title: CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model.
abstract: Slow diffusion of the lipids in conventional all-atom simulations of membrane systems makes it difficult to sample large rearrangements of lipids and protein-lipid interactions. Recently, Tajkhorshid and co-workers developed the highly mobile membrane-mimetic (HMMM) model with accelerated lipid motion by replacing the lipid tails with small organic molecules. The HMMM model provides accelerated lipid diffusion by one to two orders of magnitude, and is particularly useful in studying membrane-protein associations. However, building an HMMM simulation system is not easy, as it requires sophisticated treatment of the lipid tails. In this study, we have developed CHARMM-GUI HMMM Builder (http://www.charmm-gui.org/input/hmmm) to provide users with ready-to-go input files for simulating HMMM membrane systems with/without proteins. Various lipid-only and protein-lipid systems are simulated to validate the qualities of the systems generated by HMMM Builder with focus on the basic properties and advantages of the HMMM model. HMMM Builder supports all lipid types available in CHARMM-GUI and also provides a module to convert back and forth between an HMMM membrane and a full-length membrane. We expect HMMM Builder to be a useful tool in studying membrane systems with enhanced lipid diffusion.
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas.
authors.forename: Yifei
authors.initials: Y
authors.lastname: Qi
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas.
authors.forename: Xi
authors.initials: X
authors.lastname: Cheng
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas.
authors.forename: Jumin
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
authors.forename: Josh V
authors.initials: JV
authors.lastname: Vermaas
authors.affiliation: Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
authors.forename: Taras V
authors.initials: TV
authors.lastname: Pogorelov
authors.affiliation: Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
authors.forename: Emad
authors.initials: E
authors.lastname: Tajkhorshid
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas.
authors.forename: Soohyung
authors.initials: S
authors.lastname: Park
authors.affiliation: Department of Chemical and Biomolecular Engineering and the Biophysics Program, The University of Maryland, College Park, Maryland.
authors.forename: Jeffery B
authors.initials: JB
authors.lastname: Klauda
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas. Electronic address: wonpil@ku.edu.
authors.forename: Wonpil
authors.initials: W
authors.lastname: Im
mesh_terms: D000595:Amino Acid Sequence; D002462:Cell Membrane / Q000737:chemistry*; D008563:Membrane Lipids / Q000737:chemistry; D008565:Membrane Proteins / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D012984:Software
chemical_list: D008563:Membrane Lipids; D008565:Membrane Proteins