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Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions
KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.ORCID-id: 0000-0002-7498-7763
KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.ORCID-id: 0000-0002-2734-2794
2013 (Engelska)Ingår i: Chemistry and Physics of Lipids, ISSN 0009-3084, E-ISSN 1873-2941, Vol. 169, s. 106-112Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Cellular lipid membranes are spatially inhomogeneous soft materials. Materials properties such as pressure and surface tension thus show important microscopic-scale variation that is critical to many biological functions. We present a means to calculate pressure and surface tension in a 3D-resolved manner within molecular-dynamics simulations and show how such measurements can yield important insight. We also present the first corrections to local virial and pressure fields to account for the constraints typically used in lipid simulations that otherwise cause problems in highly oriented systems such as bilayers. Based on simulations of an asymmetric bacterial ion channel in a POPC bilayer, we demonstrate how 3D-resolved pressure can probe for both short-range and long-range effects from the protein on the membrane environment. We also show how surface tension is a sensitive metric for inter-leaflet equilibrium and can be used to detect even subtle imbalances between bilayer leaflets in a membrane-protein simulation. Since surface tension is known to modulate the function of many proteins, this effect is an important consideration for predictions of ion channel function. We outline a strategy by which our local pressure measurements, which we make available within a version of the GROMACS simulation package, may be used to design optimally equilibrated membrane-protein simulations.

Ort, förlag, år, upplaga, sidor
2013. Vol. 169, s. 106-112
Nyckelord [en]
Lipid bilayer, Molecular dynamics, Lateral pressure, Ion channel
Nationell ämneskategori
Biokemi och molekylärbiologi
Identifikatorer
URN: urn:nbn:se:kth:diva-124471DOI: 10.1016/j.chemphyslip.2013.01.001ISI: 000319310800012PubMedID: 23318532Scopus ID: 2-s2.0-84876413376OAI: oai:DiVA.org:kth-124471DiVA, id: diva2:636001
Forskningsfinansiär
EU, Europeiska forskningsrådetVetenskapsrådet
Anmärkning

QC 20130708

Tillgänglig från: 2013-07-08 Skapad: 2013-07-05 Senast uppdaterad: 2020-03-09Bibliografiskt granskad

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Hess, BerkLindahl, Erik

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Hess, BerkLindahl, Erik
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BeräkningsbiofysikScience for Life Laboratory, SciLifeLab
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Chemistry and Physics of Lipids
Biokemi och molekylärbiologi

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