Literature DB >> 28627570

Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations.

M Doktorova1, D Harries, G Khelashvili.   

Abstract

We have recently developed a novel computational methodology (termed RSF for Real-Space Fluctuations) to quantify the bending rigidity and tilt modulus of lipid membranes from real-space analysis of fluctuations in the tilt and splay degrees of freedom as sampled in molecular dynamics (MD) simulations. In this article, we present a comprehensive study that combines results from the application of the RSF method to a wide range of lipid bilayer systems that encompass membranes of different fluidities and sizes, including lipids with saturated and unsaturated lipid tails, single and multi-component lipid systems, as well as non-standard lipids such as the four-tailed cardiolipin. By comparing the material properties calculated with the RSF method to those obtained from experimental data and from other computational methodologies, we rigorously demonstrate the validity of our approach and show its robustness. This should allow for future applications of even more complex lipidic assemblies, whose material properties are not tractable by other computational techniques. In addition, we discuss the relationship between different definitions of the tilt modulus appearing in current literature to address some important unresolved discrepancies in the field.

Entities:  

Year:  2017        PMID: 28627570      PMCID: PMC5538590          DOI: 10.1039/c7cp01921a

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  61 in total

1.  Back to the future: mechanics and thermodynamics of lipid biomembranes.

Authors:  E Evans; W Rawicz; B A Smith
Journal:  Faraday Discuss       Date:  2013       Impact factor: 4.008

2.  CHARMM-GUI: a web-based graphical user interface for CHARMM.

Authors:  Sunhwan Jo; Taehoon Kim; Vidyashankara G Iyer; Wonpil Im
Journal:  J Comput Chem       Date:  2008-08       Impact factor: 3.376

3.  Introductory lecture: basic quantities in model biomembranes.

Authors:  John F Nagle
Journal:  Faraday Discuss       Date:  2013       Impact factor: 4.008

Review 4.  When Physics Takes Over: BAR Proteins and Membrane Curvature.

Authors:  Mijo Simunovic; Gregory A Voth; Andrew Callan-Jones; Patricia Bassereau
Journal:  Trends Cell Biol       Date:  2015-10-28       Impact factor: 20.808

5.  Interactions of cholesterol with lipid bilayers: the preferred configuration and fluctuations.

Authors:  A Kessel; N Ben-Tal; S May
Journal:  Biophys J       Date:  2001-08       Impact factor: 4.033

6.  Molecular origins of bending rigidity in lipids with isolated and conjugated double bonds: the effect of cholesterol.

Authors:  G Khelashvili; N Johner; G Zhao; D Harries; H L Scott
Journal:  Chem Phys Lipids       Date:  2014-01-03       Impact factor: 3.329

7.  CHARMM-GUI Membrane Builder toward realistic biological membrane simulations.

Authors:  Emilia L Wu; Xi Cheng; Sunhwan Jo; Huan Rui; Kevin C Song; Eder M Dávila-Contreras; Yifei Qi; Jumin Lee; Viviana Monje-Galvan; Richard M Venable; Jeffery B Klauda; Wonpil Im
Journal:  J Comput Chem       Date:  2014-08-07       Impact factor: 3.376

8.  Effect of chain length and unsaturation on elasticity of lipid bilayers.

Authors:  W Rawicz; K C Olbrich; T McIntosh; D Needham; E Evans
Journal:  Biophys J       Date:  2000-07       Impact factor: 4.033

Review 9.  Mechanical properties of lipid bilayers from molecular dynamics simulation.

Authors:  Richard M Venable; Frank L H Brown; Richard W Pastor
Journal:  Chem Phys Lipids       Date:  2015-07-31       Impact factor: 3.329

10.  CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.

Authors:  Jumin Lee; Xi Cheng; Jason M Swails; Min Sun Yeom; Peter K Eastman; Justin A Lemkul; Shuai Wei; Joshua Buckner; Jong Cheol Jeong; Yifei Qi; Sunhwan Jo; Vijay S Pande; David A Case; Charles L Brooks; Alexander D MacKerell; Jeffery B Klauda; Wonpil Im
Journal:  J Chem Theory Comput       Date:  2015-12-03       Impact factor: 6.006

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  28 in total

1.  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

2.  A New Computational Method for Membrane Compressibility: Bilayer Mechanical Thickness Revisited.

Authors:  Milka Doktorova; Michael V LeVine; George Khelashvili; Harel Weinstein
Journal:  Biophys J       Date:  2019-01-03       Impact factor: 4.033

Review 3.  How bilayer properties influence membrane protein folding.

Authors:  Karolina Corin; James U Bowie
Journal:  Protein Sci       Date:  2020-10-24       Impact factor: 6.725

4.  Scaling relationships for the elastic moduli and viscosity of mixed lipid membranes.

Authors:  Elizabeth G Kelley; Paul D Butler; Rana Ashkar; Robert Bradbury; Michihiro Nagao
Journal:  Proc Natl Acad Sci U S A       Date:  2020-09-03       Impact factor: 11.205

5.  On the Mechanism of Bilayer Separation by Extrusion, or Why Your LUVs Are Not Really Unilamellar.

Authors:  Haden L Scott; Allison Skinkle; Elizabeth G Kelley; M Neal Waxham; Ilya Levental; Frederick A Heberle
Journal:  Biophys J       Date:  2019-09-16       Impact factor: 4.033

6.  Accelerating Membrane Simulations with Hydrogen Mass Repartitioning.

Authors:  Curtis Balusek; Hyea Hwang; Chun Hon Lau; Karl Lundquist; Anthony Hazel; Anna Pavlova; Diane L Lynch; Patricia H Reggio; Yi Wang; James C Gumbart
Journal:  J Chem Theory Comput       Date:  2019-07-02       Impact factor: 6.006

7.  Spontaneous local membrane curvature induced by transmembrane proteins.

Authors:  Christoph Kluge; Matthias Pöhnl; Rainer A Böckmann
Journal:  Biophys J       Date:  2022-02-03       Impact factor: 4.033

8.  Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data.

Authors:  Milka Doktorova; Norbert Kučerka; Jacob J Kinnun; Jianjun Pan; Drew Marquardt; Haden L Scott; Richard M Venable; Richard W Pastor; Stephen R Wassall; John Katsaras; Frederick A Heberle
Journal:  J Phys Chem B       Date:  2020-06-16       Impact factor: 2.991

9.  How cholesterol stiffens unsaturated lipid membranes.

Authors:  Saptarshi Chakraborty; Milka Doktorova; Trivikram R Molugu; Frederick A Heberle; Haden L Scott; Boris Dzikovski; Michihiro Nagao; Laura-Roxana Stingaciu; Robert F Standaert; Francisco N Barrera; John Katsaras; George Khelashvili; Michael F Brown; Rana Ashkar
Journal:  Proc Natl Acad Sci U S A       Date:  2020-08-25       Impact factor: 11.205

Review 10.  Biomembrane Structure and Material Properties Studied With Neutron Scattering.

Authors:  Jacob J Kinnun; Haden L Scott; Rana Ashkar; John Katsaras
Journal:  Front Chem       Date:  2021-04-27       Impact factor: 5.221

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