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 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 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 A method of incorporating rate constants as kinetic constraints in molecular dynamics simulations

2020 ◽  
Vol 118 (2) ◽  
pp. e2012423118
Author(s):  
Z. Faidon Brotzakis ◽  
Michele Vendruscolo ◽  
Peter G. Bolhuis
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Rate Constants ◽  
Molecular System ◽  
Accurate Determination ◽  
Molecular Simulations ◽  
Model Systems ◽  
Wide Range ◽  
Dynamics Simulations

From the point of view of statistical mechanics, a full characterization of a molecular system requires an accurate determination of its possible states, their populations, and the respective interconversion rates. Toward this goal, well-established methods increase the accuracy of molecular dynamics simulations by incorporating experimental information about states using structural restraints and about populations using thermodynamics restraints. However, it is still unclear how to include experimental knowledge about interconversion rates. Here, we introduce a method of imposing known rate constants as constraints in molecular dynamics simulations, which is based on a combination of the maximum-entropy and maximum-caliber principles. Starting from an existing ensemble of trajectories, obtained from either molecular dynamics or enhanced trajectory sampling, this method provides a minimally perturbed path distribution consistent with the kinetic constraints, as well as modified free energy and committor landscapes. We illustrate the application of the method to a series of model systems, including all-atom molecular simulations of protein folding. Our results show that by combining experimental rate constants and molecular dynamics simulations, this approach enables the determination of transition states, reaction mechanisms, and free energies. We anticipate that this method will extend the applicability of molecular simulations to kinetic studies in structural biology and that it will assist the development of force fields to reproduce kinetic and thermodynamic observables. Furthermore, this approach is generally applicable to a wide range of systems in biology, physics, chemistry, and material science.

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.

Sign in / Sign up

Export Citation Format

Share Document