Split Membrane: A New Model to Accelerate All-Atom MD Simulation of Phospholipid Bilayers

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F25%3A00140544" target="_blank" >RIV/00216224:14740/25:00140544 - isvavai.cz</a>

Result on the web

<a href="https://pubs.acs.org/doi/10.1021/acs.jcim.4c01664" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jcim.4c01664</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jcim.4c01664" target="_blank" >10.1021/acs.jcim.4c01664</a>

Result language

angličtina

Original language name

Split Membrane: A New Model to Accelerate All-Atom MD Simulation of Phospholipid Bilayers

Original language description

All-atom molecular dynamics simulations are powerful tools for studying cell membranes and their interactions with proteins and other molecules. However, these processes occur on time scales determined by the diffusion rate of phospholipids, which are challenging to achieve in all-atom models. Here, we present a new all-atom model that accelerates lipid diffusion by splitting phospholipid molecules into head and tail groups. The bilayer structure is maintained by using external lateral potentials, which compensate for the lipid split. This split model enhances lateral lipid diffusion more than ten times, allowing faster and cheaper equilibration of large systems with different phospholipid types. The current model has been tested on membranes containing PSM, POPC, POPS, POPE, POPA, and cholesterol. We have also evaluated the interaction of the split model membranes with the Disheveled DEP domain and amphiphilic helix motif of the transcriptional repressor Opi1 as representative of peripheral proteins as well as the dimeric fragment of the epidermal growth factor receptor transmembrane domain and the Human A2A Adenosine of G protein-coupled receptors as representative of transmembrane proteins. The split model can predict the interaction sites of proteins and their preferred phospholipid type. Thus, the model could be used to identify lipid binding sites and equilibrate large membranes at an affordable computational cost.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10400 - Chemical sciences

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2025

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Chemical Information and Modeling

ISSN

1549-9596

e-ISSN

—

Volume of the periodical

65

Issue of the periodical within the volume

2

Country of publishing house

US - UNITED STATES

Number of pages

12

Pages from-to

845-856

UT code for WoS article

001393323200001

EID of the result in the Scopus database

2-s2.0-85214331944