PEPTIDE BETA-BARRELS
This invention relates to a novel form of beta-barrel pores made of self-assembling peptides, to methods of their production and to uses thereof.
It is known that some naturally occurring material polypeptides can exist in the form of beta barrels in vivo, for example porins and toxins appear as beta barrel structures embedded in cell membranes (Figl).
Beta-barrels are cylindrical nanostructures made of the beta-sheet motif, with a hole in the middle. The beta-strand segments of the polypeptide chain which make the beta-barrel are proceeded and followed by other polypeptide segments which adopt turn, loops or helical conformations and are usually protruding outside the cell membrane. These intermediate segments also connect the beta-strand segments together. The long axes of the individual beta-strands making up the beta-barrel are parallel to or at an angle substantially less than 90° from the long axis the beta-barrel cylinder.
Porins, the major outer membrane proteins of Gram-negative bacteria, are responsible for the 'molecular sieve' properties of the outer membrane of Gram- negative bacteria. Porins consist of long polypeptide chains, each being several dozen to several hundred, amino-acid residues long. Porins form large water-filled beta-barrel channels which cross the outer lipid membrane of bacteria, and which allow the diffusion of hydrophilic molecules into the periplasmic space. Porins also serve as receptor sites for the binding of phages and bacteriocins.
Toxins belong to a family of proteins/peptides which generally act by binding to membrane receptors. Toxins may cause death of the cells they attack. Toxins can consist of a large number of amino acid residues, for example, snake toxins may comprise sixty to seventy-five amino acids. A class of toxins are believed to be
characterised by their self-assembly into beta-sheet structures in the outer membranes of the cells they attack.
Thus, generally known beta barrel structures are made of long polypeptide chains or peptide molecules which are folded back upon themselves to form a barrel.
International Patent Application No WO 96/31528, Boden, et al describes peptides which self-assemble laterally in one dimension to form novel long beta-sheet tapelike polymers in a wide variety of different solvent conditions (Fig.2). Above a certain critical peptide concentration the tapes get topologically entangled and form a continuous three-dimensional gel network. These novel peptide gels possess the specific property of being able, under certain conditions, to switch from the gel state to a fluid or stiffer gel state.
We have now found that certain beta-sheet tape forming peptides can also give rise to beta barrels (Fig.3). In particular, by the appropriate selection of conditions and/or peptide structures, beta-sheet forming peptides can self assemble into beta barrel structures. Thus, we have found that, by the selection of peptides that exhibit desired hydrogen bond interactions and/or side chain interactions peptide beta barrels may be formed.
Thus, according to the invention we provide a self-assembling peptide beta barrel which comprises discrete peptide molecules each adopting a predominantly beta- strand conformation.
Moreover, we have found that peptide beta barrels can be triggered to disassemble by altering, for example, the pH. This action may be due to change of ionisation state of the amino acids in the peptide, the same charged species produced will tend to disassemble the barrel due to the repulsive like charges.
The self-assembling peptide beta barrels may be formed by using a lipid bilayer. The use of a lipid bilayer is able to influence the equilibrium between the peptide monomers and peptides in beta barrel structure. By selecting peptides which form beta sheets tapes which possess a hydrophobic width substantially the same as the thickness of the hydrophobic part of lipid bilayer, the peptide strands are able to hydrogen bond together to form a beta barrel which transverses the lipid bilayer. Such barrels will generally have a polar/hydrophilic core with an apolar/hydrophobic exterior.
According to a further feature of the invention we provide a method of preparation of a peptide beta barrel pore which comprises at least one of the following methods.
The beta barrels may be made by rationally designed peptides which self-assemble in the lipid membrane into beta barrels.
There are several alternative ways for the preparation of these beta barrels, examples of which include the following;
(i) A solution (preferably by aqueous solution) of self-assembling beta sheet forming peptides may be mixed with lipid bilayers.
The peptide concentration (c) in the solution can be low i.e. c<c* (where c* is the critical peptide concentration for self-assembly in solution); in this case the peptides will be in the monomeric state. Alternatively if c>c*, the peptides in solution will have self-assembled to form beta sheet polymers.
Upon interaction of the peptide solution with the lipid bilayers, a new equilibrium is established between peptides inserted in the bilayer and those in solution. In the bilayers, monomeric peptides may be helices, coils or beta strands. However, above a certain concentration c*barrel, the monomeric peptides spontaneously self-assemble into beta barrels.
(ii) Peptides in a self-assembled beta sheet state in solution can be switched to their monomeric state by external chemical triggering, e.g. pH change. The monomeric peptides thus generated can incorporate in a lipid bilayer, especially if the net charge of peptide is complementary to the net charge of lipid headgroups. Thus, electrostatic attraction between peptide and lipid, as well as hydrophobic interaction between peptide side-chains and lipid hydrocarbon chains, can favour formation of transmembrane self- assembled beta barrels.
(iii) A solution of peptide and lipid molecules in a common organic solvent can be prepared. The solvent may be removed by evaporation, and the dry peptide-lipid film produced may then be hydrated. In this way, lipid bilayers containing transmembrane beta barrel channel structures can be prepared.
The peptide beta barrels of the invention are advantageous, inter alia, because they can act as antimicrobial agents and bactericides, or they may be useful as drug delivery systems, as biosensors or as components in electronic devices.
The peptide beta barrels may function as antimicrobial agents or antibacterial agents and may act by forming a "hole" in the bacterium or microbe cell lipid bilayer.
As an antimicrobial agent the beta barrel peptides of the invention are especially useful in wound care. When bacteria grows in a wound site they lower the pH of the wound site. Thus if self assembling peptides are present (e.g. in a gel network state), this pH change can trigger some dissociation of the polymers to peptide monomers, which insert into the outer lipid bilayer of bacteria and form beta barrel holes. This will eventually lead to the death of the bacteria. Following elimination of the bacteria, the pH increases again to physiological values, and the peptides can reassemble, for example, into stable polymer fibrils in the wound site.
Alternatively, peptide polymers with such properties can be used to prepare antimicrobial wound dressing rather than gels which can be applied to wound site and be triggered to produce beta-barrel pore forming peptides in the cell membrane of the microbe.
Thus according to the invention we provide a wound dressing comprising a peptide as hereinbefore described.
The peptide beta-barrels can also be incorporated in the lipid bilayers of vesicles loaded with an active ingredient e.g. medicament/drug . This active compound can be small molecules, biologicals, proteonics, or DNA If these molecules can not penetrate the lipid bilayer, then the beta-barrels are the only means of release of the active compound outside the vesicle. Thus the beta-barrel in this case acts as a component of a formulation of slow or sustained release of an active compound. Of particular note, the self-assembly of the monomeric peptide into beta-barrel aggregates can be triggered in response changes to the pH if in an aqueous solution.
The peptide beta barrels may also have application in the oil industry. Specifically, our peptide beta barrels have potential application in both well construction (drilling, completion) and in reservoir stimulation (fracturing, water control). One particular application of beta-barrels in this field is the slow release of an active compound in the oil well. This can be done by incorporating the beta-barrel in lipid vesicles loaded with the appropriate active compound. The active compound will be released slowly though the beta-barrel. Increased well productivity resulting from reduced impairment of permeability in hydrocarbon-bearing formation would lead to fewer wells needing to be drilled to recover a given amount of oil. This represents significant cost savings when one considers that a typical horizontal well can cost up to £20 million. Improvements in reservoir productivity can have a dramatic impact on profitabiHty and competitiveness. Current UK north sea oil production is about
1.6m barrels per day. At today's oil prices even a 1% increase in productivity would
yield an average revenue of £2,000 per day. The cost of effective treatments would therefore be rapidly recovered.
The peptide beta-barrels can allow ion flow and current to go through them. This can be detected using appropriate techniques (see Appendix). Their conductance properties can be altered by appropriate external triggers e.g. pH changes (see appendix). Thus beta-barrels can be used as components in sensor and electronic devices.
In yet a further preferred embodiment of the invention said beta-barrel material comprises peptides with hydrophilic or hydrophobic amino-acid residues or a mixture thereof and more preferably comprises an 4-40 residue peptide ideally a peptide 10- 15 amino acid residues long.
The invention will now be described with reference to the accompanying examples and figures. .
Figure legends
Figure 1:
Natural beta-barrels formed by porin-like proteins
Figure 2:
A beta-sheet tape formed by peptides which self-assemble in one dimension.
Figure 3:
A beta-barrel pore formed by self-assembling beta-forming peptides in a lipid bilayer. Each peptide is adopting a beta-strand conformation.
Example 1
Beta-barrel forming self-assembling peptides and their conductance properties
Peptide amino acid sequence using one-letter code: DN1: QQ RFQWQFEQQ
DNl -QF QQ RFQFQWQFEQQ DN1-2E QQ RFEWEFEQQ DN1-3OQ: QQ OFOWOFQQQ
The beta barrel channel-forming peptides are reconstituted into planar lipid bilayers by fusion of lipid vesicles containing the spanning channel.
The assessment of the conductance and of the assembly states of the transmembrane peptides is made by the planar lipid bilayer method, where the ion channel activity is studied under voltage clamp conditions.
Experimental conditions: pH 7-8, Rp:!= 1/500, 450mM KC1 cis : 150mM KC1 trans
The flux of ion through the channel is indicated by the fluctuations of current levels relatively to the baseline. They open and close in a stochastic way, reflecting the probabilistic nature the ion channel activity.
DN1 (Fig. 4): Regular ion channel activities, with square-top current fluctuations, long open dwell time, and low current amplitude (0.5 pA).
DNl-QF (Fig. 5): Regular and irregular ion channel activity, with square-top current fluctuation in certain moments as also with multiple levels of channel conductance in other moments, reflecting in this last case the presence of different association states for the peptides. It shows a varied range of current amplitudes (from pA up to hundreds of pA)
DN1-2E (Fig. 6a-c): Regular and irregular ion channel activity, with square-top current fluctuations in certain moments, as also erratic behaviour in other moments, including cluster of opening events, and low to high current amplitudes (0.5pA- lOpA). On average the irregular activity is more frequent at higher voltages.
The remaining presence of irregular channel activity is due the not total neutralisation of the negative charges at this pH.
I this case, on average, we observe more regular ion channel activity when comparing (with the values of pH 7.5) for lower values of tension, but at higher tension an irregular ion channel activity is observed (however, on average, not so irregular as in the case of pH 7.5).
This indicate that the change of pH from 7.5 to 7 tend to neutralise more the negative charge of DN1-2E, and consequently produce more stable channel due the small peptide repulsion.
DNl-3ORNlQ (Fig. 7 a-c): This ion channel-forming peptide shows ion activity very irregular and with high amplitude current. This irregularity is possibly due the strong repulsion of peptides inside the bilayer that prevents the formation of a stable structure.
The ion channel activity at pH 8 still shows irregularity due the instability of the transmembrane structure, but this irregularity is less than those in the case of the pH 7.5, possibly due the diminish of the net positive charge.
At higher values of tension the high irregularity comes back.
At pH 8 the amplitude of current ranges from pA up to tenths of pA.
The occurrence of ion channel activity is much easier for DN1 and DNl-QF than to DN1-2E and DN1-3ORN1Q. hi other words, it is much easier to observe the start of
current fluctuations, and the probability of open is bigger for DNl and DNl-QF, than for DN1-2E and DN1-3ORN1Q.
This maybe due the instability of the aggregates constituted of charged peptides.
For DN1-2E at pH 8 and DN1-3ORN1Q at pH 7, the opposite behaviour is expected.