Simulation of processes in cellular membranes Abstract Many important processes in cells involve ions, e.g., fusion of synaptic vesi- cles with neuronal cell membranes is controlled by a divalent cation Ca2+ ; and the exchange of Na+ and K+ drives the the fast electrical signal transmis- sion in neurons. We have investigated model phospholipid membranes and their interactions with these biologically relevant ions. Using state-of-the-art molecular dynamics simulations, we accurately quantified their respective affinites towards neutral and negatively charged phospholipid bilayers. In order to achieve that, we developed a new model of phospholipids termed ECC-lipids, which accounts for the electronic polarization via the electronic continuum correction implemented as charge rescaling. Our simulations with this new force field reach for the first time a quantitative agreement with the experimental lipid electrometer concept for POPC as well as for POPS with all the studied cations. We have also examined the effects of transmembrane voltage on phospholipid bilayers. The electric field induced by the voltage exists exclusively in the hydrophobic region of the membrane, where it has an almost constant strength. This field affects the structure of nearby water molecules highlighting its importance in electroporation. 1

The current study investigates the effect of strain state, strain rate, and membrane planar area on phospholipid bilayer mechanoporation and failure. Using molecular dynamics, a 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer was deformed biaxially to represent injury-induced neuronal membrane mechanoporation and failure. For all studies, water forming a bridge through both phospholipid bilayer leaflets was used as a failure metric. To examine the effect of strain state, 72 phospholipid structures were subjected to equibiaxial, 2:1 non-equibiaxial, 4:1 non-equibiaxial, strip biaxial, and uniaxial tensile deformations at the von Mises strain rate of 5.45 × 108 s-1. The stress magnitude, failure strain, headgroup clustering, and damage behavior were strain state dependent. The strain state order of detrimentality in descending order was equibiaxial, 2:1 non-equibiaxial, 4:1 non-equibiaxial, strip biaxial, and uniaxial with failure von Mises strains of 0.46, 0.47, 0.53, 0.77, and 1.67, respectively. Additionally, pore nucleation, growth, and failure were used to create a Membrane Failure Limit Diagram (MFLD) to demonstrate safe and unsafe membrane deformation regions. This MFLD allowed representative equations to be derived to predict membrane failure from in-plane strains. To examine the effect of strain rate, the equibiaxial and strip biaxial strain states were repeated at multiple strain rates. Additionally, a 144 phospholipid structure, which was twice the size of the 72 phospholipid structure in the x dimension, was subjected to strip biaxial tensile deformations to examine planar area effect. The applied strain rates, planar area, and cross-sectional area had no effect on the von Mises strains at which pores greater than 0.1 nm2 were detected (0.509 plus/minus 7.8%) or the von Mises strain at failure (0.68 plus/minus 4.8%). Additionally, changes in bilayer planar and cross-sectional areas did not affect the stress response. However, a strain rate increase from 1.4 × 108 to 6.8 × 108 s-1 resulted in a yield stress increase of 44.1 MPa and a yield strain increase of 0.17. Additionally, a stress and mechanoporation behavioral transition was determined to occur at a strain rate of ~1.4 × 108 s-1. These results provide the basis to implement a more accurate mechano-physiological internal state variable continuum model that captures lower-length scale damage.

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Les principes actifs, dans leur chemin vers leur cible thérapeutique, rencontrent une ou plusieurs membranes biologiques (plasmique, intracellulaire). Les interactions entre un principe actif et ces membranes sont importantes : d’une part les propriétés pharmacocinétiques de la molécule active (transport, distribution, accumulation) en dépendent, d’autre part le principe actif peut modifier les propriétés structurales des membranes. L’étude de ces interactions est rendue difficile par la complexité des membranes en termes de composition (lipidique et protéique) et de structure (hétérogénéité de l’organisation). Par conséquent, l’utilisation de systèmes modèles simplifiés est nécessaire. Au cours de ce travail de thèse nous avons cherché à réaliser des bicouches lipidiques modèles dont les caractéristiques se rapprochaient de celles des membranes biologiques en complexifiant progressivement leur composition lipidique. Nous avons ensuite étudié l’interaction d’une molécule anti-VIH squalénisée, le ddC-SQ, avec nos modèles de membrane.Un des rôles essentiels des membranes biologiques étant de séparer deux milieux aqueux de composition ionique différente, nous avons étudié dans un premier temps l’influence de la nature du milieu d’hydratation sur les propriétés thermiques et structurales des bicouches lipidiques. A pH physiologique, nous avons mis en évidence que seuls les ions divalents (à faibles concentrations) induisaient de profondes modifications structurales en provoquant la formation de vésicules unilamellaires dans les systèmes simples. Une seconde partie de nos travaux a consisté à étudier l’interaction d’un antiviral squalénisé, le ddC-squalène (ddC-SQ), avec nos différentes bicouches modèles. Cet analogue nucléosidique a été associé de manière covalente à une chaîne de squalène afin d’améliorer ses propriétés pharmacocinétiques. Cette squalénisation confère à la molécule la capacité de s’auto-assembler en nanoparticules présentant une structure cubique bicontinue. Les résultats obtenus ont révélé que le principe actif squalénisé interagissait fortement avec les membranes à l’inverse de la molécule native. L’organisation structurale des systèmes modèles est profondément modifiée par l’insertion du ddC-SQ, ce qui pourrait influer sur l’activité du composé. / Drugs must cross one or more biological membranes (plasma membrane, intracellular membrane) to reach their intracellular target. Interactions between drug and membranes play a significant role in the pharmacokinetic properties of drug such as transport, distribution, accumulation. Moreover, drugs may alter membrane properties. The complexity of the composition (protein and lipid) and the structural properties (heterogeneity) of membranes leads to a difficult investigation of these interactions. Consequently, use of simplified model membranes is needed. In this work, model lipid bilayer systems in which the lipid organization mimics the arrangement of lipids in natural membrane have been developed. In this way, the complexity of lipid composition mixtures has been progressively increased. The primary function of membrane is to physically separate aqueous compartments from their surroundings. The intracellular and extracellular fluids differ in ionic composition. This study firstly consists to estimate the influence of aqueous medium nature on the thermodynamic and structural properties of these model membranes.In physiological conditions (pH 7.4, ionic strength 150 mM), the most significant change was obtained in the presence of divalent ions. Markedly change in lipid organization was observed and the formation of unilamellar vesicles has been evidenced (at low concentrations) in simple model bilayers. Interactions of an antiretroviral nucleoside analogue, the SQddC, with lipid systems constitute the second part of our work. Squalene has been covalently coupled to ddC, in order to improve its therapeutic index. Squalenoylation leads to amphiphilic prodrugs which self-organize as nanoparticles. ddC weakly interacts with lipid membranes while SQddC-SQ can insert into membranes between hydrophobic alkyl chains and induce disruption of lipid organization. Consequently, the efficacy and/or toxicity of this drug could change.

Abstract Coronary heart disease (CHD) is a clinical manifestation of atherosclerosis. It is a major cause of mortality and morbidity both in Finland and globally. Even after the best known treatments a significant residual risk of CHD remains. A low plasma HDL cholesterol level (HDL, high-density lipoprotein) is a common lipid abnormality in patients affected by premature CHD and also a component of the metabolic syndrome, a cluster of risk factors for atherosclerosis associated with central obesity. In this study, a phenotype of low HDL cholesterol level and premature CHD was investigated in two Northern Finnish family populations. The aim was to find new biological factors accounting for the elevated CHD risk in the phenotype. In the subjects of family population I, plasma levels of antibodies (IgG, IgM, IgA) against experimental epitopes (malondialdehyde-acetaldehyde-modified, copper-oxidized) of oxidized LDL (low-density lipoprotein) particles were measured. In the subjects of family population II, capacity of HDL fractions (total HDL, HDL2 and HDL3) to accept cholesterol from a THP-1 experimental foam cell model was assayed (cholesterol efflux). In addition, a phospholipid composition of their HDL fractions (HDL2 and HDL3) was measured using liquid chromatography-mass spectrometry. The antibody levels were not related to CHD or to HDL cholesterol level. Instead, the cholesterol efflux to HDL2 fraction was clearly impaired in CHD, which was associated with the low HDL cholesterol level of the patients. The impaired cholesterol efflux to HDL2 fraction was primarily in conjunction with the metabolic syndrome. The phospholipid composition of HDL fractions was different between the affected and the non-affected subjects. As an example, characteristic of the metabolic syndrome were elevated contents of palmitic, palmitoleic or oleic acids relative to linoleic acid in lysophosphatidylcholines and phosphatidylcholines. In conclusion, the HDL fraction is both functionally and compositionally modified in the phenotype of low HDL cholesterol level and premature CHD. Especially the cholesterol efflux capacity of the HDL2 fraction and thus its many functional properties may be impaired. There are many characteristic features in the phospholipid composition of the HDL in the phenotype which were detected in HDL2 and HDL3 fractions. / Tiivistelmä Sepelvaltimotauti on ateroskleroosin kliininen ilmenemismuoto. Se on merkittävimpiä kuolleisuuden ja sairastavuuden aiheuttajia niin Suomessa kuin maailmalla. Parhaillakin tunnetuilla hoidoilla sepelvaltimotaudille jää huomattava jäännösriski. Plasman matala HDL-kolesterolitaso (HDL, high-density lipoprotein) on yleinen lipidipoikkeavuus varhaista sepelvaltimotautia sairastavilla ja myös eräs metabolisen oireyhtymän, eli keskivartalolihavuuteen liittyvän ateroskleroosin riskitekijäkasauman, komponentti. Tässä väitöskirjassa tutkittiin matalan HDL-kolesterolitason ja varhaisen sepelvaltimotaudin fenotyyppiä kahdessa pohjoissuomalaisessa sukuaineistossa. Tavoitteena oli löytää uusia biologisia tekijöitä fenotyypin kohonneen sepelvatimotautiriskin taustalta. Ensimmäisen aineiston henkilöiden plasmasta mitattiin vasta-ainetasoja (IgG, IgM, IgA) LDL-hiukkasten (LDL, low-density lipoprotein) kokeellisia hapettuneita epitooppeja (malonidialdehydi-asetaldehydi-modioitu ja kuparilla hapetettu LDL) vastaan. Toisessa aineistossa mitattiin henkilöiden HDL-fraktioiden (kokonais-HDL, HDL2 ja HDL3) kykyä saada aikaan kolesterolin ulosvirtausta kokeellisesta THP-1 vaahtosolumallista. Lisäksi heidän HDL-fraktioidensa (HDL2, HDL3) fosfolipidikoostumus mitattiin nestekromatografi-massaspektrometri-laitteistolla. Vasta-ainetasot eivät liittyneet sepelvaltimotautiin tai HDL-kolesterolitasoon. Sen sijaan kolesterolin ulosvirtaus HDL2-fraktioon oli selkeästi alentunut sepelvaltimotaudissa, mikä liittyi potilaiden pieneen HDL-kolesterolipitoisuuteen. Alentunut ulosvirtaus HDL2-fraktioon liittyikin ensisijaisesti metaboliseen oireyhtymään. HDL-fraktioiden fosfolipidikoostumus erosi terveiden ja sairaiden välillä. Esimerkiksi metabolisessa oireryhtymässä tunnusomaista oli lysofosfatidyylikoliinien ja fosfatidyylikoliinien sisältämän palmitiinihapon, palmitoleiinihapon tai oleiinihapon suurentunut määrä suhteessa niiden sisältämän linoleenihapon määrään. Loppupäätelmä on, että matalan HDL-kolesterolitason ja varhaisen sepelvaltimotaudin fenotyypin HDL-fraktio on sekä toiminnaltaan että koostumukseltaan muuntunut. Erityisesti HDL2-fraktion kyky saada aikaan kolesterolin ulosvirtausta ja näin ollen sen monet toiminnalliset ominaisuudet voivat olla alentuneet. Fenotyypin HDL:n fosfolipidikoostumuksessa on monia tunnusomaisia piirteitä, joita havaittiin sekä HDL2- että HDL3-fraktiossa.