Literature DB >> 21441592

Lipid simulations: a perspective on lipids in action.

Ilpo Vattulainen1, Tomasz Rog.   

Abstract

In this article, we provide an overview of lipid simulations, describing how a computer can be used as a laboratory for lipid research. We briefly discuss the methodology of lipid simulations followed by a number of topical applications that show the benefit of computer modeling for complementing experiments. In particular, we show examples of cases in which simulations have made predictions of novel phenomena that have later been confirmed by experimental studies. Overall, the applications discussed in this article focus on the most recent state of the art and aim to provide a perspective of where the field of lipid simulations stands at the moment.

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Year:  2011        PMID: 21441592      PMCID: PMC3062216          DOI: 10.1101/cshperspect.a004655

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  75 in total

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2.  Toroidal pores formed by antimicrobial peptides show significant disorder.

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Review 4.  Roles of bilayer material properties in function and distribution of membrane proteins.

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5.  Molecular dynamics simulations reveal fundamental role of water as factor determining affinity of binding of beta-blocker nebivolol to beta(2)-adrenergic receptor.

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Review 6.  Cellular lipidomics.

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Journal:  EMBO J       Date:  2005-09-01       Impact factor: 11.598

Review 7.  Nebivolol: a third-generation beta-adrenergic blocker.

Authors:  Angie Veverka; Donald S Nuzum; Jamie L Jolly
Journal:  Ann Pharmacother       Date:  2006-07-05       Impact factor: 3.154

8.  Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins.

Authors:  Amy Y Shih; Ilia G Denisov; James C Phillips; Stephen G Sligar; Klaus Schulten
Journal:  Biophys J       Date:  2004-11-08       Impact factor: 4.033

9.  Lateral diffusion of lipids in complex biological membranes.

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Journal:  Proc Natl Acad Sci U S A       Date:  1987-01       Impact factor: 11.205

Review 10.  Molecular dynamics simulations of membrane channels and transporters.

Authors:  Fatemeh Khalili-Araghi; James Gumbart; Po-Chao Wen; Marcos Sotomayor; Emad Tajkhorshid; Klaus Schulten
Journal:  Curr Opin Struct Biol       Date:  2009-04-01       Impact factor: 6.809

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  9 in total

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2.  Hydrocarbons Are Essential for Optimal Cell Size, Division, and Growth of Cyanobacteria.

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Review 3.  Chemical biology approaches to membrane homeostasis and function.

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Journal:  Chimia (Aarau)       Date:  2011       Impact factor: 1.509

4.  Membrane-lipid therapy in operation: the HSP co-inducer BGP-15 activates stress signal transduction pathways by remodeling plasma membrane rafts.

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Journal:  PLoS One       Date:  2011-12-12       Impact factor: 3.240

5.  Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems.

Authors:  Matthieu Chavent; Tyler Reddy; Joseph Goose; Anna Caroline E Dahl; John E Stone; Bruno Jobard; Mark S P Sansom
Journal:  Faraday Discuss       Date:  2014-06-17       Impact factor: 4.394

6.  Microsecond molecular dynamics simulations of lipid mixing.

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Journal:  Langmuir       Date:  2014-10-01       Impact factor: 3.882

7.  Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters.

Authors:  Tomasz Róg; Adam Orłowski; Alicia Llorente; Tore Skotland; Tuulia Sylvänne; Dimple Kauhanen; Kim Ekroos; Kirsten Sandvig; Ilpo Vattulainen
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8.  Lipid nanotechnology.

Authors:  Samaneh Mashaghi; Tayebeh Jadidi; Gijsje Koenderink; Alireza Mashaghi
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Review 9.  Molecular recognition of gangliosides and their potential for cancer immunotherapies.

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  9 in total

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