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Reparameterized united atom model for molecular dynamics simulations of gel and fluid phosphatidylcholine bilayers
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.ORCID iD: 0000-0002-7448-4664
2014 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 12, 5706-5715 p.Article in journal (Refereed) Published
Abstract [en]

A new united atom parametrization of diacyl lipids like dipalmitoylphosphatidylcholine (DPPC) and the dimyristoylphosphatidylcholine (DMPC) has been constructed based on ab initio calculations to obtain fractional charges and the dihedral potential of the hydrocarbon chains, while the Lennard-Jones parameters of the acyl chains were fitted to reproduce the properties of liquid hydrocarbons. The results have been validated against published experimental X-ray and neutron scattering data for fluid and gel phase DPPC. The derived charges of the lipid phosphatidylcholine (PC) headgroup are shown to yield dipole components in the range suggested by experiments. The aim has been to construct a new force field that retains and improves the good agreement for the fluid phase and at the same time produces a gel phase at low temperatures, with properties coherent with experimental findings. The gel phase of diacyl-PC lipids forms a regular triangular lattice in the hydrocarbon region. The global bilayer tilt obtains an azimuthal value of 31 degrees and is aligned between lattice vectors in the bilayer plane. We also show that the model yields a correct heat of melting as well as decent heat capacities in the fluid and gel phase of DPPC.

Place, publisher, year, edition, pages
2014. Vol. 10, no 12, 5706-5715 p.
National Category
Physical Sciences
Research subject
Biological Physics
Identifiers
URN: urn:nbn:se:kth:diva-151393DOI: 10.1021/ct500589zISI: 000346324000052Scopus ID: 2-s2.0-84916613010OAI: oai:DiVA.org:kth-151393DiVA: diva2:748450
Funder
Swedish Research Council
Note

QC 20150220. Updates from submitted to published. Previous title "A Re-parameterized United Atom Model for Molecular Dynamics Simulations of Gel and Fluid Phosphatidylcholine Bilayers".

Available from: 2014-09-19 Created: 2014-09-19 Last updated: 2017-12-05Bibliographically approved
In thesis
1. Classical and Quantum Descriptions of Proteins, Lipids and Membranes
Open this publication in new window or tab >>Classical and Quantum Descriptions of Proteins, Lipids and Membranes
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis the properties of proteins and membranes are studied by molecular dynamics simulations. The subject is decomposed into parts addressing free energy calculations in proteins, mechanical inclusion models for lipid bilayers, phase transitions and structural correlations in lipid bilayers and atomistic lipid bilayer models. The work is based on results from large scale computer simulations, quantum mechanical and continuum models. Efficient statistical sampling and the coarseness of the models needed to describe the ordered and disordered states are of central concern.

Classical free energy calculations of zinc binding, in metalloproteins, require a quantum mechanical correction in order to obtain realistic binding energies. Classical electrostatic polarisation will influence the binding energy in a large region surrounding the ion and produce reasonable equilibrium structures in the bound state, when compared to experimental evidence.

The free energy for inserting a protein into a membrane is calculated with continuum theory. The free energy is assumed quadratic in the mismatch and depend on two elastic constants of the membrane. Under these circumstances, the free energy can then be written as a line tension multiplied by the circumference of the membrane inclusion. The inclusion model and coarse grained particle simulations of the membranes show that the thickness profile around the protein will be an exponentially damped oscillation.

Coarse-grained particle simulations of model membranes containing mixtures of phospholipid and cholesterol molecules at different conditions were performed. The gel-to-liquid crystalline phase transition is successively weakened with increasing amounts of cholesterol without disappearing even at a concentration of cholesterol as high as 60%.

A united atom parameterization of diacyl lipids was constructed. The aim was to construct a new force field that retains and improves the good agreement for the fluid phase and at the same time produces a gel phase at low temperatures, with properties coherent with experimental findings. The global bilayer tilt obtains an azimuthal value of 31and is aligned between lattice vectors in the bilayer plane. It is also shown that the model yield a correct heat of melting as well as heat capacities in the fluid and gel phase of DPPC.

 

Place, publisher, year, edition, pages
Stockholm, Sweden: KTH Royal Institute of Technology, 2014. xiv, 73 p.
Series
TRITA-FYS, ISSN 0280-316X ; 2014:55
Keyword
Quantum corrections, Coordination structure, Polarisation, Phase transitions, Kelvin differential equation, Line tension, Elastic membrane models, Molecular particle models, Zinc binding, Cholesterol and Phospholipids
National Category
Physical Sciences
Research subject
Biological Physics
Identifiers
urn:nbn:se:kth:diva-151396 (URN)978-91-7595-253-6 (ISBN)
Public defence
2014-10-03, Sal FA32, AlbaNova Universitetscentrum, Roslagstullsbacken 21, Stockholm, 10:00 (English)
Opponent
Supervisors
Funder
Swedish Research Council
Note

QC 20140919

Available from: 2014-09-19 Created: 2014-09-19 Last updated: 2014-10-07Bibliographically approved

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