[gmx-users] X ray deconvolution of membranes

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Oct 30 22:05:05 CET 2006

> I read your response to a query in gromacs list, which read
> "Since simulated membranes tend to be too thick according to the
> current deconvolution of Xray scattering data, and given the specifics
> listed above, I would personally use DPPC as an ER mimetic."
> If you could give me the reference which gives the deconvolution data and
> maybe compares it to simulation structures, I would be grateful.

Actually I may have been in error on this point. My comment was based  
on my belief that simulations generally predicted a too-small area per  
lipid in simulations. I combined this with  my expectation for an  
inverse relationship between area per lipid and membrane hydrophobic  
length. However, the area per lipid may actually be predicted within  
experimental error. My appologies.

If anybody else would care to weigh in on this one, it would be  
appreciated. Whenever I have inserted a protein into a membrane  
(limited number of times), the membrane reorders with a "dent" in  
order to accomidate the smaller hydrophobic length of the protein.

Simulations that calculate area per lipid:
  - DPPC in Lindahl and Edholm (2000) Biophys. J. 79:426-433
  - DPPC in Tieleman and Berendsen (1996) J. Chem. Phys. 105(11):4871-4880
  - DPPC in Berger et al. (1997) Biophys. J. 72:2002-2013
  - DMPC in Chiu et al. (1995) Biophys. J. 69:1230-1245

Nagle and Tristram-Nagle Biochim. Biophys. Acta 1469 (2000) 159-195  
give a good summary of experimental data.

Here are some raw data and comparisons for electron density profiles:
  - Xray/Neutron data: Weiner and White (1992) Biophys. J. 59:428-433  
and 434-447
  - Comparison to simulation: Feller et al. (1997) Biophys. J. 73:2269-2279
  - Comparison to simulation: Benz et al. (2005) Biophys. J. 88:805-817
  - Xray data: Nagle et al. Biophys. J. (1996) 70, 1419-1431
  - Comparison to simulation: Feller and MacKerell Jr. (2000) J. Phys.  
Chem. B, 104, 7510-7515
  - Comparison to simulation: Bemporad et al. (2004) Biophys. J. 87:1-13
  - simulation: Tieleman and Berendsen (1996) J. Chem. Phys. 105(11), 4871-4880

membrane protein predicted hydrophobic thickness:
  - Lomize et al. (2006) Protein Science, 15:1318-1333

solution x-ray scattering of different membrane types before and after  
protein depletion:
  - Mitra et al. (2004) PNAS vol. 101 no. 12 4083-4088

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