Membranes

From Biowerkzeug Wiki

Simulations of proteins must also represent the environment faithfully (simulations in vacuum are not appropriate in most cases and really date back to the days when computer resources were severely limited). The environment of a protein consists of the solvent and, if it's a membrane protein, of the lipid bilayer. Here we discuss methods to represent the lipid membrane.

Contents 1 Explicit lipids 1.1 All atom 1.2 United atom 2 Implicit membrane 2.1 Dielectric slab 2.2 Statistical potential-based membrane 3 References

Explicit lipids

Force-field parameters for lipids are often not distributed with the standard force field files but can be found on the lipidbook site.

All atom

All atom representations include heavy atoms and all hydrogens. See united atom for the alternative.

United atom

A united atom representation combines carbons and aliphatic hydrogens into unified particles.

Implicit membrane

Dielectric slab

Statistical potential-based membrane

The membrane is parametrized based on the distribution of amino acids along the bilayer normal [1].

References

1. Ulmschneider MB, Sansom MS, and Di Nola A. Properties of integral membrane protein structures: derivation of an implicit membrane potential. Proteins 2005 May 1; 59(2) 252-65. doi:10.1002/prot.20334 pmid:15723347. PubMed HubMed [Ulmschneider2005]