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Author:Määttä, Jukka Sakari
Title:A Novel United-Atom Force Field for Phosphatidylglycerols
Yhdistettyjen atomien voimakenttä Fosfoglyserolipideille
Publication type:Master's thesis
Publication year:2012
Pages:112 + [36]      Language:   eng
Department/School:Lääketieteellisen tekniikan ja laskennallisen tieteen laitos
Main subject:Lääketieteellinen tekniikka   (Tfy-99)
Supervisor:Koskelainen, Ari
Instructor:Salonen, Emppu
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Location:P1 Ark Aalto  229   | Archive
Keywords:molecular dynamics
simulation
phosphatidylglycerol
PG
force field
molekyylidynamiikka
simulaatio
fosfoglyseroli
PG
voimakenttä
Abstract (eng): Phosphatidylglycerols (PG)s are anionic lipids abundant both in prokaryotic membranes and in the chloroplast membrane of plants.
In humans and animals PG lipids occur in minor amounts in pulmonary lung surfactants, blood cells and mitochondrial membranes.
Similar to other negatively-charged phospholipids, PG has a very complex phase-behaviour: the phase transitions and structural organization of PG are affected both by temperature, pH, and concentration of mono- and divalent cations.
Furthermore, the glycerol moiety of the PG headgroup has a complex conformational space in aqueous media, because of the presence of vicinal hydroxyl groups that are capable of of stabilizing various conformers through hydrogen bonds (H-bonds).

In this work a novel united-atom force field is constructed for PG lipids as a part of the ongoing development of a large, consistent lipid force field library.
The torsional and partial atomic charge parameters were calculated based on high-level ab-initio quantum mechanical (QM) calculations with semi-empirical molecular mechanics (MM) studies.
The Lennard-Jones parameters were taken from the OPLS-UA force field developed by Jorgensen.
The QM and MM simulations were combined with experimental thermodynamic data of glycerol as target data for parameter optimization.
The parameters were further optimized to reproduce the structural, dynamic and elastic properties of pure DMPG and POPG lipid bilayers.
Abstract (fin): Fosfoglyserolilipidit ovat anionisia rasvoja, jotka ovat yleisiä erityisesti prokaryoottisolujen solukalvoissa sekä kasvien kloroplastikalvoissa.Nisäkkäissä PG-lipidejä esiintyy keuhkosurfaktantteina, verisoluissa sekä mitokondrioiden kalvostoissa.
PG-lipidien faasikäyttäytyminen on hyvin monimutkaista, mikä on tavallista negatiivisesti varautuneille fosfolipidieille.

Lämpötila, pH ja mono- sekä divalenttisten ioneiden konsentraatiolla on vaikutusta sekä PG-lipidien faasitransitioihin että faasien rakenteeseen.
Lisäksi PG-pääryhmän glyseroliryhmällä on hyvin kompleksinen konformaatioavaruus vesiympäristössä, koska glyserolin lähekkäiset hydroksyyliryhmät mahdollistavat monien erityyppisten konformaatioiden stabilisoinnin vetysidosten avulla.

Tässä diplomityössä rakennetaan PG-lipideille voimakenttä.
Tavoitteena on yhdistää se osaksi suurempaa, konsistenttia lipidivoimakenttäkirjastoa.
Voimakentän torsionaaliset parametrit ja osittaisvaraukset on laskettu korkean tason ab-initio kvanttimekaniikkalaskentaa (QM) sekä semiempiiristä molekyylimekaniikkaa (MM) hyväksi käyttäen.
Lennard-Jones -parametrit on otettu Jorgensenin kehittämästä OPLS-UA voimakentästä.
QM ja MM simulaatiot yhdistettiin glyserolista saatuun kokeelliseen termodynaamiseen dataan, jota käytettiin kohdedatana parametrien optimoinnissa.
Parametrejä optimoitiin lisäksi pyrkien kuvaamaan puhtaiden DMPG- ja POPG-lipidikaksoiskerrosten rakenteellisia, dynaamisia ja elastisia ominaisuuksia.
ED:2012-06-06
INSSI record number: 44671
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