Energetic and Frictional Effects in the Transport of Ions in a Cyclic Peptide Nanotube: Energetic and Frictional Effects in the Transport of Ions

doi:10.1002/bkcs.11035

Title: Energetic and Frictional Effects in the Transport of Ions in a Cyclic Peptide Nanotube: Energetic and Frictional Effects in the Transport of Ions

Authors:

Seo, Yongil ^[1]; Song, Yeonho ^[1]; Schatz, George C. ^[2]; Hwang, Hyonseok ^[1]

Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Gangwon-do 24341 Republic of Korea
Department of Chemistry, Northwestern University, Evanston IL 60208 USA

Publication Date:: 2016-12-21

Research Org.:: Energy Frontier Research Centers (EFRC) (United States). Center for Bio-Inspired Energy Science (CBES)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)

OSTI Identifier:: 1388506

DOE Contract Number:: SC0000989

Resource Type:: Journal Article

Journal Name:: Bulletin of the Korean Chemical Society

Additional Journal Information:: Journal Volume: 38; Journal Issue: 1; Related Information: CBES partners with Northwestern University (lead); Harvard University; New York University; Pennsylvania State University; University of Michigan; University of Pittsburgh; Journal ID: ISSN 1229-5949

Country of Publication:: United States

Language:: English

Subject:: catalysis (homogeneous), solar (photovoltaic), bio-inspired, charge transport, mesostructured materials, materials and chemistry by design, synthesis (novel materials), synthesis (self-assembly)

Citation Formats


                    Seo, Yongil, Song, Yeonho, Schatz, George C., and Hwang, Hyonseok. Energetic and Frictional Effects in the Transport of Ions in a Cyclic Peptide Nanotube: Energetic and Frictional Effects in the Transport of Ions.  United States: N. p., 2016. 
        Web.  doi:10.1002/bkcs.11035.

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                    Seo, Yongil, Song, Yeonho, Schatz, George C., & Hwang, Hyonseok. Energetic and Frictional Effects in the Transport of Ions in a Cyclic Peptide Nanotube: Energetic and Frictional Effects in the Transport of Ions.  United States.  doi:10.1002/bkcs.11035.

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                    Seo, Yongil, Song, Yeonho, Schatz, George C., and Hwang, Hyonseok. Wed .  
        "Energetic and Frictional Effects in the Transport of Ions in a Cyclic Peptide Nanotube: Energetic and Frictional Effects in the Transport of Ions".  United States.  doi:10.1002/bkcs.11035.

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@article{osti_1388506,

  title        = {Energetic and Frictional Effects in the Transport of Ions in a Cyclic Peptide Nanotube: Energetic and Frictional Effects in the Transport of Ions},

  author       = {Seo, Yongil and Song, Yeonho and Schatz, George C. and Hwang, Hyonseok},

  abstractNote = {},

  doi          = {10.1002/bkcs.11035},

  journal      = {Bulletin of the Korean Chemical Society},

  issn         = {1229-5949},

  number       = 1,

  volume       = 38,

  place        = {United States},

  year         = {2016},

  month        = {12}

}

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Journal Article:

DOI: 10.1002/bkcs.11035

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Title: Energetic and Frictional Effects in the Transport of Ions in a Cyclic Peptide Nanotube: Energetic and Frictional Effects in the Transport of Ions

Citation Formats

Ion transport in a gramicidin-like channel: dynamics and mobility journal, June 1991

Steered Molecular Dynamics Studies of the Potential of Mean Force of a Na + or K + Ion in a Cyclic Peptide Nanotube journal, December 2006

Calculation of ionic diffusion coefficients on the basis of migration test results journal, April 2003

Scalable molecular dynamics with NAMD journal, January 2005

K+ versus Na+ Ions in a K Channel Selectivity Filter: A Simulation Study journal, August 2002

Theory and Simulation of Ion Conduction in the Pentameric GLIC Channel journal, March 2012

Self-assembling organic nanotubes based on a cyclic peptide architecture journal, December 1993

Water Conduction through a Peptide Nanotube journal, November 2013

Transmembrane ion transport by self-assembling α,γ-peptide nanotubes journal, January 2012

Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics Simulations journal, December 2012

Ion Permeation through a Narrow Channel: Using Gramicidin to Ascertain All-Atom Molecular Dynamics Potential of Mean Force Methodology and Biomolecular Force Fields journal, May 2006

Calculation of Lipid-Bilayer Permeabilities Using an Average Force journal, January 2014

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin journal, March 1988

Transport Behavior of a Single Ca 2+ , K + , and Na + in a Water-Filled Transmembrane Cyclic Peptide Nanotube journal, May 2015

Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands journal, October 2004

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins † journal, April 1998

Potential of Mean Force Calculations for Ion Selectivity in a Cyclic Peptide Nanotube journal, March 2012

Using collective variables to drive molecular dynamics simulations journal, December 2013

Artificial transmembrane ion channels from self-assembling peptide nanotubes journal, May 1994

Energetics of ion conduction through the gramicidin channel journal, December 2003

Structure and Dynamics of Self-Assembling Peptide Nanotubes and the Channel-Mediated Water Organization and Self-Diffusion. A Molecular Dynamics Study journal, September 1995

Energetics of Ion Transport in a Peptide Nanotube journal, September 2007

Mobility and solvation of ions in channels journal, November 1996

Simulation of water transport through a lipid membrane journal, April 1994

A Synthetic Pore-Mediated Transmembrane Transport of Glutamic Acid journal, July 2001

Not Ions Alone: Barriers to Ion Permeation in Nanopores and Channels journal, November 2004

Ion Current Calculations Based on Three Dimensional Poisson−Nernst−Planck Theory for a Cyclic Peptide Nanotube journal, April 2006

Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations journal, June 1994

The Structural and Thermodynamic Basis for the Formation of Self-Assembled Peptide Nanotubes journal, January 1995

Effect of the computational domain size and shape on the self-diffusion coefficient in a Lennard-Jones liquid journal, January 2015

VMD: Visual molecular dynamics journal, February 1996

Ion transport in a model gramicidin channel. Structure and thermodynamics journal, May 1991

Ion Permeation and Selectivity of OmpF Porin: A Theoretical Study Based on Molecular Dynamics, Brownian Dynamics, and Continuum Electrodiffusion Theory journal, September 2002

Ion transport in a gramicidin-like channel: dynamics and mobility
journal, June 1991

Steered Molecular Dynamics Studies of the Potential of Mean Force of a Na ⁺ or K ⁺ Ion in a Cyclic Peptide Nanotube
journal, December 2006

Calculation of ionic diffusion coefficients on the basis of migration test results
journal, April 2003

Scalable molecular dynamics with NAMD
journal, January 2005

K+ versus Na+ Ions in a K Channel Selectivity Filter: A Simulation Study
journal, August 2002

Theory and Simulation of Ion Conduction in the Pentameric GLIC Channel
journal, March 2012

Self-assembling organic nanotubes based on a cyclic peptide architecture
journal, December 1993

Water Conduction through a Peptide Nanotube
journal, November 2013

Transmembrane ion transport by self-assembling α,γ-peptide nanotubes
journal, January 2012

Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics Simulations
journal, December 2012

Ion Permeation through a Narrow Channel: Using Gramicidin to Ascertain All-Atom Molecular Dynamics Potential of Mean Force Methodology and Biomolecular Force Fields
journal, May 2006

Calculation of Lipid-Bilayer Permeabilities Using an Average Force
journal, January 2014

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
journal, March 1988

Transport Behavior of a Single Ca ²⁺ , K ⁺ , and Na ⁺ in a Water-Filled Transmembrane Cyclic Peptide Nanotube
journal, May 2015

Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands
journal, October 2004

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins ^†
journal, April 1998

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journal, March 2012

Using collective variables to drive molecular dynamics simulations
journal, December 2013

Artificial transmembrane ion channels from self-assembling peptide nanotubes
journal, May 1994

Energetics of ion conduction through the gramicidin channel
journal, December 2003

Structure and Dynamics of Self-Assembling Peptide Nanotubes and the Channel-Mediated Water Organization and Self-Diffusion. A Molecular Dynamics Study
journal, September 1995

Energetics of Ion Transport in a Peptide Nanotube
journal, September 2007

Mobility and solvation of ions in channels
journal, November 1996

Simulation of water transport through a lipid membrane
journal, April 1994

A Synthetic Pore-Mediated Transmembrane Transport of Glutamic Acid
journal, July 2001

Not Ions Alone: Barriers to Ion Permeation in Nanopores and Channels
journal, November 2004

Ion Current Calculations Based on Three Dimensional Poisson−Nernst−Planck Theory for a Cyclic Peptide Nanotube
journal, April 2006

Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
journal, June 1994

The Structural and Thermodynamic Basis for the Formation of Self-Assembled Peptide Nanotubes
journal, January 1995

Effect of the computational domain size and shape on the self-diffusion coefficient in a Lennard-Jones liquid
journal, January 2015

VMD: Visual molecular dynamics
journal, February 1996

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journal, May 1991

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journal, September 2002