Abstract

Computer simulation studies of a variety of lipid assemblies with and without protein are proposed. Detailed potential models and high quality simulation accounting for quantum effects are included. The protein-lipid systems chosen are under current experimental investigation at University of Pennsylvania by Blasie, Opella, Degrado, and Lear. A focus is on simulating ion channels in realistic lipid bilayers.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM040712-13
Application #
6180098
Study Section
Biophysical Chemistry Study Section (BBCB)
Program Officer
Chin, Jean
Project Start
1988-07-01
Project End
2003-06-30
Budget Start
2000-07-01
Budget End
2001-06-30
Support Year
13
Fiscal Year
2000
Total Cost
$271,254
Indirect Cost

  Institution

Name
University of Pennsylvania
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
042250712
City
Philadelphia
State
PA
Country
United States
Zip Code
19104

  Publications

Donald, Jason E; Zhang, Yao; Fiorin, Giacomo et al. (2011) Transmembrane orientation and possible role of the fusogenic peptide from parainfluenza virus 5 (PIV5) in promoting fusion. Proc Natl Acad Sci U S A 108:3958-63
Delemotte, Lucie; Treptow, Werner; Klein, Michael L et al. (2010) Effect of sensor domain mutations on the properties of voltage-gated ion channels: molecular dynamics studies of the potassium channel Kv1.2. Biophys J 99:L72-4
Shinoda, Wataru; DeVane, Russell; Klein, Michael L (2010) Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field. J Phys Chem B 114:6836-49
Pantano, Diego A; Klein, Michael L (2009) Characterization of membrane-protein interactions for the leucine transporter from Aquifex aeolicus by molecular dynamics calculations. J Phys Chem B 113:13715-22
Hénin, Jérôme; Shinoda, Wataru; Klein, Michael L (2009) Models for phosphatidylglycerol lipids put to a structural test. J Phys Chem B 113:6958-63
Devane, Russell; Shinoda, Wataru; Moore, Preston B et al. (2009) A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids. J Chem Theory Comput 5:2115-2124
Treptow, Werner; Tarek, Mounir; Klein, Michael L (2009) Initial response of the potassium channel voltage sensor to a transmembrane potential. J Am Chem Soc 131:2107-9
Khurana, Ekta; DeVane, Russell H; Kohlmeyer, Axel et al. (2008) Probing peptide nanotube self-assembly at a liquid-liquid interface with coarse-grained molecular dynamics. Nano Lett 8:3626-30
Klein, Michael L; Shinoda, Wataru (2008) Large-scale molecular dynamics simulations of self-assembling systems. Science 321:798-800
Domene, Carmen; Klein, Michael L; Branduardi, Davide et al. (2008) Conformational changes and gating at the selectivity filter of potassium channels. J Am Chem Soc 130:9474-80

Showing the most recent 10 out of 31 publications