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«The Achilles heel of the bacterial membrane»

The membrane of bacteria present interesting molecules - lipid II, which does not occur in eukaryotes. This lipid is an important element in the construction of the cell wall of bacteria. He is considered a very promising target for the development of antibiotics of the future. Employees Laboratory of Biomolecular Modeling IBCh RAS R. Efremov, A. Chugunov and their colleagues by computer simulation was possible to construct a surface map portion of the membrane where the lipid. This helped to understand how an antibiotic is the most vulnerable place in the membrane of microorganisms. This research was part of the report is devoted to the A. Chugunov on X International Workshop Conference for Young Researchers «Current Aspects of Modern Microbiology»

lipid II, nisin, bacteriocins, hydrophobic membrane area

Evseev A.V.

Bacteria have a special substance - bacteriocins, which are a kind of natural antibiotics. Prokaryotes may affect each other, using these substances - such as some bacteria may kill other via bacteriocins or control the growth of colonies of competitors. These substances play an important role in microbial ecosystems.

That the bacteriocins can be useful for humans. The fact that we are completely harmless because only affect bacterial cells. Another interesting fact is that now you can help fight pathogens without harming symbionts with the human body. For example, bacteriocins secreted by symbiotic lactobacilli (Lactobacillaceae), kill pathogenic germs, but did not touch their neighbors. Many researchers believe that the use of bacteriocins will help break the deadlock resistance of pathogens to antibiotics. Therefore the study of the properties of these materials is very promising direction.

One such bacteriocin is nisin, which generates bacterium Streptococcus lactis. It is interesting that this substance discovered even before the first antibiotic penicillin. For medicinal purposes it is used rarely, mostly the substance is used both as a food additive, preservative (E234).


However, it effectively operates as a bacteriostatic and germicidal agent. Moreover, as it turned out, it affects the lowlands to an interesting element of the bacterial membrane called lipid II.

The structure of lipid II is very unusual. He has a terpene tail, then located pyrophosphate. Next, come two sugars, one of which is attached pentapeptid with an unusual structure. This original molecule serves as a carrier of a fragment of peptidoglycan, the building material of the bacterial cell wall. A grid of peptidoglycan as it covers the bacteria from all sides, like shopping bags, shopping bags, that is, it is a very important component of the bacterial cell wall. Destruction peptidoglycan grid generally leads to death of the microorganism - besides those types (they are not so many) in which it is not.

Thus, if the lipid II somehow «turn off» from this process, bacteria cannot synthesize cell wall and die. Nisin can also «catch» lipid II directly on the bacterial membrane. There are two options: the first case of nisin binds to a molecule lipid II and makes it work, and in the second embodiment, in the membrane pores form - lowlands fixed in the membrane via lipid II, and “breaks" it. In the latter case, the death of the bacteria is inevitable, since there is dissipation of ionic gradients.

Lipid II

In order to create active molecules bacteriocins that could snatch from the bacterial membrane lipid II and kill pathogens, it is necessary to study in detail all that happens on the membrane during such contact. Therefore, research staff of Laboratory of biomolecular modeling of IBCh RAS R. Efremov and A. Chugunov able to simulate the membrane fragment which contains lipid II. He built among common bacterial phospholipids - it is a complex system. Estimated time of molecular dynamics was one microsecond (1 · 10-6s). It was necessary to make billions of steps for the system consisting of hundreds of thousands of atoms in order to obtain such a calculation. Although it is impossible to see everything that happens on the membrane, but we can already say that, lipid II presence affects its properties

It is assumed that contact with Lipid II nisin occurs so - bacteriocin pyrophosphate lipid clings to it and builds a specific pattern of hydrogen bonds. leading to high affinity binding. Nevertheless, how this bacteriocin find not so often found in the membrane of a molecule?Maybe lipid II dramatically changes the properties of the portion of the membrane, where it is? Laboratory staff decided to find out, by means of constructing a site map computer Modelling membranes containing lipid II.

By the way, in spite of the popular opinion that if in all bllipidic layer membrane hydrophobic regions are inside and hydrophilic - on the surface. But now we know that it is not - according to computer modeling, on the membrane surface are also hydrophobic regions, and their area can be very high. Now, researchers have found that the surface areas of the membrane where the lipid II molecule is hydrophobic, too - they forms «hydrophobic atoll». Moreover, these areas are not uniform in relief - because of the lipid II molecule there are formed projections and depressions.

Membrane localization of lipid II

It happens that is why - pentapeptide head lipid containing «building blocks» for the cell wall is the outside of the membrane. Terpene tail hangs freely inside the latter, taking sometimes the most unusual position. Well connecting both parts pyrophosphate lipid group II as it protrudes from the membrane, and thus it is located at the boundary between the cell and the aqueous medium.

Thus, since the head that rises above the surface of the lipid membrane, its structure at this site is disrupted because of the smooth layer is formed of phospholipids rather conspicuous overhang. But this is not enough - because of the connection with the pyrophosphate group head acquires polarity and therefore forms hydrogen bonds with the polar heads of phospholipids. In addition, a positively charged lysine residue in the head lipid II attracts negatively charged fragments near lipids using electrostatics. The result is that the head of the lipid-II as it «pulls» the surrounding phospholipid molecules, and its tail is changing its location within the hydrophobic layer, thereby violating its structure. And it is formed above the atoll, centered on the island of hydrophilic (around the head of the lipid II), and the edges - a horseshoe-shaped hydrophobic region formed due to the activity of the lipid tail.

The hydrophobic membrane area around the lipid II

Based on this picture, researchers have suggested that lipid II «gives» himself bacteriocin that forms around itself a hydrophobic surface. Indeed, the molecules of the substance in the cell is very small - from one to two thousand (in gram-positive bacteria - about 20 thousand) to millions of molecules of phospholipids. It would seem that no bacteriocin simply could not find such a rare item among many prokaryotic membranes did not interest him phospholipids. However, the antimicrobial peptide has the activity of the membrane, so it first finds uneven in terms of hydrophilicity of the membrane portion, and then specifically binds to pyrophosphate. However, exactly how it is this heterogeneity, not yet known - this requires further modeling and calculations.

Thus, this study allowed us to see that in this case, the bacteria themselves give out, bacteriocins showing its most vulnerable spot. All this allows us to count on the fact that this target is very promising for the creation of fundamentally new antibiotics. It is possible that in the future the researchers based on computer calculations, will be able to offer other molecules that will be more effective to attack the «Achilles' heel» of bacterial membranes. In the case there will be only synthesize these substances and test them in practice. However, it should be noted at once that they are unlikely to work well against gram-positive bacteria, because they possess a thick cell wall, through which it is not so easy to break. But with gram-negative organisms, these agents will cope quite easily.


1) Anton Chugunov, Darya Pyrkova, Dmitry Nolde et al. Lipid-II forms potential «landing terrain» for lantibiotics in simulated bacterial membrane // Scientific Reports. 2006. V. 3. Article number: 1678. 

2) Eefjan Breukink and Ben de Kruijff. Lipid-II as a target for antibiotics // Nature Reviews Drug Discovery. 2006. V. 5. P. 321–323.

november 6, 2015

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