title: Determination of membrane-insertion free energies by molecular dynamics simulations.
abstract: The accurate prediction of membrane-insertion probability for arbitrary protein sequences is a critical challenge to identifying membrane proteins and determining their folded structures. Although algorithms based on sequence statistics have had moderate success, a complete understanding of the energetic factors that drive the insertion of membrane proteins is essential to thoroughly meeting this challenge. In the last few years, numerous attempts to define a free-energy scale for amino-acid insertion have been made, yet disagreement between most experimental and theoretical scales persists. However, for a recently resolved water-to-bilayer scale, it is found that molecular dynamics simulations that carefully mimic the conditions of the experiment can reproduce experimental free energies, even when using the same force field as previous computational studies that were cited as evidence of this disagreement. Therefore, it is suggested that experimental and simulation-based scales can both be accurate and that discrepancies stem from disparities in the microscopic processes being considered rather than methodological errors. Furthermore, these disparities make the development of a single universally applicable membrane-insertion free energy scale difficult.
authors.affiliation: Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA. gumbart@mcs.anl.gov
authors.forename: James
authors.initials: J
authors.lastname: Gumbart
authors.forename: Benoît
authors.initials: B
authors.lastname: Roux
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D002462:Cell Membrane / Q000737:chemistry / Q000378:metabolism*; D057927:Hydrophobic and Hydrophilic Interactions; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D010713:Phosphatidylcholines / Q000737:chemistry; D054466:Phospholipases A1 / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D001425:Bacterial Outer Membrane Proteins; D008565:Membrane Proteins; D010713:Phosphatidylcholines; C002448:1,2-linoleoylphosphatidylcholine; D054466:Phospholipases A1; C412876:outer membrane phospholipase A