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Pure Appl. Chem., 2013, Vol. 85, No. 1, pp. 1-13

Published online 2012-11-09

Modeling complex biological systems: From solution chemistry to membranes and channels

Benoist Laurent1, Samuel Murail1, Franck Da Silva1, Pierre-Jean Corringer2 and Marc Baaden1*

1 Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
2 Institut Pasteur, Channel-Receptors G5 Group, CNRS URA 2182, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France

Abstract: Complex biological systems are intimately linked to their environment, a very crowded and equally complex solution compartmentalized by fluid membranes. Modeling such systems remains challenging and requires a suitable representation of these solutions and their interfaces. Here, we focus on particle-based modeling at an atomistic level using molecular dynamics (MD) simulations. As an example, we discuss important steps in modeling the solution chemistry of an ion channel of the ligand-gated ion channel receptor family, a major target of many drugs including anesthetics and addiction treatments. The bacterial pentameric ligand-gated ion channel (pLGIC) called GLIC provides clues about the functional importance of solvation, in particular for mechanisms such as permeation and gating. We present some current challenges along with promising novel modeling approaches.