Structural models for the synthetic lipids were constructed and minimized using Maestro (Schrödinger LLC, New York, NY). The modeled lipids all had an extended conformation along the hydrocarbon chain. The single lipid was then translated and rotated along X and Y directions to build an initial model membrane system comprising 81 lipids. After equilibration simulations (50 ns) of this smaller membrane model, the equilibrated small membrane model was replicated along the X and Y axes to build a bigger membrane model of 729 total lipids (1458 in the case of U16). The dimensions of the bigger membrane models were in the range of 200 × 200 × 50 Å on average across the different membrane models. VMD (31) was used to make the translations and rotations of lipid in building the membrane. Membrane simulations of 100-ns duration were performed with NAMD (32), using the TIP3P explicit water model, after equilibration at temperatures of 300, 315, and 330 K, and the pressure was maintained using the Nosé-Hoover Langevin piston method at 1 atm. The temperature was maintained with the Nose-Hoover chain method, and the pressure was maintained at 1 atm. The CHARMM36 lipid force field was used with a 10 Å cutoff for van der Waals with an 8.5 Å switching distance and particle mesh Ewald for long-range electrostatics. Post-simulation trajectory analyses were carried out using R (www.R-project.org). The diffusion constants D1 and D2 were determined by fitting the mean square displacement according to the formula (33)x(t)2=4D1tr02r02+4D1t+4D2t(5)

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.