Chapter title |
Simulation of Ligand Binding to Membrane Proteins
|
---|---|
Chapter number | 20 |
Book title |
Membrane Protein Structure and Function Characterization
|
Published in |
Methods in molecular biology, January 2017
|
DOI | 10.1007/978-1-4939-7151-0_20 |
Pubmed ID | |
Book ISBNs |
978-1-4939-7149-7, 978-1-4939-7151-0
|
Authors |
Samuel Murail |
Abstract |
Membrane proteins are involved in a large variety of functions. Most of these protein functions are regulated by ligand binding with diverse modes of action: agonists, partial agonists, antagonists, and allosteric modulators, potentiators and inhibitors. From the pharmacological point of view, membrane proteins are one if not the major target for drug development. However, experimental structure determination of membrane proteins in complex or in free form still represents a great challenge. Molecular dynamics (MD) simulations commonly reach the microsecond scale on membrane systems. This numerical tool is mature enough to predict and add molecular details on the different ligand-binding modes. In the present chapter, I will present the different steps to design, simulate, and analyze a MD simulation system containing a protein embedded in a membrane and surrounded by water and ligand. As an illustration, the simulation of the ligand-gated ion channel γ-aminobutyric acid type A receptor (GABAAR) surrounded by one of its allosteric potentiators, bromoform, will be presented and discussed. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 12 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 3 | 25% |
Student > Bachelor | 2 | 17% |
Unspecified | 1 | 8% |
Student > Doctoral Student | 1 | 8% |
Student > Master | 1 | 8% |
Other | 1 | 8% |
Unknown | 3 | 25% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 4 | 33% |
Chemical Engineering | 2 | 17% |
Unspecified | 1 | 8% |
Chemistry | 1 | 8% |
Unknown | 4 | 33% |