Modeling Protein-Lipid Interactions: Recent Advances

Monique Laberge, István P. Sugár, Judit Fidy

Research output: Contribution to journalArticlepeer-review

Abstract

The lipid bilayer is the basic component of biological membranes. It functions as a relatively impermeable barrier for most water-soluble molecules. A large amount of proteins are intrinsic to the membrane or partially bound and mediate transport of specific molecules or act as receptors. The molecular modeling of lipid bilayers and proteins has now truly come of age with the widespread availability of parallel processing and advances in modeling methodologies. This chapter will discuss recent advances in specifically modeling protein-lipid interactions focusing on two computational approaches: Molecular Dynamics (MD) and Monte Carlo (MC) simulation. MD is a choice method because the protein and lipid atoms are represented explicitly as well as solvation water and the whole system is followed in time, thus providing insights on both spatial organization and temporal dynamics. Even though MC cannot provide time-dependent quantities, it represents a powerful method for sampling conformations and locations of a single peptide and also for simulating lateral diffusion of membrane lipids and proteins as well as the coupling of these distributions.

Original languageEnglish
Pages (from-to)187-235
Number of pages49
JournalAdvances in Planar Lipid Bilayers and Liposomes
Volume2
Issue numberC
DOIs
StatePublished - 2005

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