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Abstract

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Biology

Realistisk membranmodellering ved hjælp af komplekse lipidblandinger i simuleringsstudier

Published: September 1st, 2023

DOI:

10.3791/65712

1Department of Chemical and Biological Engineering, State University of New York at Buffalo, 2Department of Mathematics, State University of New York at Buffalo

Membranlipiddiversitet i struktur og sammensætning er en vigtig bidragyder til cellulære processer og kan være en markør for sygdom. Molekylære dynamiksimuleringer giver os mulighed for at studere membraner og deres interaktioner med biomolekyler ved atomistisk opløsning. Her leverer vi en protokol til at bygge, køre og analysere komplekse membransystemer.

Lipider er strukturelle byggesten i cellemembraner; Lipidarter varierer på tværs af celleorganeller og på tværs af organismer. Denne variation resulterer i forskellige mekaniske og strukturelle egenskaber i membranen, der direkte påvirker molekylerne og processerne, der forekommer ved denne grænseflade. Lipidsammensætning er dynamisk og kan tjene til at modulere cellesignaleringsprocesser. Computational tilgange bruges i stigende grad til at forudsige interaktioner mellem biomolekyler og give molekylær indsigt i eksperimentelle observerbare. Molekylær dynamik (MD) er en teknik baseret på statistisk mekanik, der forudsiger bevægelsen af atomer baseret på de kræfter, der virker på dem. MD-simuleringer kan bruges til at karakterisere interaktionen mellem biomolekyler. Her introducerer vi kort teknikken, skitserer praktiske trin for begyndere, der er interesseret i at simulere lipiddobbeltlag, demonstrerer protokollen med begyndervenlig software og diskuterer alternativer, udfordringer og vigtige overvejelser om processen. Vi understreger især relevansen af at bruge komplekse lipidblandinger til at modellere en cellemembran af interesse for at fange de passende hydrofobe og mekaniske miljøer i simulering. Vi diskuterer også nogle eksempler, hvor membransammensætning og egenskaber modulerer interaktionerne mellem dobbeltlag og andre biomolekyler.

Lipider er vigtige bestanddele af membraner, som giver grænser for celler og muliggør intracellulær ruminddeling 1,2,3. Lipider er amfifile, med en polær hovedgruppe og to hydrofobe fedtsyrehaler; Disse samles selv i et dobbeltlag for at minimere kontakt mellem de hydrofobe kæder og vand 3,4. Forskellige kombinationer af hydrofile hovedgrupper og hydrofobe haler resulterer i forskellige klasser af lipider i biologiske membraner, såsom glycerophospholipider, sfingolipider og steroler (figur 1)

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1. Opbygning af systemkoordinater

  1. Naviger til CHARMM-GUI.org (C-GUI) ved hjælp af en webbrowser. I topmenuen skal du navigere til Input Generator og derefter vælge Membrane Builder fra de lodrette indstillinger i venstre side af skærmen.
  2. Hvis du vil bygge et dobbeltlag, skal du vælge Dobbeltlagsgenerator.
    BEMÆRK: Første gang brugere skal aktivere deres gratis konto, før de bygger deres første sæt koordinater.
  3. Væ.......

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For at illustrere brugen af protokollen og de resultater, der kan opnås, diskuteres en sammenligningsundersøgelse for membranmodeller for det endoplasmatiske retikulum (ER). De to modeller i denne undersøgelse var (i) PI-modellen, som indeholder de fire øverste lipidarter, der findes i ER, og (ii) PI-PS-modellen, som tilføjede de anioniske phosphatidylserin (PS) lipidarter. Disse modeller blev senere brugt i en undersøgelse af et viralt protein, og hvordan det interagerer med membranen, interessen for PS er blevet .......

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Eksperimentelle teknikker kan visualisere biomolekyler ved høj opløsning ved hjælp af kryo-elektronmikroskopi (cryo-EM)58, fluorescensteknikker og atomkraftmikroskopi (AFM)59. Det er imidlertid udfordrende at fange samspillet og dynamikken i molekylære interaktioner, der ligger til grund for biologiske veje, sygdomspatogenese og terapeutisk levering på atom- eller aminosyreniveau. Her blev MD-simuleringers muligheder for at studere lipidmembraner og de vigtigste trin t.......

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Forfatterne takker Jinhui Li og Ricardo X. Ramirez for deres simuleringsbaner og diskussioner under skrivningen af dette manuskript. O.C. blev støttet af University at Buffalo Presidential Fellowship og National Institute of Health's Initiative for Maximizing Student Development Training Grant 1T32GM144920-01 tildelt Margarita L. Dubocovich (PI).

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NameCompanyCatalog NumberComments
Anaconda3Anaconda Inc (Python & related libraries)N/A
CHARMM-GUI.orgIm lab, Lehigh UniversityN/A
GROMACSGROMACS development teamN/A
Linux HPC ClusterUB CCRN/A
MATLABMathWorksN/A
VMDTheoretical and Computational Biophysics GroupN/A

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Tags

Realistisk membranmodellering
Komplekse lipidblandinger
Simuleringsunders gelser
Cellemembraner
Lipidarter
Mekaniske egenskaber
Strukturelle egenskaber
Membransammens tning
Cellesignaleringsprocesser
Beregningsmetoder
Biomolekyl re interaktioner
Molekyl r dynamik
MD simuleringer
Lipiddobbeltlag
Begyndervenlig software
Hydrofob milj
Mekanisk milj
Membranegenskaber
Biomolekyleinteraktioner

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