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Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0002-4591-9809
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0002-7498-7763
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0002-2734-2794
2013 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 8, 3527-3537 p.Article in journal (Refereed) Published
Abstract [en]

The accuracy of electrostatic interactions in molecular dynamics advanced tremendously with the introduction of particle-mesh Ewald (PME) summation almost 20 years ago. Lattice summation electrostatics is now the de facto standard for most types of biomolecular simulations, and in particular, for lipid bilayers, it has been a critical improvement due to the large charges typically present in zwitterionic lipid headgroups. In contrast, Lennard-Jones interactions have continued to be handled with increasingly longer cutoffs, partly because few alternatives have been available despite significant difficulties in tuning cutoffs and parameters to reproduce lipid properties. Here, we present a new Lennard-Jones PME implementation applied to lipid bilayers. We confirm that long-range contributions are well approximated by dispersion corrections in simple systems such as pentadecane (which makes parameters transferable), but for inhomogeneous and anisotropic systems such as lipid bilayers there are large effects on surface tension, resulting in up to 5.5% deviations in area per lipid and order parameters-far larger than many differences for which reparameterization has been attempted. We further propose an approximation for combination rules in reciprocal space that significantly reduces the computational cost of Lennard-Jones PME and makes accurate treatment of all nonbonded interactions competitive with simulations employing long cutoffs. These results could potentially have broad impact on important applications such as membrane proteins and free energy calculations.

Place, publisher, year, edition, pages
2013. Vol. 9, no 8, 3527-3537 p.
Keyword [en]
Molecular-Dynamics Simulations, Isotropic Periodic Sum, Particle Mesh Ewald, Atom Force-Field, Electrostatic Interactions, Liquid Water, Potentials, Temperature, Truncation, Parameters
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-128488DOI: 10.1021/ct400140nISI: 000323193500028Scopus ID: 2-s2.0-84882349032OAI: oai:DiVA.org:kth-128488DiVA: diva2:648091
Funder
EU, European Research Council, 209825Swedish Foundation for Strategic Research Swedish Research Council, 2010-491 2010-5107Swedish e‐Science Research Center
Note

QC 20130913

Available from: 2013-09-13 Created: 2013-09-12 Last updated: 2017-12-06Bibliographically approved
In thesis
1. Exploring the Interactive Landscape of Lipid Bilayers
Open this publication in new window or tab >>Exploring the Interactive Landscape of Lipid Bilayers
2014 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

One of the most important aspects for all life on this planet is theact to keep their cellular processes in a state where they do notreach equilibrium. One part in the upholding of this imbalanced stateis the barrier between the cells and their surroundings, created bythe cell membrane. In addition to experiments, the investigation ofprocesses occuring in the cell membrane can be performed by usingmolecular dynamics simulations. Through this method we can obtain anatomistic description of the dynamics associated with events that arenot accessible to experimental setups. Molecular dynamics relies onthe integration of Newton's equations of motion in order to sample therelevant parts of phase-space for the system, and therefore it isdependent on a correct description of the interactions between all thesimulated particles. In this thesis I first present an improved methodfor the calculation of long-range interactions in molecular dynamicssimulations, followed by a study of cholesterol's impact on thepermeation of small solutes across a lipid bilayer.

The first paper presents a previously derived modification to theparticle-mesh Ewald method, which makes it possible to apply thisto long-range Lennard-Jones interactions. Old implementations of themethod have been haunted by an extreme performance degradation andhere I propose a solution to this problem by applying a modifiedinteraction potential. I further show that the historical treatmentof long-range interactions in simulations of lipid bilayers hasnon-negligible effects on their structural properties.In the second paper, this modification is improved such that the smallerrors introduced by the modified interaction potential becomenegligible. Furthermore, I demonstrate that I have also improved theimplementation of the method so that it now only incurs a performanceloss of roughly 15% compared to conventional simulations using theGromacs simulation package.The third paper presents a simulation study of cholesterol's effect onthe permeation of six different solutes across a variety of lipidbilayers. I analyze the effect of different head groups, tail lengths,and tail saturation by performing simulations of the solutes in fourdifferent bilayers, with cholesterol contents between 0% and50%. Analysis of the simulations shows that the impact of the surfacearea per lipid on the partitioning of the solute could be lower thanpreviously thought. Furthermore, a model with a laterallyinhomogeneous permeability in cholesterol-containing membranes isproposed, which could explain the large differences betweenpermeabilities from experiments and calculated partition coefficientsin simulations.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2014. xi, 38 p.
Series
TRITA-FYS, ISSN 0280-316X ; 2014:24
Keyword
Molecular Dynamics, lipid bilayer, cholesterol, permeability, long-range interactions, Lennard-Jones, dispersion, particle-mesh Ewald
National Category
Biophysics
Research subject
Biological Physics
Identifiers
urn:nbn:se:kth:diva-145559 (URN)978-91-7595-174-4 (ISBN)
Presentation
2014-06-13, FB54, Roslagstullsbacken 21, AlbaNova, Stockholm, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

QC 20140609

Available from: 2014-06-09 Created: 2014-05-22 Last updated: 2014-06-09Bibliographically approved
2. Computational modeling of biological barriers
Open this publication in new window or tab >>Computational modeling of biological barriers
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

One of the most important aspects for all life on this planet is the act to keep their biological processes in a state where they do not reach equilibrium. One part in the upholding of this imbalanced state is the barrier between the cells and their surroundings, created by the cell membrane. Additionally, terrestrial animal life often requires a barrier that protects the organism's body from external hazards and water loss. As an alternative to experiments, the investigation of the processes occurring at these barriers can be performed by using molecular dynamics simulations. Through this method we can obtain an atomistic description of the dynamics associated with events that are not accessible to experimental setups.

 In this thesis the first paper presents an improved particle-mesh Ewald method for the calculation of long-range Lennard-Jones interactions in molecular dynamics simulations, which solves the historical performance problem of the method. The second paper demonstrate an improved implementation, with a higher accuracy, that only incurs a performance loss of roughly 15% compared to conventional simulations using the Gromacs simulation package. Furthermore, the third paper presents a study of cholesterol's effect on the permeation of six different solutes across a variety of lipid bilayers. A laterally inhomogeneous permeability in cholesterol-containing membranes is proposed as an explanation for the large differences between experimental permeabilities and calculated partition coefficients in simulations. The fourth paper contains a coarse-grained simulation study of a proposed structural transformation in ceramide bilayer structures, during the formation of the stratum corneum. The simulations show that glycosylceramides are able to stabilize a three-dimensionally folded bilayer structure, while simulations with ceramides collapse into a lamellar bilayer structure.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2016. xii, 49 p.
Series
TRITA-FYS, ISSN 0280-316X ; 2016:10
Keyword
Molecular dynamics, cholesterol, lipid bilayer, permeability, long-range interactions, Lennard-Jones, dispersion, particle-mesh Ewald, stratum corneum, skin formation
National Category
Biophysics
Research subject
Biological Physics
Identifiers
urn:nbn:se:kth:diva-183362 (URN)978-91-7595-884-2 (ISBN)
Public defence
2016-04-15, sal F3, Lindstedtsvägen 26, KTH, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

QC 20160308

Available from: 2016-03-08 Created: 2016-03-08 Last updated: 2016-03-09Bibliographically approved

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Wennberg, Christian L.Hess, BerkLindahl, Erik

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