Systematic molecular dynamics searching in a lipid bilayer: Application to the glycophorin A and oncogenic ErbB-2 transmembrane domains

Andrew J. Beevers; Andreas Kukol

doi:10.1016/j.jmgm.2005.12.008

Systematic molecular dynamics searching in a lipid bilayer: Application to the glycophorin A and oncogenic ErbB-2 transmembrane domains

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2005.12.008 ◽

2006 ◽

Vol 25 (2) ◽

pp. 226-233 ◽

Cited By ~ 16

Author(s):

Andrew J. Beevers ◽

Andreas Kukol

Keyword(s):

Molecular Dynamics ◽

Lipid Bilayer ◽

Transmembrane Domains ◽

Glycophorin A

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Investigation on the Interaction between Plexin Intracellular Plus Transmembrane Domains with GTPases and with the Lipid Bilayer using All-Atom Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/j.bpj.2014.11.2739 ◽

2015 ◽

Vol 108 (2) ◽

pp. 500a

Author(s):

Liqun Zhang ◽

Buck Matthias

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Lipid Bilayer ◽

Transmembrane Domains ◽

Dynamics Simulations

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Molecular dynamics simulation of a hydrated diphytanol phosphatidylcholine lipid bilayer containing an alpha-helical bundle of four transmembrane domains of the Influenza A virus M2 protein

Faraday Discussions ◽

10.1039/a806675b ◽

1999 ◽

Vol 111 ◽

pp. 200-208

Author(s):

Thomas Husslein ◽

Preston B. Moore ◽

Qingfong Zhong ◽

Dennis M. Newns ◽

p C. Pattnaik ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Lipid Bilayer ◽

Influenza A Virus ◽

Influenza A ◽

Transmembrane Domains ◽

Dynamics Simulation ◽

M2 Protein ◽

Helical Bundle

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Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.1c00380 ◽

2021 ◽

Author(s):

Masatake Sugita ◽

Satoshi Sugiyama ◽

Takuya Fujie ◽

Yasushi Yoshikawa ◽

Keisuke Yanagisawa ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Membrane Permeability ◽

Lipid Bilayer ◽

Cyclic Peptides ◽

Large Scale ◽

Enhanced Sampling ◽

Permeability Prediction ◽

Dynamics Simulations

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An Alamethicin Channel in a Lipid Bilayer: Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/s0006-3495(99)77337-6 ◽

1999 ◽

Vol 76 (4) ◽

pp. 1757-1769 ◽

Cited By ~ 136

Author(s):

D. Peter Tieleman ◽

Herman J.C. Berendsen ◽

Mark S.P. Sansom

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Lipid Bilayer ◽

Dynamics Simulations

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1P242 1I1435 Analysis of the effect of water molecules on lipid bilayer dynamics in aqueous salt solutions using molecular dynamics simulations(Biol & Artifi memb.:Dynamics,Oral Presentations,The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s62_2 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S62

Author(s):

Rina Kagawa ◽

Yoshinori Hirano ◽

Kenji Yasuoka ◽

Masato Yasui

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Annual Meeting ◽

Lipid Bilayer ◽

Water Molecules ◽

Salt Solutions ◽

Aqueous Salt Solutions ◽

Biophysical Society ◽

Dynamics Simulations ◽

Oral Presentations

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Coarse-Grained Molecular Dynamics Simulations of Cobra Cytotoxin A3 Interactions with a Lipid Bilayer: Penetration of Loops into Membranes

The Journal of Physical Chemistry B ◽

10.1021/jp107599v ◽

2011 ◽

Vol 115 (5) ◽

pp. 796-802 ◽

Cited By ~ 11

Author(s):

Zhi-Yuan Su ◽

Yeng-Tseng Wang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Lipid Bilayer ◽

Coarse Grained ◽

Dynamics Simulations ◽

Coarse Grained Molecular Dynamics

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Permeability of drugs and hormones through a lipid bilayer: insights from dual-resolution molecular dynamics

Soft Matter ◽

10.1039/c0sm00136h ◽

2010 ◽

Vol 6 (16) ◽

pp. 3797 ◽

Cited By ~ 98

Author(s):

Mario Orsi ◽

Jonathan W. Essex

Keyword(s):

Molecular Dynamics ◽

Lipid Bilayer

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1N1348 Quantitation of molecular dynamics and interactions in T cell activation by single-molecule microscopy with a lipid bilayer system(Bioimaging 1,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s66_5 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S66-S67

Author(s):

Yuma Ito ◽

Kumiko Sakata-Sogawa ◽

Makio Tokunaga

Keyword(s):

Molecular Dynamics ◽

T Cell ◽

Annual Meeting ◽

Lipid Bilayer ◽

T Cell Activation ◽

Single Molecule ◽

Cell Activation ◽

Single Molecule Microscopy ◽

Bilayer System ◽

Biophysical Society

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A multi-scale molecular dynamics simulation of PMAL facilitated delivery of siRNA

RSC Advances ◽

10.1039/c5ra10965e ◽

2015 ◽

Vol 5 (83) ◽

pp. 68227-68233 ◽

Cited By ~ 9

Author(s):

Jipeng Li ◽

Yiyun Ouyang ◽

Xian Kong ◽

Jingying Zhu ◽

Diannan Lu ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Lipid Bilayer ◽

Dynamics Simulation ◽

Lipid Bilayer Membranes ◽

Bilayer Membranes ◽

Multi Scale

PMAL as a novel carrier for the delivery of siRNA into lipid bilayer membranes.

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Molecular dynamics studies of lipid bilayer with gramicidin A: Effects of gramicidin a on membrane structure and hydrophobic match

International Journal of Quantum Chemistry ◽

10.1002/qua.23252 ◽

2011 ◽

Vol 112 (1) ◽

pp. 161-170 ◽

Cited By ~ 1

Author(s):

Hiroaki Saito ◽

Taku Mizukami ◽

Shuhei Kawamoto ◽

Takeshi Miyakawa ◽

Masashi Iwayama ◽

...

Keyword(s):

Molecular Dynamics ◽

Lipid Bilayer ◽

Membrane Structure ◽

Gramicidin A

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