scholarly journals Molecular dynamics simulations of carbon nanotube porins in lipid bilayers

2018 ◽  
Vol 209 ◽  
pp. 341-358 ◽  
Author(s):  
Martin Vögele ◽  
Jürgen Köfinger ◽  
Gerhard Hummer
Keyword(s):  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Dynamics Simulations

Carbon nanotube porins embedded in lipid membranes are studied by molecular dynamics simulations.

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

2017 ◽  
Vol 19 (25) ◽  
pp. 16806-16818 ◽  
Author(s):  
M. Doktorova ◽  
D. Harries ◽  
G. Khelashvili
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Real Space ◽  
Fluctuation Analysis ◽  
Bending Rigidity ◽  
Wide Range ◽  
Dynamics Simulations

Computational methodology that allows to extract bending rigidity and tilt modulus for a wide range of single and multi-component lipid bilayers from real-space analysis of fluctuations in molecular dynamics simulations.

scholarly journals Imaging phase separation in model lipid membranes through the use of BODIPY based molecular rotors

2015 ◽  
Vol 17 (28) ◽  
pp. 18393-18402 ◽  
Author(s):  
Michael R. Dent ◽  
Ismael López-Duarte ◽  
Callum J. Dickson ◽  
Niall D. Geoghegan ◽  
Jonathan M. Cooper ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Phase Separation ◽  
Fluorescence Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Molecular Rotors ◽  
Model Lipid Membranes ◽  
Dynamics Simulations

Viscosity in the phase-separated lipid bilayers is investigated through the use of fluorescence spectroscopy and molecular dynamics simulations.

Anesthetics significantly increase the amount of intramembrane water in lipid membranes

Soft Matter ◽  
2020 ◽  
Vol 16 (42) ◽  
pp. 9674-9682
Author(s):  
Sebastian Himbert ◽  
Lili Zhang ◽  
Richard J. Alsop ◽  
Viviana Cristiglio ◽  
Giovanna Fragneto ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Diffraction ◽  
Molecular Dynamics Simulations ◽  
Water Content ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Water Distribution ◽  
Dynamics Simulations

We studied the effect anesthetics on the water distribution in lipid bilayers by combining all-atom molecular dynamics simulations and neutron diffraction experiments. We found that anesthetics increase the intramembrane water content by up to 25%.

scholarly journals Effect of lipid saturation on amyloid-beta peptide partitioning and aggregation in neuronal membranes: molecular dynamics simulations

2019 ◽  
Vol 48 (8) ◽  
pp. 813-824 ◽  
Author(s):  
Nikolaos Ntarakas ◽  
Inna Ermilova ◽  
Alexander P. Lyubartsev
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Neuronal Membranes ◽  
Chemical Background ◽  
Dynamics Simulations ◽  
Polyunsaturated Lipids

Abstract Aggregation of amyloid-$$\beta $$β (Aβ) peptides, cleaved from the amyloid precursor protein, is known as a precursor of the Alzheimer’s disease (AD). It is also known that Alzheimer’s disease is characterized by a substantial decrease of the amount of polyunsaturated lipids in the neuronal membranes of the frontal gray matter. To get insight into possible interconnection of these phenomena, we have carried out molecular dynamics simulations of two fragments of A$$\beta $$β peptide, A$$\beta $$β$$_{1-28}$$1-28 and A$$\beta $$β$$_{26-40}$$26-40, in four different lipid bilayers: two monocomponent ones (14:0-14:0 PC, 18:0-22:6 PC), and two bilayers containing mixtures of 18:0-18:0 PE, 22:6-22:6 PE, 16:0-16:0 PC and 18:1-18:1 PC lipids of composition mimicking neuronal membranes in a “healthy” and “AD” brain. The simulations showed that the presence of lipids with highly unsaturated 22:6cis fatty acids chains strongly affects the interaction of amyloid-$$\beta $$β peptides with lipid membranes. The polyunsaturated lipids cause stronger adsorption of A$$\beta $$β-peptides by the membrane and lead to weaker binding between peptides when the latter form aggregates. This difference in the behaviour observed in monocomponent bilayers is propagated in a similar fashion to the mixed membranes mimicking composition of neuronal membranes in “healthy” and “AD” brains, with “healthy” membrane having higher fraction of polyunsaturated lipids. Our simulations give strong indication that it can be physical–chemical background of the interconnection between amyloid fibrillization causing Alzheimer’s disease, and content of polyunsaturated lipids in the neuronal membranes.

Influence of the gallate moiety on the interactions between green tea polyphenols and lipid membranes elucidated by molecular dynamics simulations

2021 ◽  
pp. 106592
Author(s):  
Rong-zu Nie ◽  
Mei-zhu Dang ◽  
Zhen-zhen Ge ◽  
Yin-qiang Huo ◽  
Bo Yu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Green Tea ◽  
Lipid Membranes ◽  
Tea Polyphenols ◽  
Green Tea Polyphenols ◽  
Dynamics Simulations

scholarly journals Molecular Dynamics Simulations of Human Islet Amyloid Polypeptide (IAPP) Oligomers and their Interactions with Lipid Bilayers

2011 ◽  
Vol 100 (3) ◽  
pp. 200a-201a ◽  
Author(s):  
Jun Zhao ◽  
Xiang Yu ◽  
Chao Zhao ◽  
Qiuming Wang ◽  
Jie Zheng
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Islet Amyloid Polypeptide ◽  
Human Islet ◽  
Islet Amyloid ◽  
Human Islet Amyloid Polypeptide ◽  
Dynamics Simulations

scholarly journals Molecular Dynamics Simulations of Human Beta-Defensin Type 3 Crossing Different Lipid Bilayers

ACS Omega ◽  
2021 ◽  
Author(s):  
Rabeta Yeasmin ◽  
Ann Brewer ◽  
Lela R Fine ◽  
Liqun Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Dynamics Simulations ◽  
Type 3
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