinity of sodium over potassium to protein surfaces.

Authors:  Lubos Vrbka; Jirí Vondrásek; Barbara Jagoda-Cwiklik; Robert Vácha; Pavel Jungwirth
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-10       Impact factor: 11.205

3.  Ion leakage through transient water pores in protein-free lipid membranes driven by transmembrane ionic charge imbalance.

Authors:  Andrey A Gurtovenko; Ilpo Vattulainen
Journal:  Biophys J       Date:  2007-01-05       Impact factor: 4.033

4.  Ion pairing as a possible clue for discriminating between sodium and potassium in biological and other complex environments.

Authors:  Barbara Jagoda-Cwiklik; Robert Vacha; Mikael Lund; Monika Srebro; Pavel Jungwirth
Journal:  J Phys Chem B       Date:  2007-12-05       Impact factor: 2.991

5.  Specific anion and cation binding to lipid membranes investigated on a solid supported membrane.

Authors:  Juan J Garcia-Celma; Lina Hatahet; Werner Kunz; Klaus Fendler
Journal:  Langmuir       Date:  2007-08-24       Impact factor: 3.882

6.  Effects of alkali cations and halide anions on the DOPC lipid membrane.

Authors:  Robert Vácha; Shirley W I Siu; Michal Petrov; Rainer A Böckmann; Justyna Barucha-Kraszewska; Piotr Jurkiewicz; Martin Hof; Max L Berkowitz; Pavel Jungwirth
Journal:  J Phys Chem A       Date:  2009-07-02       Impact factor: 2.781

7.  Structural determinants of water permeability through the lipid membrane.

Authors:  John C Mathai; Stephanie Tristram-Nagle; John F Nagle; Mark L Zeidel
Journal:  J Gen Physiol       Date:  2008-01       Impact factor: 4.086

8.  Theory of passive permeability through lipid bilayers.

Authors:  John F Nagle; John C Mathai; Mark L Zeidel; Stephanie Tristram-Nagle
Journal:  J Gen Physiol       Date:  2008-01       Impact factor: 4.086

9.  Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl.

Authors:  Parag Mukhopadhyay; Luca Monticelli; D Peter Tieleman
Journal:  Biophys J       Date:  2004-03       Impact factor: 4.033

10.  Biomolecular simulations of membranes: physical properties from different force fields.

Authors:  Shirley W I Siu; Robert Vácha; Pavel Jungwirth; Rainer A Böckmann
Journal:  J Chem Phys       Date:  2008-03-28       Impact factor: 3.488

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  16 in total

1.  Molecular dynamics simulations of lipid membrane electroporation.

Authors:  Lucie Delemotte; Mounir Tarek
Journal:  J Membr Biol       Date:  2012-05-30       Impact factor: 1.843

2.  Vibrational spectroscopy of water in hydrated lipid multi-bilayers. I. Infrared spectra and ultrafast pump-probe observables.

Authors:  S M Gruenbaum; J L Skinner
Journal:  J Chem Phys       Date:  2011-08-21       Impact factor: 3.488

3.  Accurate In Silico Modeling of Asymmetric Bilayers Based on Biophysical Principles.

Authors:  Milka Doktorova; Harel Weinstein
Journal:  Biophys J       Date:  2018-09-15       Impact factor: 4.033

4.  Vibrational spectroscopy of water in hydrated lipid multi-bilayers. II. Two-dimensional infrared and peak shift observables within different theoretical approximations.

Authors:  Scott M Gruenbaum; Piotr A Pieniazek; J L Skinner
Journal:  J Chem Phys       Date:  2011-10-28       Impact factor: 3.488

5.  Partitioning of 2,6-Bis(1H-Benzimidazol-2-yl)pyridine fluorophore into a phospholipid bilayer: complementary use of fluorescence quenching studies and molecular dynamics simulations.

Authors:  Alexander Kyrychenko; Igor Yu Sevriukov; Zoya A Syzova; Alexey S Ladokhin; Andrey O Doroshenko
Journal:  Biophys Chem       Date:  2010-12-13       Impact factor: 2.352

6.  The HIV-1 nucleocapsid protein recruits negatively charged lipids to ensure its optimal binding to lipid membranes.

Authors:  Noémie Kempf; Viktoriia Postupalenko; Saurabh Bora; Pascal Didier; Youri Arntz; Hugues de Rocquigny; Yves Mély
Journal:  J Virol       Date:  2014-11-19       Impact factor: 5.103

7.  Developing initial conditions for simulations of asymmetric membranes: a practical recommendation.

Authors:  Sooyhung Park; Wonpil Im; Richard W Pastor
Journal:  Biophys J       Date:  2021-10-13       Impact factor: 4.033

8.  Specific binding of chloride ions to lipid vesicles and implications at molecular scale.

Authors:  Volker Knecht; Benjamin Klasczyk
Journal:  Biophys J       Date:  2013-02-19       Impact factor: 4.033

9.  How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets?

Authors:  Soohyung Park; Andrew H Beaven; Jeffery B Klauda; Wonpil Im
Journal:  J Chem Theory Comput       Date:  2015-07-14       Impact factor: 6.006

10.  Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations.

Authors:  Fatemeh Khalili-Araghi; Brigitte Ziervogel; James C Gumbart; Benoît Roux
Journal:  J Gen Physiol       Date:  2013-10       Impact factor: 4.086

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