Title :

Membrane-associated proteins and peptides

Author(s) :

Lensink, Marc [Auteur]

Journal title :

Methods in molecular biology (Clifton, N.J.)

Abbreviated title :

Methods Mol. Biol.

Volume number :

1215

Pages :

109-124

Publication date :

2015

ISSN :

1940-6029

English keyword(s) :

Deuterium
Solvents
Phosphatidylethanolamines
Salts
Lipid Bilayers
Protein Structure, Secondary
Peptides
1,2-Dipalmitoylphosphatidylcholine
Lipids
Membrane Protein
Molecular Dynamics Simulation

HAL domain(s) :

Chimie/Chimie théorique et/ou physique

English abstract : [en]

This chapter discusses the practical aspects of setting up molecular dynamics simulations of membrane-associated proteins and peptides, and the analysis thereof. Topology files for selected lipids are provided and selected ...
Show more >This chapter discusses the practical aspects of setting up molecular dynamics simulations of membrane-associated proteins and peptides, and the analysis thereof. Topology files for selected lipids are provided and selected analysis tools presented. These include tools for the creation of lipid bilayers of mixed lipid content (DOPE) and easy extraction of lipid coordinates (g_zcoor, g_xycoor), the calculation of helical axes (g_helixaxis) and aromatic order parameters (g_arom), the determination of peptide- or protein-interacting lipids (g_under), and the investigation of lipid-specific interactions through the calculation of lipid-bridged residue-residue contacts (g_prolip).Show less >

Language :

Anglais

Administrative institution(s) :

CNRS
Université de Lille

Collections :

• Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576

Research team(s) :

Computational Molecular Systems Biology

Submission date :

2020-02-12T15:11:24Z