title: CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems.
abstract: Micelle Builder in CHARMM-GUI, http://www.charmm-gui.org/input/micelle , is a web-based graphical user interface to build pure/mixed micelle and protein/micelle complex systems for molecular dynamics (MD) simulation. The robustness of Micelle Builder is tested by simulating four detergent-only homogeneous micelles of DHPC (dihexanoylphosphatidylcholine), DPC (dodecylphosphocholine), TPC (tetradecylphosphocholine), and SDS (sodium dodecyl sulfate) and comparing the calculated micelle properties with experiments and previous simulations. As a representative protein/micelle model, Pf1 coat protein is modeled and simulated in DHPC micelles with three different numbers of DHPC molecules. While the number of DHPC molecules in direct contact with Pf1 protein converges during the simulation, distinct behavior and geometry of micelles lead to different protein conformations in comparison to that in bilayers. It is our hope that CHARMM-GUI Micelle Builder can be used for simulation studies of various protein/micelle systems to better understand the protein structure and dynamics in micelles as well as distribution of detergents and their dynamics around proteins.
authors.affiliation: Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, USA.
authors.forename: Xi
authors.initials: X
authors.lastname: Cheng
authors.forename: Sunhwan
authors.initials: S
authors.lastname: Jo
authors.forename: Hui Sun
authors.initials: HS
authors.lastname: Lee
authors.forename: Jeffery B
authors.initials: JB
authors.lastname: Klauda
authors.forename: Wonpil
authors.initials: W
authors.lastname: Im
mesh_terms: D036022:Capsid Proteins / Q000737:chemistry; D003196:Computer Graphics; D008823:Micelles; D056004:Molecular Dynamics Simulation; D010742:Phospholipid Ethers / Q000737:chemistry / Q000494:pharmacology; D010767:Phosphorylcholine / Q000031:analogs & derivatives / Q000737:chemistry / Q000494:pharmacology; D011487:Protein Conformation / Q000187:drug effects; D011506:Proteins / Q000737:chemistry*; D012967:Sodium Dodecyl Sulfate / Q000737:chemistry / Q000494:pharmacology; D012984:Software; D014584:User-Computer Interface
chemical_list: C052298:1,2-dihexadecyl-sn-glycero-3-phosphocholine; D036022:Capsid Proteins; D008823:Micelles; D010742:Phospholipid Ethers; D011506:Proteins; C071283:coat protein, Pseudomonas phage Pf1; D010767:Phosphorylcholine; D012967:Sodium Dodecyl Sulfate; C031166:n-tetradecylphosphorylcholine