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Literature DB >> 34302674

Identification and Characterization of Specific Protein-Lipid Interactions Using Molecular Simulation.

Robin A Corey¹, Mark S P Sansom², Phillip J Stansfeld³.

Abstract

Interactions with lipids can dramatically shape and define the activity of membrane proteins. Here, we describe tools that allow the identification of these interactions using molecular dynamics simulation. Additionally, we provide the details of how to use different methods to probe the affinity of these interactions.

Entities: Chemical

Keywords: Free energy calculations; Lipids; Membrane proteins; Molecular dynamics; Protein–lipid interactions

Mesh：

Substances：

Year: 2021 PMID： 34302674 DOI： 10.1007/978-1-0716-1468-6_8

Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745

46 in total

1. SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics.

Authors: Leonardo Darré; Matías Rodrigo Machado; Astrid Febe Brandner; Humberto Carlos González; Sebastián Ferreira; Sergio Pantano
Journal: J Chem Theory Comput Date: 2015-02-10 Impact factor: 6.006

Identification and Characterization of Specific Protein-Lipid Interactions Using Molecular Simulation.

1. SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics.

2. The MARTINI force field: coarse grained model for biomolecular simulations.

Review 3. The complex and intriguing lives of PIP2 with ion channels and transporters.

4. The MARTINI Coarse-Grained Force Field: Extension to Proteins.

5. Protein-phospholipid interplay revealed with crystals of a calcium pump.

Review 6. Lipid rafts as a membrane-organizing principle.

7. Crystal structure of the mammalian GIRK2 K+ channel and gating regulation by G proteins, PIP2, and sodium.

8. Structural basis of PIP2 activation of the classical inward rectifier K+ channel Kir2.2.

9. PIP(2)-binding site in Kir channels: definition by multiscale biomolecular simulations.

10. Defining how multiple lipid species interact with inward rectifier potassium (Kir2) channels.

1. Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?