Peptide ion channels: design and creation of function

DNA scaffolds support stable and uniform peptide nanopores

The assembly of peptides into membrane-spanning nanopores might be promoted by scaffolds to pre-organize the structures. Such scaffolds could enable the construction of uniform pores of various sizes and pores with controlled permutations around a central axis. Here, we show that DNA nanostructures can serve as scaffolds to arrange peptides derived from the octameric polysaccharide transporter Wza to form uniform nanopores in planar lipid bilayers. Our ring-shaped DNA scaffold is assembled from short synthetic oligonucleotides that are connected to Wza peptides through flexible linkers. When scaffolded, the Wza peptides form conducting nanopores of which only octamers are stable and of uniform conductance. Removal of the DNA scaffold by cleavage of the linkers leads to a rapid loss of the nanopores from the lipid bilayer, which shows that the scaffold is essential for their stability. The DNA scaffold also adds functionality to the nanopores by enabling reversible and permanent binding of complementary tagged oligonucleotides near the nanopore entrance.

Molecular Evolution in a Peptide-Vesicle System

Based on a new model of a possible origin of life, we propose an efficient and stable system undergoing structural reproduction, self-optimization, and molecular evolution. This system is being formed under realistic conditions by the interaction of two cyclic processes, one of which offers vesicles as the structural environment, with the other supplying peptides from a variety of amino acids as versatile building blocks. We demonstrate that structures growing in a combination of both cycles have the potential to support their own existence, to undergo chemical and structural evolution, and to develop unpredicted functional properties. The key mechanism is the mutual stabilization of the peptides by the vesicles and of the vesicles by the peptides together with a constant production and selection of both. The development of the proposed system over time would not only represent one of the principles of life, but could also be a model for the formation of self-evolving structures ultimately leading to the first living cell. The experiment yields clear evidence for a vesicle-induced accumulation of membrane-interacting peptide which could be identified by liquid chromatography combined with high-resolution mass spectroscopy. We found that the selected peptide has an immediate effect on the vesicles, leading to (i) reduced vesicle size, (ii) increased vesicle membrane permeability, and (iii) improved thermal vesicle stability.

Selection of Prebiotic Molecules in Amphiphilic Environments

A basic problem in all postulated pathways of prebiotic chemistry is the low concentration which generally is expected for interesting reactants in fluid environments. Even though compounds, like nucleobases, sugars or peptides, principally may form spontaneously under environmental conditions, they will always be rapidly diluted in an aqueous environment. In addition, any such reaction leads to side products which often exceed the desired compound and generally hamper the first steps of a subsequent molecular evolution. Therefore, a mechanism of selection and accumulation of relevant prebiotic compounds seems to be crucial for molecular evolution. A very efficient environment for selection and accumulation can be found in the fluid continuum circulating in tectonic fault zones. Vesicles which form spontaneously at a depth of approximately 1 km present a selective trap for amphiphilic molecules, especially for peptides composed of hydrophilic and hydrophobic amino acids in a suitable sequence. The accumulation effect is shown in a numeric simulation on a simplified model. Further, possible mechanisms of a molecular evolution in vesicle membranes are discussed. Altogether, the proposed scenario can be seen as an ideal environment for constant, undisturbed molecular evolution in and on cell-like compartments.

Development of toroidal nanostructures by self-assembly: rational designs and applications

Toroidal nanostructures are symmetrical ring-shaped structures with a central internal pore. Interestingly, in nature, many transmembrane proteins such as β-barrels and α-helical bundles have toroidal shapes. Because of this similarity, toroidal nanostructures can provide a template for the development of transmembrane channels. However, because of the lack of guiding principles for the construction of toroids, researchers have not widely studied the self-assembly of toroidal nanostructures as compared with the work on other supramolecular architectures. In this Account, we describe our recent efforts to construct toroidal nanostructures through the self-assembly of rationally designed building blocks. In one strategy for building these structures, we induce interfacial curvatures within the building blocks. When we laterally graft a bulky hydrophilic segment onto a p-oligophenyl rod or β-sheet peptides, the backbones of the self-assembled structures can bend in response to the steric effect of these large side groups, driving the p-oligophenyl rod or β-sheet peptides to form nanosized toriods. In another strategy, we can build toroids from bent-shaped building blocks by stacking the macrocycles. Aromatic segments with an internal angle of 120° can associate with each other in aqueous solution to form a hexameric macrocycle. Then these macrocycles can stack on top of each other via hydrophobic and π-π interactions and form highly uniform toroidal nanostructures. We provide many examples that illustrate these guiding principles for constructing toroidal nanostructures in aqueous solution. Efforts to create toroidal nanostructures through the self-assembly of elaborately designed molecular modules provide a fundamental approach toward the development of artificial transmembrane channels. Among the various toroids that we developed, a few nanostructures can insert into lipid membranes and allow limited transport in vesicles.

Extramembrane control of ion channel peptide assemblies, using alamethicin as an example

Ion channels allow the influx and efflux of specific ions through a plasma membrane. Many ion channels can sense, for example, the membrane potential (the voltage gaps between the inside and the outside of the membrane), specific ligands such as neurotransmitters, and mechanical tension within the membrane. They modulate cell function in response to these stimuli. Researchers have focused on developing peptide- and non-peptide-based model systems to elucidate ion-channel protein functions and to create artificial sensing systems. In this Account, we employed a typical peptide that forms ion channels,alamethicin, as a model to evaluate our methodologies for controlling the assembly states of channel-forming molecules in membranes. As alamethicin self-assembles in membranes, it prompts channel formation, but number of peptide molecules in these channels is not constant. Using planar-lipid bilayer methods, we monitored the association states of alamethicin in real time. Many ligand-gated, natural-ion channel proteins have large extramembrane domains. As these proteins interact with specific ligands, those conformational alterations in the extramembrane domains are transmitted to the transmembrane, pore-forming domains to open and close the channels. We hypothesized that if we conjugated suitable extramembrane segments to alamethicin, ligand binding to the extramembrane segments could alter the structure of the extramembrane domains and influence the association states or association numbers of alamethicin in the membranes. We could then assess those changes by using single-channel current recording. We found that we could modulate channel assembly and eventual ion flux with attached leucine-zipper extramembrane peptide segments. Using conformationally switchable leucine-zipper extramembrane segments that respond to Fe(3+), we fabricated an artificial Fe(3+)-sensitive ion channel; a decrease in the helical content of the extramembrane segment led to an increase in the channel current. When we added a calmodulin C-terminus segment, we formed a channel that was sensitive to Ca(2+). This result demonstrated that we could prepare artificial channels that were sensitive to specific ligands by adding appropriate extramembrane segments from natural protein motifs that respond to external stimuli. In conclusion, our research points to the possibility of creating tailored sensor or signal transduction systems through the conjugation of a conformationally switchable extramembrane peptide/protein segment to a suitable transmembrane peptide segment.

Construction of a Ca(2+)-gated artificial channel by fusing alamethicin with a calmodulin-derived extramembrane segment

Using native chemical ligation, we constructed a Ca(2+)-gated fusion channel protein consisting of alamethicin and the C-terminal domain of calmodulin. At pH 5.4 and in the absence of Ca(2+), this fusion protein yielded a burst-like channel current with no discrete channel conductance levels. However, Ca(2+) significantly lengthened the specific channel open state and increased the mean channel current, while Mg(2+) produced no significant changes in the channel current. On the basis of 8-anilinonaphthalene-1-sulfonic acid (ANS) fluorescent measurement, Ca(2+)-stimulated gating may be related to an increased surface hydrophobicity of the extramembrane segment of the fusion protein.

Metal-assisted channel stabilization: disposition of a single histidine on the N-terminus of alamethicin yields channels with extraordinarily long lifetimes

Alamethicin, a member of the peptaibol family of antibiotics, is a typical channel-forming peptide with a helical structure. The self-assembly of the peptide in the membranes yields voltage-dependent channels. In this study, three alamethicin analogs possessing a charged residue (His, Lys, or Glu) on their N-termini were designed with the expectation of stabilizing the transmembrane structure. A slight elongation of channel lifetime was observed for the Lys and Glu analogs. On the other hand, extensive stabilization of certain channel open states was observed for the His analog. This stabilization was predominantly observed in the presence of metal ions such as Zn(2+), suggesting that metal coordination with His facilitates the formation of a supramolecular assembly in the membranes. Channel stability was greatly diminished by acetylation of the N-terminal amino group, indicating that the N-terminal amino group also plays an important role in metal coordination.

Helical membrane peptides to modulate cell function

In recent years there has been an abundance of research into the potential of helical peptides to influence cell function. These peptides have been used to achieve a variety of different outcomes from cell repair to cell death, depending upon the peptide sequence and the nature of its interactions with cell membranes and membrane proteins. In this critical review, we summarise several mechanisms by which helical peptides, acting as either transporters, inhibitors, agonists or antibiotics, can have significant effects on cell membranes and can radically affect the internal mechanisms of the cell. The various approaches to peptide design are discussed, including the role of naturally-occurring proteins in the design of these helical peptides and current breakthroughs in the use of non-natural (and therefore more stable) peptide scaffolds. Most importantly, the current successful applications of these peptides, and their potential uses in the field of medicine, are reviewed (131 references).

Ligand-induced extramembrane conformation switch controlling alamethicin assembly and the channel current

In this review, we describe our approach to creating artificial receptor-channel proteins or sensor systems, using an extramembrane segment conformationally switchable by external stimuli. Alamethicin is known to self-assemble in membranes to form ion channels with various open states. Employment of an alpha-helical leucine-zipper segment resulted in the effective modulation of the association states of alamethicin to produce a single predominant channel-open state. A decrease in the helical content of the extramembrane segments was found to induce a channel-current increase. Therefore, conformational changes in the extramembrane segments induced by the interaction with ligands can be reflected in the current levels.

Vertical and directional insertion of helical peptide into lipid bilayer membrane

A novel helical hexadecapeptide carrying a poly(ethylene glycol) (PEG) chain at the N terminal was synthesized. The N and C terminals of the compound are labeled with a fluorescein isothiocyanate (FITC) group and an N-ethylcarbazolyl group (ECz), respectively. An octapeptide carrying the same groups and a hexadecapeptide without a PEG chain were also synthesized and used as control. A mixture of the peptide and dimyristoylphosphatidylcholine was sonicated in a buffer to prepare the liposome. The orientation as well as direction of the helical segment in the lipid bilayer were analyzed by quenching experiments of the FITC and the ECz fluorescence. The results clearly indicated that the helical segment of the peptide penetrated into the lipid bilayer with vertical orientation in both the gel and liquid crystalline states of the lipid bilayer. Notably, the bulky N terminal was left behind in the outer aqueous phase of liposome, meaning that the C terminal of the peptide points to the inner aqueous phase of liposome. The insertion mode of the helical peptide into a bilayer membrane is therefore well-regulated in terms of the orientation and the directionality by designing the balance between the PEG chain and the helix length. The methodology presented here will initiate a way to construct artificial functional molecular systems that can induce vectorial transport phenomena as seen in biological systems.

Analysis of peptide design in four-, five-, and six-helix bundle template assembled synthetic protein molecules

Four-, five-, and six-helix bundle template assembled synthetic proteins (TASPs) have been synthesized using disulfide bonds between cavitand templates and peptides, and characterized in terms of stability and structural specificity. The peptide sequence (CGGGEELLKKLEE LLKKG) used was originally designed for a four-helix bundle. The TASPs were analyzed using CD spectroscopy, chemical denaturation studies, NMR spectroscopy, sedimentation equilibria studies, and hydrophobic dye binding studies to determine the effect of a single peptide sequence when incorporated into bundles with different numbers of helices. If the design was indeed idealized for a four-helix bundle, then the five- and six-helix bundles should be less stable and manifest lower conformational specificity. The TASPs all demonstrated high stability and cooperative unfolding. However, the four-helix bundle was found to be significantly more stable and nativelike compared to the five- and six-helix bundles. This suggests that the peptide sequence is specific to the four-helix bundle, as designed. This result demonstrates the ability to design de novo proteins with specified structure, not just generic stability.

Characterization of de novo four-helix bundles by molecular dynamics simulations

We have investigated the structure and dynamics of three cavitand-based four-helix bundles (caviteins) by computer simulation. In these systems, designed de novo, each of the four helices contain the identical basis sequence EELLKKLEELLKKG (N1). Each cavitein consists of a rigid macrocycle (cavitand) with four aryl linkages, to each of which is connected an N1 peptide by means of a linker peptide. The three caviteins studied here differ only in the linker peptide, which consist of one, two, or three glycine residues. Previous experimental work has shown that these systems exhibit very different behavior in terms of stability and oligomerization states despite the small differences in the linker peptide. Given that to date no three-dimensional structure is available for these caviteins, we have undertaken a series of molecular dynamics (MD) simulations in explicit water to try to rationalize the large differences in the experimentally observed behavior of these systems. Our results provide insight, for the first time, into why and how the cavitein with a single glycine linker forms dimers. In addition, our results indicate why although the two- and three-glycine-linked caviteins have similar stabilities, they have different native-like characteristics: the cavitein with three glycines can form a supercoiled helix, whereas the one with two glycines cannot. These findings may provide a useful guide in the rational de novo design of novel proteins with finely tunable structures and functions in the future.

Functional engineered channels and pores (Review)

Significant progress has been made in membrane protein engineering over the last 5 years, based largely on the re-design of existing scaffolds. Engineering techniques that have been employed include direct genetic engineering, both covalent and non-covalent modification, unnatural amino acid mutagenesis and total synthesis aided by chemical ligation of unprotected fragments. Combinatorial mutagenesis and directed evolution remain, by contrast, underemployed. Techniques for assembling and purifying heteromeric multisubunit pores have been improved. Progress in the de novo design of channels and pores has been slower. But, we are at the beginning of a new era in membrane protein engineering based on the accelerating acquisition of structural information, a better understanding of molecular motion in membrane proteins, technical improvements in membrane protein refolding and the application of computational approaches developed for soluble proteins. In addition, the next 5 years should see further advances in the applications of engineered channels and pores, notably in therapeutics and sensor technology.

Gramicidin-based channel systems for the detection of protein-ligand interaction

To detect protein-ligand interaction a gramicidin-based sensor was developed. Biotin was tagged to the C-terminus of gramicidin (Gram-bio 1). The biotin-moiety, which faces the electrolyte, gave little effect on single-channel conductance. Streptavidin added to the electrolyte was detected by Gram-bio 1 through the monitoring channel current using the planar bilayer system. The suppression of macroscopic currents and the acceleration of their decaying time course were observed in a concentration dependent manner. In the single-channel level, however, no significant effect on the single-channel conductance and the open dwell time was observed upon addition of streptavidin. Therefore, streptavidin neither blocked the open channel nor changed the stability of the conducting dimer. Insertion of a linker between gramicidin and biotin did not change the streptavidin-sensitivity of the current reduction. We conclude that the binding of streptavidin to the Gram-bio 1 shifted the distribution of the complex from the membrane to the electrolyte and, thus, reduced the formation of conducting dimer of Gram-bio 1 in the membrane. Interaction of biotin with an anti-biotin antibody was also observed using this system, indicating that this system is applicable for the detection of protein-ligand interaction having a binding constant of approximately 10(8-9) M(-1) or more. Both the adamantane-tagged gramicidin for detection of beta-cyclodextrin and the Strep Tag-II-tagged gramicidin for detection of streptavidin (binding constant: approximately 10(5) M(-1) or less) failed to respond. Thus, high-affinity ligands upon tagging to gramicidin render the gramicidin-based sensor able to execute as a real-time monitoring system for protein-ligand interaction.

De Novo Design of Peptide Immunogens That Mimic the Coiled Coil Region of Human T-cell Leukemia Virus Type-1 Glycoprotein 21 Transmembrane Subunit for Induction of Native Protein Reactive Neutralizing Antibodies

Peptide vaccines able to induce high affinity and protective neutralizing antibodies must rely in part on the design of antigenic epitopes that mimic the three-dimensional structure of the corresponding region in the native protein. We describe the design, structural characterization, immunogenicity, and neutralizing potential of antibodies elicited by conformational peptides derived from the human T-cell leukemia virus type 1 (HTLV-1) gp21 envelope glycoprotein spanning residues 347-374. We used a novel template design and a unique synthetic approach to construct two peptides (WCCR2T and CCR2T) that would each assemble into a triple helical coiled coil conformation mimicking the gp21 crystal structure. The peptide B-cell epitopes were grafted onto the epsilon side chains of three lysyl residues on a template backbone construct consisting of the sequence acetyl-XGKGKGKGCONH2 (where X represents the tetanus toxoid promiscuous T cell epitope (TT) sequence 580-599). Leucine substitutions were introduced at the a and d positions of the CCR2T sequence to maximize helical character and stability as shown by circular dichroism and guanidinium hydrochloride studies. Serum from an HTLV-1-infected patient was able to recognize the selected epitopes by enzyme-linked immunosorbent assay (ELISA). Mice immunized with the wild-type sequence (WCCR2T) and the mutant sequence (CCR2T) elicited high antibody titers that were capable of recognizing the native protein as shown by flow cytometry and whole virus ELISA. Sera and purified antibodies from immunized mice were able to reduce the formation of syncytia induced by the envelope glycoprotein of HTLV-1, suggesting that antibodies directed against the coiled coil region of gp21 are capable of disrupting cell-cell fusion. Our results indicate that these peptides represent potential candidates for use in a peptide vaccine against HTLV-1.

Studies on the aggregation and possible channel formation in membranes of a cyclic hexapeptide, cyclo (D-Ala-L-Pro-L-Ala)2

The interaction of zwitterionic lipid DMPC and DPPC with cyclic hexapeptide, cyclo (D-Ala-L-Pro-L-Ala)2 was studied using circular dichroism (CD) and differential scanning calorimetry (DSC). Preliminary membrane conductance results showed that the peptide has a tendency to form channels inside the lipid bilayer. CD studies indicated that as the lipid/peptide (L/P) ratio (DMPC/peptide) was increased, the magnitude of the negative CD band having a lambda(max) around 200 nm decreased. At a L/P ratio of 210:1, this band disappeared completely, indicating dramatic conformational changes in the peptide on interaction with the lipid bilayer. Reduction of the phase transition temperature and the maximum heat capacity of the lipid bilayer (DPPC) for gel-to-liquid crystalline phase transition indicates a strong interaction of the peptide with the lipid bilayer.

Channel properties of template assembled alamethicin tetramers

The multiple conductance levels displayed by the antibiotic alamethicin in planar lipid bilayers is explained by a dynamic 'barrel-stave' model, the conducting pore resulting from the aggregation of up to ten helical amphipathic helical monomers. However, the precise assignment of an oligomerization state to a particular single-channel conductance substate is far from being experimentally clear. In addition, it could be useful to tailor a given channel geometry to selectively allow the permeation of solutes with different molecular sizes, whilst retaining a high voltage-dependence. To control the aggregation state of the channel, the TASP (template assembled synthetic proteins) strategy was applied to synthesize structurally defined oligomers, i.e. dimer, trimer, tetramer. The modulation of conductance properties of three alamethicin tetramers with the length and flexibility of the linkers of the 'open' or linear template is described. It is shown that the introduction of an alanine between the contiguous lysines to which are tethered C-terminally modified alamethicin helical monomers stabilizes the open channel states, whereas the alanine substitution by Pro-Gly, a reverse beta-turn promoting motif, increases voltage-dependence and leads to single-channel conductance values more in line with the expected ones from a tetrameric bundle.

How did cells get their size?

Cells exercise size homeostasis, and the origins of their ability to do so is the topic of this essay. Before there were cells, there were protocells. The most basic questions about protocells as objects are: What were they made of, and how big were they? Asking how big they were implies that the answer to the first part includes a boundary. The best candidate for that boundary is a self-assembling lipid bilayer. Therefore, protocells are defined here as Darwinian liposomes-bilayer vesicles with mutable on-board replicases linked to phenotypes. Because liposomes undergo spontaneous fission and fusion, and are subject to osmotic forces, size regulation in the earliest protocells would essentially have been liposome physics. For successful protocells, averting osmotic lysis would have been the first order of business. However, from the outset size mattered too, because of sex and reproduction (i.e., genome mixing and genome copying in entities with phenotypes). Protocell fission and fusion would have blended seamlessly into protocell sex and reproduction, making any gene product that furnished control over protocell size changes doubly adaptive. A recurrent theme is the feedback role of bilayer tension in protocell size control. Ways in which primitive peptides and their aggregates (e.g., channels) might have allowed liposomes to gain improved volume and surface area homeostasis are suggested. Domain-swapped proteins that polymerize as filaments are discussed as the origin of cytoskeleton structures that diversify and stabilize liposome shapes and sizes. Throughout, attention is paid to the question of set points for cell size.

Modulating ion channel properties of transmembrane peptide nanotubes through heteromeric supramolecular assemblies

A selective heteromeric supramolecular assembly process is devised to create functional single channels of altered ion conductance, charge selectivity, and rectification. The hollow transmembrane tubular structure produced spontaneously from the self-assembly of cyclic-d,l-alpha-peptides in lipid bilayers is modified by designer cyclic peptide "cap" subunits that bind site-selectively at the mouth of the channel assembly.

Detection of protein-ligand interaction on the membranes using C-terminus biotin-tagged alamethicin

C-terminal biotin-tagged alamethicin, which has several alpha-aminoisobutyric acid (Aib) residues in its sequence, was synthesized by the preparation of the protected peptide segment using the 2-chlorotrityl resin, followed by conjugation with biotin hydrazide. Suppression of the channel current of the biotin-tagged alamethicin by the addition of streptavidin to the electrolyte was monitorable in real time using the planar lipid-bilayer method. The system was also applicable to the detection of interaction of the biotin-tagged alamethicin with the anti-biotin antibody.

A comparison of three- and four-helix bundle TASP molecules

We have designed, synthesized and characterized three- and four-helix bundle template-assembled synthetic proteins CTASPs). The TASPs were synthesized using disulphide bonds between the peptides and either the cyclotribenzylene (CTB) template, or the cavitand (BOWL) template, to form the three- and four helix bundles, respectively. The TASPs were constructed using peptides that were linked via their N-termini (peptide CGGGEELLKKXEELLKKG, where X = L, I, Nle or V), or via their C-termini (peptide GEELLKKLEELLKKGGGC). Each TASP was assayed for its structure, stability, 'native-like' characteristics and whether it was a monomer in solution. All TASPs were found to be highly helical, and highly resistant to chemical denaturation using guanidine hydrochloride (GnHCl). Analysis of the GnHCl-induced unfolding curves of the different TASPs demonstrated stability differences based on the number of helices in the bundle, the end of the helix that was attached to the template, and the identity of the core amino acid. The TASPs all had molten-globule structure, which is (generally) consistent with a degenerate sequence in the core. The four-helix bundle TASPs appeared to be monomers in solution, whereas there is some evidence that the three-helix bundle TASPs are weakly self-associating.

Ionic Rectification Properties of a Bipolar Interface Consisting of a Cationic Surfactant and Cation-Exchange Membrane

A novel bipolar interface that consists of cationic surfactant and cation-exchange membrane was successfully prepared in an aqueous electrolyte system. This bipolar interface shows a ionic rectification behavior similar to that observed in bipolar membranes. However, different from bipolar membranes, this system has a total rectification behavior, where we cannot observe the occurrence of a water-splitting phenomenon, which always occurs in the bipolar membrane process under reverse bias conditions.

Alamethicin-leucine zipper hybrid peptide: a prototype for the design of artificial receptors and ion channels

In this report, we describe a novel concept of extramembrane control of channel peptide assembly and the eventual channel current modulation. Alamethicin is a peptide antibiotic, which usually forms ion channels in various association states. By introducing an extramembrane leucine zipper segment (Alm-LeuZ), the association number of alamethicin was effectively controlled to produce a single predominant channel open state. The assembly was estimated to be a tetramer, by comparison of the channel conductance with that of the template-assembled Alm-LeuZ tetramer, which was prepared by the conjugation of a maleimide-functionalized peptide template with cysteine-derivatized Alm-LeuZ segments. Employment of an extramembrane segment of a random conformation provided higher levels of channel conductance. The result exemplified the possibility of channel current control by a conformational switch of the extramembrane segments.

A coiled coil with a fluorous core

The design, synthesis, and structural characterization of a highly fluorinated peptide system based on the coiled coil region of the yeast transcription factor GCN4 is described. All four leucine residues (a position) and three valine residues (d position) were replaced by the unnatural amino acids 5,5,5-trifluoroleucine and 4,4,4-trifluorovaline, respectively. The peptide is highly alpha-helical at low micromolar concentrations as judged by circular dichroism spectra, sediments as a dimeric species in the 5-30 microM concentration range, and exhibits a dimer melting temperature that is 15 degrees C higher than a control peptide with a hydrocarbon core. Furthermore, the apparent free energy of unfolding as calculated from guanidinium hydrochloride denaturation experiments is larger by approximately 1.0 kcal/mol for the fluorinated peptide than its hydrocarbon counterpart. We conclude that additional stability is derived from sequestering the more hydrophobic trifluoromethyl groups from aqueous solvent. These studies introduce a new paradigm in the design of molecular self-assembling systems, one based on orthogonal solubility properties of liquid phases.

Molecular design and synthesis of artificial ion channels based on cyclic peptides containing unnatural amino acids

A series of novel cyclic peptides composed of 3 to 5 dipeptide units with alternating natural-unnatural amino acid units, have been designed and synthesized, employing 5-(N-alkanoylamino)-3-aminobenzoic acid with a long alkanoyl chain as the unnatural amino acid. All cyclic peptides with systematically varying pore size, shape, and lipophilicity are found to form ion channels with a conductance of ca. 9 pS in aqueous KCl (500 mM) upon examination by the voltage clamp method. These peptide channels are cation selective with the permeability ratio P(Cl(-))/P(K(+)) of around 0.17. The ion channels formed by the neutral, cationic, and anionic cyclic peptides containing L-alanine, L-lysine, and L-aspartate, respectively, show the monovalent cation selectivity with the permeability ratio P(Na(+))/P(K(+)) of ca. 0.39. On the basis of structural information provided by voltage-dependent blockade of the single channel current of all the tested peptides by Ca(2+), we inferred that each channel is formed from a dimer of the peptide with its peptide ring constructing the channel entrance and its alkanoyl chains lining across the membrane to build up the channel pore. The experimental results are consistent with an idea that the rate of ion conduction is determined by the nature of the hydrophobic alkanoyl chain region, which is common to all the channels.

Channel-forming, self-assembling, bishelical amphiphilic peptides: design, synthesis and crystal structure of Py(Aibn)2, n=2,3,4

The design, synthesis, characterization and self-assembling properties of a new class of amphiphilic peptides, constructed from a bifunctional polar core attached to totally hydrophobic arms, are presented. The first series of this class, represented by the general structure Py(Aibn)2 (Py=2,6-pyridine dicarbonyl unit; Aib=alpha, alpha'-dimethyl glycine; n=1-4), is prepared in a single step by the condensation of commercially available 2,6-pyridine dicarbonyl dichloride with the methyl ester of homo oligoAib peptide (Aibn-OMe) in the presence of triethyl amine. 1H NMR VT and ROESY studies indicated the presence of a common structural feature of 2-fold symmetry and an NH...N hydrogen bond for all the members. Whereas the Aib3 segment in Py(Aib3)2 showed only the onset of a 3(10)-helical structure, the presence of a well-formed 3(10)-helix in both Aib4 arms of Py(Aib4)2 was evident in the 1H NMR of the bispeptide. X-ray crystallographic studies have shown that in the solid state, whereas Py(Aib2)2 molecules organize into a sheet-like structure and Py(Aib3)2 molecules form a double-stranded string assembly, the tetra Aib bispeptide, Py(Aib4)2, is organized to form a tetrameric assembly which in turn extends into a continuous channel-like structure. The channel is totally hydrophobic in the interior and can selectively encapsulate lipophilic ester (CH3COOR, R=C2H5, C5H11) molecules, as shown by the crystal structures of the encapsulating channel. The crystal structure parameters are: 1b, Py(Aib2)2, C25H37N5O8, sp. gr. P2(1)2(1)2(1), a=9.170(1) A, b=16.215(2) A, c=20.091(3) A, R=4.80; 1c, Py(Aib3)2, C33H51N7O10H2O, sp. gr. P1, a=11.040(1) A, b=12.367(1) A, c=16.959(1) A, alpha =102.41 degrees, beta =97.29 degrees, gamma =110.83 degrees, R1=6.94; 1 da, Py(Aib4)2.et ac, C41H65N9O12.1.5H2O.C4H8O2, sp. gr. P1, a=16.064(4) A, b=16.156 A, c=21.655(5) A, alpha =90.14(1)degrees, beta=101.38(2) degrees, gamma=97.07(1)degrees, Z=4, R1=9.03; 1db, Py(Aib4)2.amylac, C41H65N9O12.H2O.C7H14O2, P2(1)/c, a=16.890(1) A, b=17.523(1)A, c=20.411(1) A, beta=98.18 degrees, Z=4, R=11.1 (with disorder).

Design, synthesis, and crystal structure of self-assembling norbornene (NBE)-supported two-helix bundles: a unique example of Janus helicity in the solid-state structure of NBE(Aib(5))(2)

Norbornene-supported bis-helical peptides with the general structure NBE(Aib(n) )(2) (NBE: 2,3-trans-norbornene dicarbonyl unit; Aib: alpha,alpha'-dimethyl glycine unit; n = 4,5) have been synthesized and examined for self-assembly preferences in the solid state. An x-ray study has revealed a phenomenon of Janus helicity in the solid state structure of NBE(Aib(5))(2). The lower homologue NBE(Aib(4))(2), however, shows an identical screw sense for both the helical arms. The difference in the handedness of left and right arms is reflected in the self-assembly patterns. Thus, while the NBE(Aib(4))(2) molecule self-assembles to form an infinite hydrogen-bonded superhelical ladder, the Janus molecule NBE(Aib(5))(2) crystallizes as individual units surrounded by water molecules. The structures of Z-Aib(4)-OMe and Z-Aib(5)-OMe are also presented to compare their conformations with the helical arms of the title compound and also to the already known structures of other X-Aib(n) -Y compounds. The helices in all the molecules are the 3(10)-type.