Limits...
Liquid but durable: molecular dynamics simulations explain the unique properties of archaeal-like membranes.

Chugunov AO, Volynsky PE, Krylov NA, Boldyrev IA, Efremov RG - Sci Rep (2014)

Bottom Line: These are the properties that have most likely determined the evolutionary fate of Archaea, and it may be possible for bionanotechnology to adopt these from nature.We conclude that the branched structure defines dense packing and low water permeability of archaeal-like membranes, while at the same time ensuring a liquid-crystalline state, which is vital for living cells.This makes tetraether lipid systems promising in bionanotechnology and material science, namely for design of new and unique membrane nanosystems.

View Article: PubMed Central - PubMed

Affiliation: M.M. Shemyakin &Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997.

ABSTRACT
Archaeal plasma membranes appear to be extremely durable and almost impermeable to water and ions, in contrast to the membranes of Bacteria and Eucaryota. Additionally, they remain liquid within a temperature range of 0-100°C. These are the properties that have most likely determined the evolutionary fate of Archaea, and it may be possible for bionanotechnology to adopt these from nature. In this work, we use molecular dynamics simulations to assess at the atomistic level the structure and dynamics of a series of model archaeal membranes with lipids that have tetraether chemical nature and "branched" hydrophobic tails. We conclude that the branched structure defines dense packing and low water permeability of archaeal-like membranes, while at the same time ensuring a liquid-crystalline state, which is vital for living cells. This makes tetraether lipid systems promising in bionanotechnology and material science, namely for design of new and unique membrane nanosystems.

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Free volume inside the membranes.The fraction of free volume is given as a percentage with respect to the total volume of the membrane slice, depending on the Z coordinate of the slice (for details of the calculation, see Computational methods). Five free volume profiles are presented for the bolalipid systems and two profiles for the phospholipid systems, colored and styled according to the legend. Shaded areas are standard deviations. This series of profiles was obtained at 350 K. Vertical lines show the average positions of lipids' chemical groups (choline head, phosphate, glycerol, etc.). An analogous plot for 310 K is shown in Fig. S5.
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f6: Free volume inside the membranes.The fraction of free volume is given as a percentage with respect to the total volume of the membrane slice, depending on the Z coordinate of the slice (for details of the calculation, see Computational methods). Five free volume profiles are presented for the bolalipid systems and two profiles for the phospholipid systems, colored and styled according to the legend. Shaded areas are standard deviations. This series of profiles was obtained at 350 K. Vertical lines show the average positions of lipids' chemical groups (choline head, phosphate, glycerol, etc.). An analogous plot for 310 K is shown in Fig. S5.

Mentions: In MD trajectories, we have observed water molecules that spontaneously permeate most of the membranes under study. This process seems stochastic, nearly always involving single water molecules, and not exhibiting formation of any kind of the pore of H-bonding networks of waters in the central part of the membranes. The permeation of water across hydrophobic layers requires the formation of dynamic (semi)continuous void spaces between the lipids' hydrophobic tails26. To uncover the structure and characteristics of the voids inside the various membranes, we have developed an algorithm to “map” such voids in three dimensions (see Computational methods). This allows us to plot the profiles of free volume depending on the Z coordinate in the membrane (Z is the distance from the membrane's middle plane). Fig. 6 depicts these profiles for all the examined systems at 350 K. Three-dimensional picture of these voids is provided in fig. S6. The main observation is free volume peaks in the bilayer center for phospholipids; additionally, the corresponding voids are fluctuating fast. However, this is a direct consequence of the chemical structure: lipids' tails from opposite leaflets are not chemically linked. At the same time, the water–membrane interface is organized similarly in phospholipids and branched bolalipid mimetics m8r0 and m6r2.


Liquid but durable: molecular dynamics simulations explain the unique properties of archaeal-like membranes.

Chugunov AO, Volynsky PE, Krylov NA, Boldyrev IA, Efremov RG - Sci Rep (2014)

Free volume inside the membranes.The fraction of free volume is given as a percentage with respect to the total volume of the membrane slice, depending on the Z coordinate of the slice (for details of the calculation, see Computational methods). Five free volume profiles are presented for the bolalipid systems and two profiles for the phospholipid systems, colored and styled according to the legend. Shaded areas are standard deviations. This series of profiles was obtained at 350 K. Vertical lines show the average positions of lipids' chemical groups (choline head, phosphate, glycerol, etc.). An analogous plot for 310 K is shown in Fig. S5.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4264030&req=5

f6: Free volume inside the membranes.The fraction of free volume is given as a percentage with respect to the total volume of the membrane slice, depending on the Z coordinate of the slice (for details of the calculation, see Computational methods). Five free volume profiles are presented for the bolalipid systems and two profiles for the phospholipid systems, colored and styled according to the legend. Shaded areas are standard deviations. This series of profiles was obtained at 350 K. Vertical lines show the average positions of lipids' chemical groups (choline head, phosphate, glycerol, etc.). An analogous plot for 310 K is shown in Fig. S5.
Mentions: In MD trajectories, we have observed water molecules that spontaneously permeate most of the membranes under study. This process seems stochastic, nearly always involving single water molecules, and not exhibiting formation of any kind of the pore of H-bonding networks of waters in the central part of the membranes. The permeation of water across hydrophobic layers requires the formation of dynamic (semi)continuous void spaces between the lipids' hydrophobic tails26. To uncover the structure and characteristics of the voids inside the various membranes, we have developed an algorithm to “map” such voids in three dimensions (see Computational methods). This allows us to plot the profiles of free volume depending on the Z coordinate in the membrane (Z is the distance from the membrane's middle plane). Fig. 6 depicts these profiles for all the examined systems at 350 K. Three-dimensional picture of these voids is provided in fig. S6. The main observation is free volume peaks in the bilayer center for phospholipids; additionally, the corresponding voids are fluctuating fast. However, this is a direct consequence of the chemical structure: lipids' tails from opposite leaflets are not chemically linked. At the same time, the water–membrane interface is organized similarly in phospholipids and branched bolalipid mimetics m8r0 and m6r2.

Bottom Line: These are the properties that have most likely determined the evolutionary fate of Archaea, and it may be possible for bionanotechnology to adopt these from nature.We conclude that the branched structure defines dense packing and low water permeability of archaeal-like membranes, while at the same time ensuring a liquid-crystalline state, which is vital for living cells.This makes tetraether lipid systems promising in bionanotechnology and material science, namely for design of new and unique membrane nanosystems.

View Article: PubMed Central - PubMed

Affiliation: M.M. Shemyakin &Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997.

ABSTRACT
Archaeal plasma membranes appear to be extremely durable and almost impermeable to water and ions, in contrast to the membranes of Bacteria and Eucaryota. Additionally, they remain liquid within a temperature range of 0-100°C. These are the properties that have most likely determined the evolutionary fate of Archaea, and it may be possible for bionanotechnology to adopt these from nature. In this work, we use molecular dynamics simulations to assess at the atomistic level the structure and dynamics of a series of model archaeal membranes with lipids that have tetraether chemical nature and "branched" hydrophobic tails. We conclude that the branched structure defines dense packing and low water permeability of archaeal-like membranes, while at the same time ensuring a liquid-crystalline state, which is vital for living cells. This makes tetraether lipid systems promising in bionanotechnology and material science, namely for design of new and unique membrane nanosystems.

Show MeSH