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A MARTINI extension for Pseudomonas aeruginosa PAO1 lipopolysaccharide
Affiliation:1. Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences H-1117 Budapest, Magyar tudósok körútja 2, Hungary;2. Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland;1. SLOWPOKE Nuclear Reactor Facility, University of Alberta, Edmonton, AB, T6G 2G7 Canada;2. Department of Physics, University of Alberta, Edmonton, AB, T6G 2E1 Canada;1. Department of Pharmaceutical Health Care, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji 670-8524, Japan;2. Department of Pathology, Hyogo College of Medicine, 1-1 Mukogawa-cho, Nishinomiya 663-8501, Japan;3. Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan;4. Department of Anesthesiology, Hyogo College of Medicine, Nishinomiya 663-8501, Japan;1. Department of Otolaryngology, University of Arizona College of Medicine, Tucson, AZ 85724, United States;2. Department of Medicine, University of Arizona College of Medicine, Tucson, AZ 85724, United States;3. Molecular Biology and Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM 87108, United States;4. Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD 21201, United States;3. From the Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, Ohio 45237,;4. the Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, Ohio 45237,;5. the Department of Medicine and Atherosclerosis Research Unit, University of Alabama at Birmingham, Birmingham, Alabama 35294,;6. the Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Paraná, Brazil 81350-010, and
Abstract:We report a course-grained, large scale simulation of the outer membrane from Pseudomonas aeruginosa. Using the MARTINI force field approach of 4-to-1 atom mapping, we simulate an asymmetrically constructed bilayer with over 1100 rough lipopolysaccharide (LPS) and 3100 16:0-18:1-phosphatidylethanolamine. We achieve 90-fold improvement in computational efficiency on a system much larger than reasonable for all-atom simulation. We also compare a coarse-grained LPS/LPS bilayer simulation with known parameters determined from neutron diffraction.
Keywords:Lipopolysaccharide  POPE  MARTINI  Coarse grain  GROMACS  Molecular dynamics
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