Literature DB >> 20438090

Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field.

Wataru Shinoda1, Russell DeVane, Michael L Klein.   

Abstract

A new coarse-grained (CG) intermolecular force field is presented for a series of zwitterionic lipids. The model is an extension of our previous work on nonionic surfactants and is designed to reproduce experimental surface/interfacial properties as well as distribution functions from all-atom molecular dynamics (MD) simulations. Using simple functional forms, the force field parameters are optimized for multiple lipid molecules, simultaneously. The resulting CG lipid bilayers have reasonable molecular areas, chain order parameters, and elastic properties. The computed surface pressure vs area (pi-A) curve for a dipalmitoyl phosphatidylcholine (DPPC) monolayer demonstrates a significant improvement over the previous CG models. The DPPC monolayer has a longer persistence length than a polyethyleneglycol (PEG) lipid monolayer, exhibiting a long-lived curved monolayer surface under negative tension. The bud ejected from an oversaturated DPPC monolayer has a large bicelle-like structure, which is different from the micellar bud formed from an oversaturated PEG lipid monolayer. We have successfully observed vesicle formation during CG-MD simulations, starting from an aggregate of dimyristoyl phosphatidylcholine (DMPC) molecules. Depending on the aggregate size, the lipid assembly spontaneously transforms into a closed vesicle or a bicelle. None of the various intermediate structures between these extremes seem to be stable. An attempt to observe fusion of two vesicles through the application of an external adhesion force was not successful. The present CG force field also supports stable multilamellar DMPC vesicles.

Entities:  

Mesh:

Substances:

Year:  2010        PMID: 20438090      PMCID: PMC2876730          DOI: 10.1021/jp9107206

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  42 in total

1.  Rigid-body dynamics in the isothermal-isobaric ensemble: a test on the accuracy and computational efficiency.

Authors:  Wataru Shinoda; Masuhiro Mikami
Journal:  J Comput Chem       Date:  2003-06       Impact factor: 3.376

2.  Entropy-driven tension and bending elasticity in condensed-fluid membranes.

Authors: 
Journal:  Phys Rev Lett       Date:  1990-04-23       Impact factor: 9.161

3.  A consistent model for thermal fluctuations and protein-induced deformations in lipid bilayers.

Authors:  Grace Brannigan; Frank L H Brown
Journal:  Biophys J       Date:  2005-12-02       Impact factor: 4.033

4.  A detailed look at vesicle fusion.

Authors:  A F Smeijers; A J Markvoort; K Pieterse; P A J Hilbers
Journal:  J Phys Chem B       Date:  2006-07-06       Impact factor: 2.991

5.  An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.

Authors:  Jeffery B Klauda; Bernard R Brooks; Alexander D MacKerell; Richard M Venable; Richard W Pastor
Journal:  J Phys Chem B       Date:  2005-03-24       Impact factor: 2.991

6.  A single bicontinuous cubic phase induced by fusion peptides.

Authors:  Marc Fuhrmans; Volker Knecht; Siewert J Marrink
Journal:  J Am Chem Soc       Date:  2009-07-08       Impact factor: 15.419

7.  Multiscale modeling of lipids and lipid bilayers.

Authors:  Alexander P Lyubartsev
Journal:  Eur Biophys J       Date:  2005-08-31       Impact factor: 1.733

8.  Phase behavior of model lipid bilayers.

Authors:  Marieke Kranenburg; Berend Smit
Journal:  J Phys Chem B       Date:  2005-04-14       Impact factor: 2.991

9.  Effect of chain length and unsaturation on elasticity of lipid bilayers.

Authors:  W Rawicz; K C Olbrich; T McIntosh; D Needham; E Evans
Journal:  Biophys J       Date:  2000-07       Impact factor: 4.033

10.  Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles.

Authors:  Siewert J Marrink; Alan E Mark
Journal:  J Am Chem Soc       Date:  2003-12-10       Impact factor: 15.419

View more
  41 in total

1.  Interdigitation between Triglycerides and Lipids Modulates Surface Properties of Lipid Droplets.

Authors:  Amélie Bacle; Romain Gautier; Catherine L Jackson; Patrick F J Fuchs; Stefano Vanni
Journal:  Biophys J       Date:  2017-04-11       Impact factor: 4.033

2.  The cellular membrane as a mediator for small molecule interaction with membrane proteins.

Authors:  Christopher G Mayne; Mark J Arcario; Paween Mahinthichaichan; Javier L Baylon; Josh V Vermaas; Latifeh Navidpour; Po-Chao Wen; Sundarapandian Thangapandian; Emad Tajkhorshid
Journal:  Biochim Biophys Acta       Date:  2016-05-06

3.  Janus dendrimersomes coassembled from fluorinated, hydrogenated, and hybrid Janus dendrimers as models for cell fusion and fission.

Authors:  Qi Xiao; Samuel E Sherman; Samantha E Wilner; Xuhao Zhou; Cody Dazen; Tobias Baumgart; Ellen H Reed; Daniel A Hammer; Wataru Shinoda; Michael L Klein; Virgil Percec
Journal:  Proc Natl Acad Sci U S A       Date:  2017-08-07       Impact factor: 11.205

4.  Prediction of self-assemblies of sodium dodecyl sulfate and fragrance additives using coarse-grained force fields.

Authors:  Chunwei Yang; Zhe Shen; Liang Wu; Haiqiu Tang; Lifeng Zhao; FengLei Cao; Huai Sun
Journal:  J Mol Model       Date:  2017-06-22       Impact factor: 1.810

5.  Energetics of liposomes encapsulating silica nanoparticles.

Authors:  Duangkamon Baowan; Henrike Peuschel; Annette Kraegeloh; Volkhard Helms
Journal:  J Mol Model       Date:  2013-02-24       Impact factor: 1.810

6.  Coarse-grained model for PEGylated lipids: effect of PEGylation on the size and shape of self-assembled structures.

Authors:  Hwankyu Lee; Richard W Pastor
Journal:  J Phys Chem B       Date:  2011-05-27       Impact factor: 2.991

7.  Computer simulations of protein-membrane systems.

Authors:  Jennifer Loschwitz; Olujide O Olubiyi; Jochen S Hub; Birgit Strodel; Chetan S Poojari
Journal:  Prog Mol Biol Transl Sci       Date:  2020-02-26       Impact factor: 3.622

8.  Coexistence of Lipid Phases Stabilizes Interstitial Water in the Outer Layer of Mammalian Skin.

Authors:  Christopher M MacDermaid; Kyle Wm Hall; Russell H DeVane; Michael L Klein; Giacomo Fiorin
Journal:  Biophys J       Date:  2020-02-12       Impact factor: 4.033

9.  Molecular modeling to predict peptide accessibility for peptide-functionalized hydrogels.

Authors:  Xianfeng Li; Jia Jia; Ying Mei; Robert A Latour
Journal:  Biointerphases       Date:  2017-08-18       Impact factor: 2.456

10.  Coarse-Grained Molecular Models of Water: A Review.

Authors:  Kevin R Hadley; Clare McCabe
Journal:  Mol Simul       Date:  2012-07-04       Impact factor: 2.178

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.