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Dynamics in atomistic simulations of phospholipid membranes: Nuclear magnetic resonance relaxation rates and lateral diffusion
KTH, School of Engineering Sciences (SCI), Theoretical Physics.ORCID iD: 0000-0001-6732-2571
KTH, School of Engineering Sciences (SCI), Theoretical Physics.ORCID iD: 0000-0002-7448-4664
2006 (English)In: Journal of chemical physics, ISSN 0021-9606, Vol. 125, 204703- p.Article in journal (Refereed) Published
Abstract [en]

It is shown that a long, near microsecond, atomistic simulation can shed some light upon the dynamical processes occurring in a lipid bilayer. The analysis focuses on reorientational dynamics of the chains and lateral diffusion of lipids. It is shown that the reorientational correlation functions exhibits an algebraic decay (rather than exponential) for several orders of magnitude in time. The calculated nuclear magnetic resonance relaxation rates agree with experiments for carbons at the C7 position while there are some differences for C3. Lateral diffusion can be divided into two stages. In a first stage occurring at short times, t < 5 ns, the center of mass of the lipid moves due to conformational changes of the chains while the headgroup position remains relatively fixed. In this stage, the center of mass can move up to similar to 0.8 nm. The fitted short-time diffusion coefficient is D-1=13x10(-7) cm(2) s(-1) On a longer time scale, the diffusion coefficient becomes D-2=0.79x10(-7) cm(2) s(-1).

Place, publisher, year, edition, pages
2006. Vol. 125, 204703- p.
Keyword [en]
elastic neutron-scattering, particle mesh ewald, molecular-dynamics, lipid-bilayers, nmr relaxation, h-2, distributions, spectroscopy, temperature, length
National Category
Physical Sciences
URN: urn:nbn:se:kth:diva-6730DOI: 10.1063/1.2393240ISI: 000242408100040ScopusID: 2-s2.0-33751556346OAI: diva2:11522
QC 20100927Available from: 2007-01-10 Created: 2007-01-10 Last updated: 2010-09-27Bibliographically approved
In thesis
1. Atomistic computer simulations of lipid bilayers
Open this publication in new window or tab >>Atomistic computer simulations of lipid bilayers
2006 (English)Doctoral thesis, comprehensive summary (Other scientific)
Abstract [en]

Computer simulation has become an important tool for the study of biomolecular systems. This thesis deals with molecular dynamics simulations of one-component lipid bilayers, which may serve as models for biological membranes.

The main scientific contributions are:

• It is possible to analyze the electrostatic contribution to the surface tension at a lipid-water interface in terms of dipole-dipole interactions between lipid headgroup shielded by a dielectric medium (water). The interaction can be divided into two parts. The in-plane components of the dipoles give rise to a positive, i.e. contractive

contribution to the surface tension, albeit rather short ranged due to them being fluctuating dipoles. The normal components give rise to a negative, i.e. expansive contribution that will dominate the interaction at large distances.

• Simulated membrane areas are extremely sensitive to details, especially the treatment of long-range electrostatic interactions. When cut-offs are used for the electrostatics, the exact definition of charge groups play an important role. Furthermore, using Ewald summation for the long-range interactions seems to have an overall stabilizing effect, and the area becomes less sensitive to other factors, such as system size and hydration.

• Using atomistic simulations it is possible to study formation and evolution of a hydrophilic trans-membrane pore in detail. Free energy of pore nucleation and expansion can be calculated using potentials of mean constraint force. The resulting free energy profile shows no local maximum between the intact and pre-pore states, contrary to what is suggested by experiments.

• The present force field reproduces even the slowest dynamics in the lipid chains, as reflected in NMR relaxation rates. Furthermore, since the simulated system was relatively small, the experimentally observed variation of relaxation rates with Larmor frequency cannot be explained by large scale collective dynamics, or it would not have shown up in the simulation.

• Lipid lateral diffusion can be studied in detail on all relevant time scales by molecular dynamics. Using simple assumptions, the different diffusion coefficients measured on short and long times respectively can be connected in an analytic expression that fit calculated mean square displacements on timescales ranging from picoseconds to hundreds of nanoseconds.

Place, publisher, year, edition, pages
Stockholm: KTH, 2006. vi, 61 p.
Trita-FYS, ISSN 0280-316X ; 2006:82
National Category
Physical Sciences
urn:nbn:se:kth:diva-4264 (URN)978-91-7178-551-0 (ISBN)
Public defence
2007-01-17, FA 32, AlbaNova, Roslagstullsbacken 21, Stockholm, 10:15
QC 20100927Available from: 2007-01-10 Created: 2007-01-10 Last updated: 2011-12-08Bibliographically approved

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