Carbon nanotube porin diffusion in mixed composition supported lipid bilayers

Sullivan, Kylee; Zhang, Yuliang; Lopez, Joseph; Lowe, Mary; Noy, Aleksandr

doi:10.1038/s41598-020-68059-2

Title: Carbon nanotube porin diffusion in mixed composition supported lipid bilayers

Abstract

Carbon nanotube porins (CNTPs), short pieces of carbon nanotubes capable of self-inserting into a lipid bilayer, represent a simplified model of biological membrane channels. We have used high-speed atomic force microscopy (HS-AFM) and all-atom molecular dynamics (MD) simulations to study the behavior of CNTPs in a mixed lipid membrane consisting of DOPC lipid with a variable percentage of DMPC lipid added to it. HS-AFM data reveal that the CNTPs undergo diffusive motion in the bilayer plane. Motion trajectories extracted from the HS-AFM movies indicate that CNTPs exhibit diffusion coefficient values broadly similar to values reported for membrane proteins in supported lipid bilayers. The data also indicate that increasing the percentage of DMPC leads to a marked slowing of CNTP diffusion. MD simulations reveal a CNTP-lipid assembly that diffuses in the membrane and show trends that are consistent with the experimental observations.

Authors:: Sullivan, Kylee; Zhang, Yuliang; Lopez, Joseph; Lowe, Mary; Noy, Aleksandr

Publication Date:: Fri Jul 17 00:00:00 EDT 2020

Research Org.:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Molecular Foundry

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Materials Sciences & Engineering Division; National Science Foundation (NSF)

OSTI Identifier:: 1638906

Alternate Identifier(s):: OSTI ID: 1642362

Report Number(s):: LLNL-JRNL-800281
Journal ID: ISSN 2045-2322; 11908; PII: 68059

Grant/Contract Number:: AC52-07NA27344; SCW1607; AC02-05CH11231; 1626262

Resource Type:: Published Article

Journal Name:: Scientific Reports

Additional Journal Information:: Journal Name: Scientific Reports Journal Volume: 10 Journal Issue: 1; Journal ID: ISSN 2045-2322

Publisher:: Nature Publishing Group

Country of Publication:: United Kingdom

Language:: English

Subject:: 77 NANOSCIENCE AND NANOTECHNOLOGY; Biophysics; Nanoscale biophysics

Citation Formats


                    Sullivan, Kylee, Zhang, Yuliang, Lopez, Joseph, Lowe, Mary, and Noy, Aleksandr. Carbon nanotube porin diffusion in mixed composition supported lipid bilayers.  United Kingdom: N. p., 2020. 
Web.  doi:10.1038/s41598-020-68059-2.

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                    Sullivan, Kylee, Zhang, Yuliang, Lopez, Joseph, Lowe, Mary, & Noy, Aleksandr. Carbon nanotube porin diffusion in mixed composition supported lipid bilayers.  United Kingdom.  https://doi.org/10.1038/s41598-020-68059-2

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                    Sullivan, Kylee, Zhang, Yuliang, Lopez, Joseph, Lowe, Mary, and Noy, Aleksandr. Fri .  
"Carbon nanotube porin diffusion in mixed composition supported lipid bilayers".  United Kingdom.  https://doi.org/10.1038/s41598-020-68059-2.

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@article{osti_1638906,

  title        = {Carbon nanotube porin diffusion in mixed composition supported lipid bilayers},

  author       = {Sullivan, Kylee and Zhang, Yuliang and Lopez, Joseph and Lowe, Mary and Noy, Aleksandr},

  abstractNote = {Carbon nanotube porins (CNTPs), short pieces of carbon nanotubes capable of self-inserting into a lipid bilayer, represent a simplified model of biological membrane channels. We have used high-speed atomic force microscopy (HS-AFM) and all-atom molecular dynamics (MD) simulations to study the behavior of CNTPs in a mixed lipid membrane consisting of DOPC lipid with a variable percentage of DMPC lipid added to it. HS-AFM data reveal that the CNTPs undergo diffusive motion in the bilayer plane. Motion trajectories extracted from the HS-AFM movies indicate that CNTPs exhibit diffusion coefficient values broadly similar to values reported for membrane proteins in supported lipid bilayers. The data also indicate that increasing the percentage of DMPC leads to a marked slowing of CNTP diffusion. MD simulations reveal a CNTP-lipid assembly that diffuses in the membrane and show trends that are consistent with the experimental observations.},

  doi          = {10.1038/s41598-020-68059-2},

  journal      = {Scientific Reports},

  number       = 1,

  volume       = 10,

  place        = {United Kingdom},

  year         = {Fri Jul 17 00:00:00 EDT 2020},

  month        = {Fri Jul 17 00:00:00 EDT 2020}

}

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Title: Carbon nanotube porin diffusion in mixed composition supported lipid bilayers

Abstract

Citation Formats

Characterization of the motion of membrane proteins using high-speed atomic force microscopy journal, July 2012

CHARMM-GUI: A web-based graphical user interface for CHARMM journal, March 2008

Scalable molecular dynamics with NAMD journal, January 2005

Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature journal, November 2011

Video imaging of walking myosin V by high-speed atomic force microscopy journal, October 2010

A high-speed atomic force microscope for studying biological macromolecules journal, October 2001

Real-Time Monitoring of Lipid Exchange via Fusion of Peptide Based Lipid-Nanodiscs journal, April 2018

Single-Unit Imaging of Membrane Protein-Embedded Nanodiscs from Two Oriented Sides by High-Speed Atomic Force Microscopy journal, January 2019

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field journal, December 2015

Real-time dynamics of carbon nanotube porins in supported lipid membranes visualized by high-speed atomic force microscopy journal, June 2017

Observing Membrane Protein Diffusion at Subnanometer Resolution journal, April 2003

Comparison of simple potential functions for simulating liquid water journal, July 1983

Stochastic transport through carbon nanotubes in lipid bilayers and live cell membranes journal, October 2014

Understanding the diversity of membrane lipid composition journal, February 2018

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations journal, August 2014

A cationic polymethacrylate-copolymer acts as an agonist for β-amyloid and an antagonist for amylin fibrillation journal, January 2019

Apparent molar heat capacities of phospholipids in aqueous dispersion. Effects of chain length and head group structure journal, November 1983

Lateral Diffusion of Proteins in Membranes journal, March 1987

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SINGLE-PARTICLE TRACKING:Applications to Membrane Dynamics journal, June 1997

High speed atomic force microscopy to investigate the interactions between toxic Aβ 1-42 peptides and model membranes in real time: impact of the membrane composition journal, January 2019

Nanoscale Dynamics of Amyloid β-42 Oligomers As Revealed by High-Speed Atomic Force Microscopy journal, October 2016

Constant pressure molecular dynamics simulation: The Langevin piston method journal, September 1995

CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature journal, July 2014

Structure of Carbon Nanotube Porins in Lipid Bilayers: An in Situ Small-Angle X-ray Scattering (SAXS) Study journal, June 2016

A smooth particle mesh Ewald method journal, November 1995

High-Speed Atomic Force Microscopy Reveals Rotary Catalysis of Rotorless F1-ATPase journal, August 2011

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Molecular dynamics simulations of carbon nanotube porins in lipid bilayers journal, January 2018

Synthesis, lipid membrane incorporation, and ion permeability testing of carbon nanotube porins journal, September 2016

Dynamics of Nucleosomes Assessed with Time-Lapse High-Speed Atomic Force Microscopy journal, September 2011

Hydration of DOPC bilayers by differential scanning calorimetry journal, April 1994

Lateral diffusion of proteins and lipids in the plasma membrane of rose protoplast journal, February 1989

Filming Biomolecular Processes by High-Speed Atomic Force Microscopy journal, January 2014

The morphology of lipid membranes journal, August 1995

Lateral diffusion of lipids and proteins in bilayer membranes journal, September 1984

VMD: Visual molecular dynamics journal, February 1996

Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-Ray Scattering Data journal, September 2008

Characterization of the motion of membrane proteins using high-speed atomic force microscopy
journal, July 2012

CHARMM-GUI: A web-based graphical user interface for CHARMM
journal, March 2008

Scalable molecular dynamics with NAMD
journal, January 2005

Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature
journal, November 2011

Video imaging of walking myosin V by high-speed atomic force microscopy
journal, October 2010

A high-speed atomic force microscope for studying biological macromolecules
journal, October 2001

Real-Time Monitoring of Lipid Exchange via Fusion of Peptide Based Lipid-Nanodiscs
journal, April 2018

Single-Unit Imaging of Membrane Protein-Embedded Nanodiscs from Two Oriented Sides by High-Speed Atomic Force Microscopy
journal, January 2019

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
journal, December 2015

Real-time dynamics of carbon nanotube porins in supported lipid membranes visualized by high-speed atomic force microscopy
journal, June 2017

Observing Membrane Protein Diffusion at Subnanometer Resolution
journal, April 2003

Comparison of simple potential functions for simulating liquid water
journal, July 1983

Stochastic transport through carbon nanotubes in lipid bilayers and live cell membranes
journal, October 2014

Understanding the diversity of membrane lipid composition
journal, February 2018

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations
journal, August 2014

A cationic polymethacrylate-copolymer acts as an agonist for β-amyloid and an antagonist for amylin fibrillation
journal, January 2019

Apparent molar heat capacities of phospholipids in aqueous dispersion. Effects of chain length and head group structure
journal, November 1983

Lateral Diffusion of Proteins in Membranes
journal, March 1987

Carbon nanotube as a gramicidin analogue
journal, January 2011

SINGLE-PARTICLE TRACKING:Applications to Membrane Dynamics
journal, June 1997

High speed atomic force microscopy to investigate the interactions between toxic Aβ _1-42 peptides and model membranes in real time: impact of the membrane composition
journal, January 2019

Nanoscale Dynamics of Amyloid β-42 Oligomers As Revealed by High-Speed Atomic Force Microscopy
journal, October 2016

Constant pressure molecular dynamics simulation: The Langevin piston method
journal, September 1995

CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature
journal, July 2014

Structure of Carbon Nanotube Porins in Lipid Bilayers: An in Situ Small-Angle X-ray Scattering (SAXS) Study
journal, June 2016

A smooth particle mesh Ewald method
journal, November 1995

High-Speed Atomic Force Microscopy Reveals Rotary Catalysis of Rotorless F1-ATPase
journal, August 2011

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
journal, June 2010

Molecular dynamics simulations of carbon nanotube porins in lipid bilayers
journal, January 2018

Synthesis, lipid membrane incorporation, and ion permeability testing of carbon nanotube porins
journal, September 2016

Dynamics of Nucleosomes Assessed with Time-Lapse High-Speed Atomic Force Microscopy
journal, September 2011

Hydration of DOPC bilayers by differential scanning calorimetry
journal, April 1994

Lateral diffusion of proteins and lipids in the plasma membrane of rose protoplast
journal, February 1989

Filming Biomolecular Processes by High-Speed Atomic Force Microscopy
journal, January 2014

The morphology of lipid membranes
journal, August 1995

Lateral diffusion of lipids and proteins in bilayer membranes
journal, September 1984

VMD: Visual molecular dynamics
journal, February 1996

Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-Ray Scattering Data
journal, September 2008