Modulation of Membrane Lipid Receptors Explored via Multiscale Computer Simulations

Sami Rissanen

Modulation of Membrane Lipid Receptors Explored via Multiscale Computer Simulations

Sami Rissanen

Tutkimustuotos: Väitöskirja › Collection of Articles

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Abstrakti

Tässä työssä käsitellään GM1 ja fosfatidyyli-inositoli-4,5-bisfosfaatti (PI(4,5)P₂) lipidireseptoreita. GM1 on gangliosidi, joka esiintyy solukalvon ulommaisella puolella ja vastaanottaa solun ulkopuolelta tulevia signaaleja. PI(4,5)P₂ on tärkeä fosfatidyyliinositoli ja esiintyy solukalvon sytosolisella osalla. Soluille elintärkeisiin toimintoihin osallistumisen takia lipidireseptoreiden vuorovaikutukset muiden lipidien sekä proteiinien kanssa ovat olleet monien tutkimusten kohteena. Suuresta huomiosta ja panostuksesta huolimatta reseptoreiden toiminnallisista yksityiskohdista tiedetään kuitenkin edelleen verrattain vähän. Tämä johtuu nykyisten kokeellisten menetelmien haasteista tutkia pieniä nanoskaaloja sekä niiden nopeaa dynamiikkaa. Tässä työssä käytetään atomistisia sekä karkeistettuja molekyylidynamiikkasimulaatioita kyseisten lipidireseptoreiden rakenteellisten ja dynaamisten ominaisuuksien selvittämiseen.

Väitöstyön ensimmäisessä osassa tutkitaan PI(4,5)P₂-reseptorin vuorovaikutuksia integriinin kanssa. Simulaatiot paljastivat uuden mekanismin, jolla PI(4,5)P₂ yhdessä talin-proteiinin kanssa voi häiritä integriinin kalvossa olevan osan vakautta. Tulokset tarjoavat uuden mahdollisen selityksen sille, miten integriinien aktivoitumista voidaan säädellä solukalvoissa.

Jälkimmäinen osa tästä väitöstyöstä keskittyy lipidireseptorien toimintamekanismien säätelyyn. Ensiksi tutkitaan koleratoksiinin sitoutumista sekä sen luonnolliseen GM1reseptoriin että sen ﬂuoresoivaksi muokattuun GM1-vastinpariin. Tulokset osoittavat selkeän eron proteiinin sitoutumisessa näiden reseptorien välillä, korostaen yleisesti käytettyjen ﬂuoresoivien aineiden merkitystä ja vaikutusta tutkittaviin kohteisiin. Seuraavaksi selvitetään sytosolissa olevan kalsiumin vaikutus PI(4,5)P₂-reseptoriin ja sen aiheuttamiin muutoksiin proteiinin sitoutumisessa. Tulokset yhdistetään myös solusignalointireittiin kokeellisen yhteistyön kautta. Viimeiseksi tutkitaan perusperiaatetta siitä, miten PI(4,5)P₂-reseptori sitoo tiettyjä proteiineja pelkästään solukalvossa, mutta ei muissa solun soluelimissä. Tulokset havainnollistavat, että solukalvon kolesteroli parantaa proteiinien sitoutumista PI(4,5)P₂-reseptoriin. Tämä voi selittää soluelinten identiteettiä, kun jo ennestään tiedetään, että kolesterolikonsentraatio muuttuu eri solukalvoissa ja on korkeimmillaan juuri plasmakalvossa.

Kokonaisuutena tämä työ tarjoaa uusia näkemyksiä lipidireseptorien toiminnallisuudesta sekä lipidi–proteiini -vuorovaikutusten säätelystä. Työ korostaa laskennallisten ja kokeellisten tutkimusten yhteistyön tärkeyttä ja hyödyllisyyttä.

Alkuperäiskieli	Englanti
Kustantaja	Tampere University of Technology
Sivumäärä	92
ISBN (elektroninen)	978-952-15-4301-2
ISBN (painettu)	978-952-15-4272-5
Tila	Julkaistu - 13 jouluk. 2018
OKM-julkaisutyyppi	G5 Artikkeliväitöskirja

Julkaisusarja

Nimi	Tampere University of Technology. Publication
Vuosikerta	1606
ISSN (painettu)	1459-2045

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abstract = "This work focuses on two lipid receptors known as GM1 and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). GM1 is a ganglioside present in the outer plasma membrane, sensing signals from the outside of the cell, while PI(4,5)P2 is an important phosphoinositide found in the inner leaﬂet of the plasma membrane. Due to their vital role in cellular life, studies of the lipid–lipid and lipid–protein interactions of these receptors have become an attractive venture for researchers. Nevertheless, despite a signiﬁcant amount of work, the molecular details of these interactions have remained largely unknown due to the limited temporal and spatial resolution of the current experimental methods. Here we overcome this problem by using atomistic and coarse-grained molecular dynamics simulations applied to explore the structural and dynamical properties of these lipid receptors in various membranes.In the ﬁrst part of this Thesis, the functional properties of PI(4,5)P2 were studied through lipid–protein interactions between PI(4,5)P2, talin, and integrin. The simulations revealed a new means on how PI(4,5)P2 together with talin interferes with the stability of the integrin transmembrane domains, suggesting a new mechanism for the ﬁrst steps of integrin activation.The second part of this Thesis focuses on various mechanisms that can alter and regulate lipid receptor binding properties. First, the binding of cholera toxin to GM1 and the ﬂuorescent analog of the receptor was examined. A clear diﬀerence in the behavior between the native and the labeled GM1 was observed. These results highlight the importance of artifacts that ﬂuorescent labeling can cause. Second, the intracellular calcium was shown to aﬀect the PI(4,5)P2 headgroup tilting and the related ligand binding. Importantly, these results were directly linked to cell signaling events through experimental ﬁndings observed by our collaborators. Finally, the fundamental question as to how the PI(4,5)P2 receptor is recognized only in the plasma membrane but not in the other cell compartments was explored. Enhanced ligand binding to cholesterol-rich PI(4,5)P2 membranes was found, suggesting that the steep cholesterol gradient along the secretory pathway in a cell may be a part of the machinery coordinating the speciﬁc cell organelle recognition.Altogether, the Thesis provides novel insight on the function of lipid receptors, modulation of lipid–protein interactions, and highlights the added value gained by bridging scientiﬁc computing and novel computing tools with experimental science.",

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AB - This work focuses on two lipid receptors known as GM1 and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). GM1 is a ganglioside present in the outer plasma membrane, sensing signals from the outside of the cell, while PI(4,5)P2 is an important phosphoinositide found in the inner leaﬂet of the plasma membrane. Due to their vital role in cellular life, studies of the lipid–lipid and lipid–protein interactions of these receptors have become an attractive venture for researchers. Nevertheless, despite a signiﬁcant amount of work, the molecular details of these interactions have remained largely unknown due to the limited temporal and spatial resolution of the current experimental methods. Here we overcome this problem by using atomistic and coarse-grained molecular dynamics simulations applied to explore the structural and dynamical properties of these lipid receptors in various membranes.In the ﬁrst part of this Thesis, the functional properties of PI(4,5)P2 were studied through lipid–protein interactions between PI(4,5)P2, talin, and integrin. The simulations revealed a new means on how PI(4,5)P2 together with talin interferes with the stability of the integrin transmembrane domains, suggesting a new mechanism for the ﬁrst steps of integrin activation.The second part of this Thesis focuses on various mechanisms that can alter and regulate lipid receptor binding properties. First, the binding of cholera toxin to GM1 and the ﬂuorescent analog of the receptor was examined. A clear diﬀerence in the behavior between the native and the labeled GM1 was observed. These results highlight the importance of artifacts that ﬂuorescent labeling can cause. Second, the intracellular calcium was shown to aﬀect the PI(4,5)P2 headgroup tilting and the related ligand binding. Importantly, these results were directly linked to cell signaling events through experimental ﬁndings observed by our collaborators. Finally, the fundamental question as to how the PI(4,5)P2 receptor is recognized only in the plasma membrane but not in the other cell compartments was explored. Enhanced ligand binding to cholesterol-rich PI(4,5)P2 membranes was found, suggesting that the steep cholesterol gradient along the secretory pathway in a cell may be a part of the machinery coordinating the speciﬁc cell organelle recognition.Altogether, the Thesis provides novel insight on the function of lipid receptors, modulation of lipid–protein interactions, and highlights the added value gained by bridging scientiﬁc computing and novel computing tools with experimental science.

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BT - Modulation of Membrane Lipid Receptors Explored via Multiscale Computer Simulations

PB - Tampere University of Technology

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Modulation of Membrane Lipid Receptors Explored via Multiscale Computer Simulations

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