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Biology

Modellazione realistica delle membrane utilizzando miscele lipidiche complesse negli studi di simulazione

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

La diversità dei lipidi di membrana nella struttura e nella composizione è un importante contributo ai processi cellulari e può essere un marcatore di malattia. Le simulazioni di dinamica molecolare ci permettono di studiare le membrane e le loro interazioni con le biomolecole a risoluzione atomistica. Qui forniamo un protocollo per costruire, eseguire e analizzare sistemi a membrana complessi.

I lipidi sono elementi costitutivi strutturali delle membrane cellulari; Le specie lipidiche variano tra gli organelli cellulari e tra gli organismi. Questa varietà si traduce in diverse proprietà meccaniche e strutturali nella membrana che hanno un impatto diretto sulle molecole e sui processi che si verificano in questa interfaccia. La composizione lipidica è dinamica e può servire a modulare i processi di segnalazione cellulare. Gli approcci computazionali sono sempre più utilizzati per prevedere le interazioni tra biomolecole e fornire informazioni molecolari agli osservabili sperimentali. La dinamica molecolare (MD) è una tecnica basata sulla meccanica statistica che prevede il movimento degli atomi in base alle forze che agiscono su di essi. Le simulazioni MD possono essere utilizzate per caratterizzare l'interazione delle biomolecole. Qui, introduciamo brevemente la tecnica, delineiamo i passaggi pratici per i principianti che sono interessati a simulare i doppi strati lipidici, dimostriamo il protocollo con un software adatto ai principianti e discutiamo le alternative, le sfide e le considerazioni importanti del processo. In particolare, sottolineiamo l'importanza dell'utilizzo di miscele lipidiche complesse per modellare una membrana cellulare di interesse per catturare gli ambienti idrofobici e meccanici appropriati nella simulazione. Discutiamo anche alcuni esempi in cui la composizione e le proprietà della membrana modulano le interazioni dei doppi strati con altre biomolecole.

I lipidi sono i principali costituenti delle membrane, che forniscono confini per le cellule e consentono la compartimentazione intracellulare 1,2,3. I lipidi sono anfifilici, con un gruppo di teste polari e due code di acidi grassi idrofobici; Questi si auto-assemblano in un doppio strato per ridurre al minimo il contatto delle catene idrofobiche con l'acqua 3,4. Varie combinazioni di gruppi di teste idrofile e code idrofobiche danno luogo a diverse classi di lipidi nelle membrane biologiche, come glicerofosfosfolipi....

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1. Costruire le coordinate del sistema

  1. Passare a CHARMM-GUI.org (C-GUI) utilizzando un browser Web. Nel menu in alto, vai a Generatore di input, quindi seleziona Generatore di membrane dalle opzioni verticali sul lato sinistro dello schermo.
  2. Per creare un bilayer, selezionare Bilayer Builder.
    NOTA: gli utenti per la prima volta devono attivare il proprio account gratuito prima di creare il primo set di coordinate.
  3. Selezio.......

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Per illustrare l'uso del protocollo e i risultati che si possono ottenere, viene discusso uno studio comparativo per modelli di membrana per il reticolo endoplasmatico (ER). I due modelli in questo studio erano (i) il modello PI, che contiene le prime quattro specie lipidiche trovate nel reticolo endoplasmatico, e (ii) il modello PI-PS, che ha aggiunto le specie lipidiche anioniche fosfatidilserina (PS). Questi modelli sono stati successivamente utilizzati in uno studio su una proteina virale e su come interagisce con la.......

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Le tecniche sperimentali possono visualizzare le biomolecole ad alta risoluzione utilizzando la microscopia crioelettronica (cryo-EM)58, le tecniche di fluorescenza e la microscopia a forza atomica (AFM)59. Tuttavia, è difficile catturare l'interazione e la dinamica delle interazioni molecolari che sono alla base dei percorsi biologici, della patogenesi della malattia e della somministrazione terapeutica a livello atomico o amminoacidico. In questo articolo, sono state dis.......

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Gli autori ringraziano Jinhui Li e Ricardo X. Ramirez per le loro traiettorie di simulazione e le discussioni durante la stesura di questo manoscritto. O.C. è stato sostenuto dalla University at Buffalo Presidential Fellowship e dal National Institute of Health's Initiative for Maximizing Student Development Training Grant 1T32GM144920-01 assegnato a 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

Modellazione realistica della membrana
Miscele lipidiche complesse
Studi di simulazione
Membrane cellulari
Specie lipidiche
Propriet meccaniche
Propriet strutturali
Composizione della membrana
Processi di segnalazione cellulare
Approcci computazionali
Interazioni biomolecolari
Dinamica molecolare
Simulazioni MD
Doppi strati lipidici
Software per principianti
Ambiente idrofobico
Ambiente meccanico
Propriet della membrana
Interazioni biomolecolari

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