Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 40, Issue 18, Pages 1727-1734Publisher
WILEY
DOI: 10.1002/jcc.25823
Keywords
outer membrane; gram-negative bacteria; lipopolysaccharide; beta-Barrel; molecular dynamics
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Funding
- National & Kapodistrian University of Athens
- Greek Research & Technology Network (GRNET) in the National HPC facility-ARIS [PR004006- BioMemPro-MD]
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Outer membranes are a crucial component of Gram-negative bacteria, containing standard lipids in their inner leaflet, lipopolysaccharides (LPSs) in their outer leaflet, and transmembrane beta-barrels known as outer membrane proteins (OMPs). OMPs regulate functions such as substrate transport and cell movement, while LPSs act as a protective barrier for bacteria and can cause toxic reactions in humans. However, the experimental study of outer membranes is challenging. Molecular dynamics simulations are often used for the computational study of membrane systems, but the preparation of complex, LPS-rich outer membranes is not straightforward. The Gram-Negative Outer Membrane Modeler (GNOMM) is an automated pipeline for preparing simulation systems of OMPs embedded in LPS-containing membranes in four different force fields. Given the physiological and clinical importance of outer membranes and their components, GNOMM can be a useful tool in the study of their structure, function, and implications in diseases. GNOMM is available at . (c) 2019 Wiley Periodicals, Inc.
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