Study of structural dynamics of nuclear receptor PPARγ with molecular dynamics simulations

Cernatič, Filip (author), Stote, Roland (mentor), Podlipnik, Črtomir (co-mentor)

PPARγ is a nuclear receptor protein that has a central role in promoting adipocyte growth and differentiation, as well as regulating serum glucose and triglyceride levels. Under normal physiological conditions, PPARγ is a target of several post-translational modifications (PTMs) that modulate its transcriptional activity. One particular PTM, phosphorylation of Ser245 in the ligand-binding domain (LBD) by cyclin-dependent kinase 5 (CDK5) leads to down-regulation of specific genes that promote insulin sensitivity, increasing the risk of type 2 diabetes and cardiovascular diseases. Earlier studies have shown that some PPARγ ligands can lead to the inhibition of Ser245 phosphorylation by CDK5 and restore the basal gene expression of PPARγ and increase insulin sensitivity. The mechanism of this inhibition from the molecular point of view is not completely understood. While it has been previously suggested that ligand binding leads to the establishment of a series of interactions that effectively prevent the formation of PPARγ-CDK5 interaction surface, to date, there are no experimental structures to support this hypothesis. To that end, we used molecular dynamics simulations to investigate the effects of different ligands on the structure and dynamics of this region of the protein. Using both classical and accelerated dynamics approaches, we studied PPARγ-ligand complexes containing ligands with three different activation profiles, the full agonist rosiglitazone, partial agonist MRL24 and a non-agonist decanoic acid, that resembles an endogenous PPARγ ligand. Our observations show that the binding of a ligand to the active site of PPARγ correlates well with the global stability of PPARγ LBD, especially in the case of rosiglitazone, effectively restricting the dynamics and conformational space of residues, encompassing the PPARγ-CDK5 interaction surface. Further research is required to discern the difference between ligands of distinct inhibitory and agonistic profiles on the dynamical and conformational properties of PPARγ.

• Language: English
• Keywords: nuclear receptor, PPARγ, CDK5, phosphorylation, molecular dynamics
• Work type: Master's thesis/paper
• Typology: 2.09 - Master's Thesis
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Year: 2020
• PID: 20.500.12556/RUL-124095
• COBISS.SI-ID: 52092675
• Publication date in RUL: 29.12.2020

Secondary language

• Language: Slovenian
• Title: Študija strukturne dinamike jedrnega receptorja PPARγ s simulacijami molekulske dinamike

Abstract

PPARγ je jedrni receptor, ki ima osrednjo vlogo pri promociji rasti in diferenciacije adipocitov ter regulaciji nivoja glukoze in trigliceridov v krvi. Pri normalnih fizioloških pogojih je PPARγ tarča številnih post-translacijskih modifikacij, ki uravnavajo transkripcijsko aktivnost tega receptorja. Postranslacijska modifikacija PPARγ s strani od ciklina odvisne kinaze 5 (CDK5) vodi v supresijo specifičnih genov za povečevanje inzulinske občutljivosti, kar vodi k povečanemu tveganju za pojav sladkorne bolezni tipa 2 in srčno-žilnih obolenj. Predhodne študije so pokazale, da inhibicija fosforilacije PPARγ s strani CDK5, z vezavo liganda v aktivno mesto PPARγ povrne bazalni nivo transkripcije in ponovno poveča inzulinsko občutljivost posameznika. Mehanizem inhibicije na molekulski ravni ni popolnima razjasnjen. Čeprav se domneva, da se z vezavo liganda v aktivno mesto PPARγ vzpostavijo kritične interakcije med ligandom in proteinom, ki preprečijo molekulsko prepoznavanje CDK5, do sedaj še ni bilo nobenih eksperimentalnih izsledkov, ki bi potrjevale to hipotezo. V ta namen smo s simulacijami molekulske dinamike preučili vpliv različnih ligandov na strukturo in dinamiko interakcijske površine PPARγ za interakcijo s CDK5. S pomočjo metod klasične in pospešene molekulske dinamike smo podrobneje preučili komplekse PPARγ z ligandi treh aktivacijskih profilov, polnim agonistom rosiglitazone, delnim agonistom MRL24 in neagonistom dekanojsko kislino iz skupine srednjeverižnih maščobnih kislin. Naša opažanja so, da vezava liganda v aktivno mesto PPARγ dobro korelira z globalno stabilnostjo ligand-vezavne domene PPARγ. Nadaljnje raziskave bi bile potrebne za razločevanje razlik med ligandi z različnimi inhibitornimi in agonističnimi lastnostmi pri njihoven vplivu na dinamiko in konformacijske lastnosti PPARγ.

• Keywords: jedrni receptor, PPARγ, CDK5, fosforilacija, molekulska dinamika