tag:blogger.com,1999:blog-1283194685237019772.post7653337416967304281..comments2024-03-26T17:11:28.045+02:00Comments on The NMRlipids Project: NMRlipids III: Quantifying intermolecular interactions in binary lipid mixturesmarkus.http://www.blogger.com/profile/05973383391755193687noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-1283194685237019772.post-65287343016654971762020-03-12T15:48:05.835+02:002020-03-12T15:48:05.835+02:00Since I extended the Slipids, MacRog, and CHARMM36...Since I extended the Slipids, MacRog, and CHARMM36 POPC + cholesterol simulations to 500 ns [1-5], I decided to calculate the diffusion coefficients of POPC from them. They have also been experimentally measured at 313 K using NMR [6], and thus could perhaps fit in this manuscript. I plotted the data here: <br /><br />https://www.dropbox.com/s/5y7wv6osbeizuac/diffusion_popc_chol.pdf?dl=0<br /><br />It seems that C36 and Slipids capture the effects of cholesterol, but MacRog does not. I'd be happy to extract the values for Berger and Lipid14 as well, but ~500 ns simulations are required. <br /><br />There is an obvious problem though, as the hydrodynamic correction [7] should be included. This is tedious to estimate, as each model with each cholesterol concentration would have to be simulated for long enough times (~500 ns) at multiple system sizes. The correction is added (not multiplied) to the curves. However, since the membrane viscosity is not constant over cholesterol concentrations, the correction is not equal for them either. If anyone has ideas on how to proceed, please let me know. Or we can just ditch these data entirely.<br /><br />[1] https://zenodo.org/record/3252052<br />[2] https://zenodo.org/record/3243328<br />[3] https://zenodo.org/record/3243329<br />[4] https://zenodo.org/record/3237420<br />[5] https://zenodo.org/record/3238157<br />[6] DOI:10.1016/S0006-3495(03)70033-2<br />[7] DOI:10.1021/acs.jpcb.6b05102Matti Javanainenhttps://www.blogger.com/profile/13300446060709340277noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-54406535810300448362019-06-14T19:12:52.207+03:002019-06-14T19:12:52.207+03:00As suggested, the order parameter slopes could be ...As suggested, the order parameter slopes could be used to compare the effect of cholesterol between different experiments even though the experimental conditions would not match excatly. One motivation for this would to get another experimental data set for the order parameter changes with cholesterol, in addition to the data by Ferreira et al. Therefore, I calculated the slopes from the measurements of DMPC order parameters as a function of cholesterol published by Urbina et al. https://doi.org/10.1016/0005-2736(95)00117-L and Douliez et al. https://dx.doi.org/10.1016%2FS0006-3495(95)80350-4 (todo point 4). The results are shown here:<br />https://github.com/NMRLipids/NmrLipidsCholXray/blob/master/FIGS/slopesEXP.pdf<br /><br />Taking into account the uncertainties in the assignment, the results from different DMPC experiments are roughly similar. The slopes from POPC experiments are clearly smaller. This can be explained by the stronger dependence of membrane properties on cholesterol in saturated DMPC membrane than in POPC with one monounsaturated chain, as also observed in Lipid14 simulations by Madej et al. http://dx.doi.org/10.1021/acs.jpcb.5b04924.<br /><br />In addition to the data by Ferreira et al., POPC order parameters upon addition of cholesterol are measured using SDROSS 13C experiments by Leftin et al. However, it seems to me that they report inconsistent results in their two publications (compare Fig. 4 in Leftin14.pdf http://dx.doi.org/10.1016/j.bpj.2014.07.044 and Fig. 7 in http://dx.doi.org/10.1016/j.jmb.2013.04.002)<br /><br />In conclusion, the two independent DMPC measurements upon addition of cholesterol are roughly similar. For POPC we do not have independent experiments, unless we can figure out why two publications by Leftin et al. seem to give different results for POPC/chol (1:1) mixture.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-18072064551390249382019-05-13T01:18:56.611+03:002019-05-13T01:18:56.611+03:00Depending on what Jesper has already in his reposi...Depending on what Jesper has already in his repositories, I can contribute to the lipid14 simulations as well. Batuhan Kavhttps://www.blogger.com/profile/16276244213761216101noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-67427120170160712702019-05-10T18:39:32.498+03:002019-05-10T18:39:32.498+03:00Regarding lipid14 simulations: I have experimented...Regarding lipid14 simulations: I have experimented with running lipid14 in amber before and can run some dynamics trajectories that are needed. I am responding to the issue-7 thread to see exactly where we are on this and what is missing still.Jesper Madsenhttps://www.blogger.com/profile/00989014794393139185noreply@blogger.com