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Molecular Dynamic Simulations of Biological Membranes
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Biological membranes mainly constituent lipid molecules along with some proteins and steroles. The properties of the pure lipid bilayers as well as in the presence of other constituents (in case of two or three component systems) are very important to be studied carefully to model these systems and compare them with the realistic systems. Molecular dynamic simulations provide a good opportunity to model such systems and to study them at microscopic level where experiments fail to do. In this thesis we study the structural and dynamic properties of the pure phospholipid bilayers and the phase behavior of phospholipid bilayers when other constituents are present in them. Material and structural properties like area per lipid and area compressibility of the phospholipids show a big scatter in experiments. These properties are studied for different system sizes and it was found that the increasing undulations in large systems effect these properties. A correction was applied to area per lipid and area compressibility using the Helfrich theory in Fourier space. Other structural properties like order of the lipid chains, electron density and radial distribution functions are calculated which give the structure of the lipid bilayer along the normal and in the lateral direction. These properties are compared to the X-ray and neutron scattering experiments after Fourier transform. Thermodynamic properties like heat capacity and heat of melting are also calculated from derivatives of energies available in molecular dynamics. Heat capacity on the other hand include quantum effect and are corrected for that by applying quantum correction using normal mode analysis for a simple as well as ambiguous system like water. Here it is done for SPC/E water model. The purpose of this study is to further apply the quantum corrections on macromolecules like lipids by using this technique. Furthermore the phase behavior of two component systems (phospholipids/cholesterol) is also studied. Phase transition in these systems is observed at different cholesterol concentrations as a function of temperature by looking at different quantities (as an order parameter) like the order of chains, area per molecule and partial specific area. Radial distribution functions are used to look at the in plane structure for different phases having a different lateral or positional order. Adding more cholesterol orders the lipid chains changing a liquid disordered system into a liquid ordered one and turning a solid ordered system into a liquid ordered one. Further more the free energy of domain formation is calculated to investigate the two phasecoexistence in binary systems. Free energy contains two terms. One is bulk freeenergy which was calculated by the chemical potential of cholesterol moleculein a homogeneous system which is favorable for segregation. Second is thefree energy of having an interface which is calculated from the line tension of the interface of two systems with different cholesterol concentration which in unfavorable for domain formation. The size of the domains calculated from these two contributions to the free energy gives the domains of a few nm in size. Though we could not find any such domains by directly looking at our simulations.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2012. , vii, 78 p.
Series
Trita-FYS, ISSN 0280-316X ; 2012:68
Keyword [en]
phospholipids, area compressibility, undulations, quantum corrections, cholesterol, phase transition, segregation
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-102268ISBN: 978-91-7501-455-5 (print)OAI: oai:DiVA.org:kth-102268DiVA: diva2:551948
Public defence
2012-09-24, Sal FA31, AlbaNova, Roslagstullsbacken 21, Stockholm, 13:00 (English)
Opponent
Supervisors
Note

QC 20120913

Available from: 2012-09-13 Created: 2012-09-12 Last updated: 2012-09-13Bibliographically approved
List of papers
1. Undulation Contributions to the Area Compressibility in Lipid Bilayer Simulations
Open this publication in new window or tab >>Undulation Contributions to the Area Compressibility in Lipid Bilayer Simulations
2009 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 97, no 10, 2754-2760 p.Article in journal (Refereed) Published
Abstract [en]

It is here shown that there is a considerable system size-dependence in the area compressibility calculated from area fluctuations in lipid bilayers. This is caused by the contributions to the area fluctuations from undulations. This is also the case in experiments. At present, such a contribution, in most cases, is subtracted from the experimental values to obtain a true area compressibility. This should also be done with the simulation values. Here, this is done by extrapolating area compressibility versus system size, down to very small (zero) system size, where undulations no longer exist. The area compressibility moduli obtained from such simulations do not agree with experimental true area compressibility moduli as well as the uncorrected ones from contemporary or earlier simulations, but tend, instead, to be similar to 50% too large. As a byproduct, the bending modulus can be calculated from the slope of the compressibility modulus versus system-size. The values obtained in this way for the bending modulus are then in good agreement with experiment.

Identifiers
urn:nbn:se:kth:diva-18969 (URN)10.1016/j.bpj.2009.08.048 (DOI)000271917700013 ()2-s2.0-72149118772 (Scopus ID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved
2. Quantum Corrections to Classical Molecular Dynamics Simulations of Water and Ice
Open this publication in new window or tab >>Quantum Corrections to Classical Molecular Dynamics Simulations of Water and Ice
2011 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, no 9, 2903-2909 p.Article in journal (Refereed) Published
Abstract [en]

Classical simulations of simple water models reproduce many properties of the liquid and ice but overestimate the heat capacity by about 65% at ordinary temperatures and much more for low temperature ice. This is due to the fact that the atomic vibrations are quantum mechanical. The application of harmonic quantum corrections to the molecular motion results in good heat capacities for the liquid and for ice at low temperatures but a successively growing positive deviation from experimental results for ice above 200 K that reaches 15% just below melting. We suggest that this deviation is due to the lack of quantum corrections to the anharmonic motions. For the liquid, the anharmonicities are even larger but also softer and thus in less need of quantum correction. Therefore, harmonic quantum corrections to the classically calculated liquid heat capacities result in agreement with the experimental values. The classical model underestimates the heat of melting by 15%, while the application of quantum corrections produces fair agreement. On the other hand, the heat of vaporization is overestimated by 10% in the harmonically corrected classical model.

Keyword
particle mesh ewald, liquid water, model, tip4p/2005, spectra, range
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-41790 (URN)10.1021/ct2003034 (DOI)000294790400026 ()2-s2.0-80052786849 (Scopus ID)
Funder
Swedish Research CouncilSwedish e‐Science Research Center
Note
QC 20111003Available from: 2011-10-03 Created: 2011-10-03 Last updated: 2017-12-08Bibliographically approved
3. Phase Transitions in Coarse-Grained Lipid Bilayers Containing Cholesterol by Molecular Dynamics Simulations
Open this publication in new window or tab >>Phase Transitions in Coarse-Grained Lipid Bilayers Containing Cholesterol by Molecular Dynamics Simulations
2012 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 103, no 10, 2125-2133 p.Article in journal (Refereed) Published
Abstract [en]

Coarse-grained simulations of model membranes containing mixtures of phospholipid and cholesterol molecules at different concentrations and temperatures have been performed. A random mixing without tendencies for segregation or formation of domains was observed on spatial scales corresponding to a few thousand lipids and timescales up to several micro-seconds. The gel-to-liquid crystalline phase transition is successively weakened with increasing amounts of cholesterol without disappearing completely even at a concentration of cholesterol as high as 60%. The phase transition temperature increases slightly depending on the cholesterol concentration. The gel phase system undergoes a transition with increasing amounts of cholesterol from a solid-ordered phase into a liquid-ordered one. In the solid phase, the amplitude of the oscillations in the radial distribution function decays algebraically with a prefactor that goes to zero at the solid-liquid transition.

Keyword
particle mesh ewald, liquid water, model, tip4p/2005, spectra, range
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-102277 (URN)10.1016/j.bpj.2012.10.014 (DOI)000311419000011 ()2-s2.0-84869465857 (Scopus ID)
Funder
Swedish Research CouncilSwedish e‐Science Research Center
Note

QC 20130107. Updated from accepted to published.

Available from: 2012-09-12 Created: 2012-09-12 Last updated: 2017-12-07Bibliographically approved
4. Free energy for cholesterol insertion into lipid bilayers studied by molecular dynamic simulations
Open this publication in new window or tab >>Free energy for cholesterol insertion into lipid bilayers studied by molecular dynamic simulations
(English)Article in journal (Other academic) Submitted
Abstract [en]

Lipid bilayers consisting of binary mixtures of phospholipids and cholesterol are studied above and below the main phase transition temperature using coarse grained (CG) and united atom (UA) models by molecular dynamics simulations. The purpose is to explore whether phase segregation into cholesterol-rich and cholesterol-poor domains is favorable from a free energy point of view and what the required size of these domains would be. We observe directly in simulations that phase separated fluid phase systems mix in less than 200 ns. Since, the dynamics is about 2 orders of magnitude slower in the gel phase mixing was not observed in such system. The chemical potential for cholesterol insertion was calculated from simulations. This resulted in a small bulk free energy of about 0.3kBT per lipid that favors phase separation while a small line tension (a couple of pN) between cholesterol-rich and -poor regions favors mixing. Although a simple continuum theory would indicate stabilization of domains as small as 1-2 nm in size, this was not observed in direct simulations.

Keyword
Cholesterol, phospholipids, domain formation, line tension
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-102276 (URN)
Note

QS 2012

Available from: 2012-09-12 Created: 2012-09-12 Last updated: 2012-09-13Bibliographically approved

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