De novo design, synthesis, and characterization of a pore-forming small globular protein and its insertion into lipid bilayers

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.

Structural Design and Characterization of a Channel-forming Peptide

A 16-residue polypeptide model with the sequence acetyl-YALSLAATLLKEAASL-OH was derived by rational de novo peptide design. The designed sequence consists of amino acid residues with high propensity to adopt an alpha helical conformation, and sequential order was arranged to produce an amphipathic surface. The designed sequence was chemically synthesized using a solid-phase method and the polypeptide was purified by reverse-phase liquid chromatography. Molecular mass analysis by electro-spray ionization mass spectroscopy confirmed the correct designed sequence. Structural characterization by circular dichroism spectroscopy demonstrated that the peptide adopts the expected alpha helical conformation in 50% acetonitrile solution. Liposome binding assay using Small Unilamellar Vesicle (SUV) showed a marked release of entrapped glucose by interaction between the lipid membrane and the tested peptide. The channel-forming activity of the peptide was revealed by a planar lipid bilayer experiment. An analysis of the conducting current at various applied potentials suggested that the peptide forms a cationic ion channel with an intrinsic conductance of 188 pS. These results demonstrate that a simple rational de novo design can be successfully employed to create short peptides with desired structures and functions.

An artificially designed pore-forming protein with anti-tumor effects

Protein engineering is an emerging area that has expanded our understanding of protein folding and laid the groundwork for the creation of unprecedented structures with unique functions. We previously designed the first native-like pore-forming protein, small globular protein (SGP). We show here that this artificially engineered protein has membrane-disrupting properties and anti-tumor activity in several cancer animal models. We propose and validate a mechanism for the selectivity of SGP toward cell membranes in tumors. SGP is the prototype for a new class of artificial proteins designed for therapeutic applications.

Smart and genetically engineered biomaterials and drug delivery systems

The design, synthesis, and properties of novel stimuli-sensitive and genetically engineered biomaterials and drug delivery systems are reviewed. Two approaches to their engineering are presented. One approach is to improve the traditional methods of synthesis, as demonstrated by the example of controlled copolymerization of alpha-amino acid N-carboxyanhydrides. The other approach, discussed in more detail, uses genetic engineering methods. The design of hybrid hydrogel systems whose components derive from at least two distinct classes of molecules, e.g., synthetic macromolecules and protein domains, is assessed. The design of self-assembling block copolymers is discussed in detail. Finally, the pharmaceutics related applications of these materials are presented.

Roles of peptide-peptide charge interaction and lipid phase separation in helix-helix association in lipid bilayer

The roles of peptide-peptide charged interaction and lipid phase separation in helix-helix association in lipid bilayers were investigated using a model peptide, P(24), as a transmembrane alpha-helical peptide, and its four analogues. Fluorescence amino acids, tryptophan (P(24)W) and pyrenylalanine (P(24)Pya), were introduced into the sequence of P(24), respectively. Association of these peptides permits the resonance excitation energy transfer between tryptophan in P(24)W and pyrenylalanine in P(24)Pya or excimer formation between P(24)Pya themselves. To evaluate the effect of charged interaction on the association between alpha-helical transmembrane segments in membrane proteins, charged amino acids, glutamic acid (P(24)EW) and lysine (P(24)KPya), were introduced into P(24)W and P(24)Pya, respectively. Energy transfer experiments indicated that the charged interaction between the positive charge of lysine residue in P(24)KPya and the negative charge of glutamic acid residue in P(24)EW did not affect the aggregation of transmembrane peptides in lipid membranes. As the content ratio of sphingomyelin (SM) and cholesterol (Ch) was increased in the egg phosphatidylcholine (PC), the stronger excimer fluorescence spectra of P(24)Pya were observed, indicating that the co-existence of SM and Ch in PC liposomes, that is, the raft of SM and Ch, promotes the aggregation of the alpha-helical transmembrane peptides in lipid bilayers. Since the increase in the contents of SM and Ch leads to the decrease in the content of liquid crystalline-order phase, the moving area of transmembrane peptides might be limited in the liposomes, resulting in easy formation of the excimer in the presence of the lipid-raft.

Study on the packing geometry, stoichiometry, and membrane interaction of three analogs related to a pore-forming small globular protein

A de novo designed pore-forming small globular protein (SGP) with antitumor activity consists of four helices: 3 basic amphipathic helices composed of Leu and Lys surrounding a central hydrophobic helix composed of oligoalanine. These helices are connected by a beta-turn-forming sequence and two beta-turn-unfavorable ones (S. Lee, T. Kiyota, T. Kunitake, E. Matsumoto, S. Yamashita, K. Anzai, and G. Sugihara Biochemistry 1997, Vol. 36, pp. 3782-3791). In the present work, we designed and synthesized three new SGP analogs in order to study the stoichiometric packing geometry and stability of SGP. The replacement of alanines in the central helix of SGP with leucines (SGP-L), which make the helix much larger in size and more hydrophobic, resulted in an equilibrium of monomeric-trimeric structure. The replacement of some Lys residues by Glu residues in the hydrophilic regions of the amphipathic helices (SGP-E) led to a decrease in helical content and the formation of an equilibrium of monomeric-trimeric structure. The alteration of beta-turn regions with Gly residues, which makes these regions flexible (SGP-G), established an equilibrium of monomeric-dimeric states in buffer. The hydrophobic alpha-helix of SGP-L penetrated into the lipid bilayers in a manner that stabilized model membranes and biomembranes, whereas the central helices of SGP-G and -E destabilized them by forming channels. SGP and its analogs may be a useful model to study the role of the hydrophobic and hydrophilic regions in the formation of monomer-oligomer of proteins and to better understand the insertion of membrane targeting proteins into biomembranes.

The coiled coils in the design of protein-based constructs: hybrid hydrogels and epitope displays

Recombinant DNA technology provides a powerful tool for producing protein-based biomaterials. Genetically engineered coiled coils have been used as a structural module for the construction of a variety of bio-based systems useful in drug delivery studies. Two of such approaches developed in the authors' laboratory were described here. One approach was to assemble hybrid hydrogels from coiled coil protein domains and synthetic polymers. Preliminary results showed that temperature-sensitive volume transition of the hybrid hydrogels could be triggered by the thermal unfolding of the engineered coiled coil protein domains. The other approach, discussed in detail, was to construct an epitope display model system based on a coiled coil stem loop peptide self-assembled on a solid substrate. This model construct displayed a constrained nonapeptide sequence, which was found to mediate specific binding with immunocompetent cells bearing complementary surface receptors. These novel approaches will likely find important applications in the rational design of more effective drug delivery systems.

Topological diversity of artificial beta-barrels in water

Rigid-rod beta-barrels are composed of interdigitating, short, amphiphilic peptide strands flanked by stabilizing rigid-rod "staves". We here report studies on the topological diversity of these recently devised artificial beta-barrels with regard to their length. For this purpose, homologous p-octiphenyl, p-sexiphenyl, and p-quarterphenyl rods were equipped with complementary tripeptide strands based on the sequences Lys-Leu-Lys and Glu-Leu-Glu. The stability of rigid-rod beta-barrels of different length was determined by denaturation with guanidinium chloride. Free energies of delta GH2O = -5.2 kcalmol-1, delta GH2O = -2.9 kcalmol-1, and delta GH2O < -0.3 kcalmol-1 found for homologous p-octiphenyl, p-sexiphenyl, and p-quarterphenyl beta-barrels demonstrated strong dependence of beta-barrel stability on beta-barrel length. These results revealed a very qualitative minimal (approximately 23 A) and an "ideal" beta-barrel length (approximately 34 A), synergistic formation (alpha = 1.4) and remarkable stability for "ideal" p-octiphenyl beta-barrels exceeding that of several proteins and most synthetic models. Rigid-rod beta-barrels with p-oligophenyl "staves" longer than approximately 34 A will be very difficult to make and study because of rapidly decreasing rod solubilities. However, a strategy to bypass this apparent upper limitation of beta-barrel length is introduced: supramolecular matching of mismatched rods yielded elongated beta-barrels (61 A) of acceptable stability (delta GH2O = 2.2 - 3.1 kcalmol-1).

Morphological behavior of acidic and neutral liposomes induced by basic amphiphilic alpha-helical peptides with systematically varied hydrophobic-hydrophilic balance

Lipid-peptide interaction has been investigated using cationic amphiphilic alpha-helical peptides and systematically varying their hydrophobic-hydrophilic balance (HHB). The influence of the peptides on neutral and acidic liposomes was examined by 1) Trp fluorescence quenched by brominated phospholipid, 2) membrane-clearing ability, 3) size determination of liposomes by dynamic light scattering, 4) morphological observation by electron microscopy, and 5) ability to form planar lipid bilayers from channels. The peptides examined consist of hydrophobic Leu and hydrophilic Lys residues with ratios 13:5, 11:7, 9:9, 7:11, and 5:13 (abbreviated as Hels 13-5, 11-7, 9-9, 7-11, and 5-13, respectively; Kiyota, T., S. Lee, and G. Sugihara. 1996. Biochemistry. 35:13196-13204). The most hydrophobic peptide (Hel 13-5) induced a twisted ribbon-like fibril structure for egg PC liposomes. In a 3/1 (egg PC/egg PG) lipid mixture, Hel 13-5 addition caused fusion of the liposomes. Hel 13-5 formed ion channels in neutral lipid bilayer (egg PE/egg PC = 7/3) at low peptide concentrations, but not in an acidic bilayer (egg PE/brain PS = 7/3). The peptides with hydrophobicity less than Hel 13-5 (Hels 11-7 and Hel 9-9) were able to partially immerse their hydrophobic part of the amphiphilic helix in lipid bilayers and fragment liposome to small bicelles or micelles, and then the bicelles aggregated to form a larger assembly. Peptides Hel 11-7 and Hel 9-9 each formed strong ion channels. Peptides (Hel 7-11 and Hel 5-13) with a more hydrophilic HHB interacted with an acidic lipid bilayer by charge interaction, in which the former immerses the hydrophobic part in lipid bilayer, and the latter did not immerse, and formed large assemblies by aggregation of original liposomes. The present study clearly showed that hydrophobic-hydrophilic balance of a peptide is a crucial factor in understanding lipid-peptide interactions.

Combining hydrophobicity and helicity: a novel approach to membrane protein structure prediction

In spite of the overwhelming numbers and critical biological functions of membrane proteins, only a few have been characterized by high-resolution structural techniques. From the structures that are known, it is seen that their transmembrane (TM) segments tend to fold most often into alpha-helices. To evaluate systematically the features of these TM segments, we have taken two approaches: (1) using the experimentally-measured residence behavior of specifically designed hydrophobic peptides in RP-HPLC, a scale was derived based directly on the properties of individual amino acids incorporated into membrane-interactive helices: and (2) the relative alpha-helical propensity of each of the 20 amino acids was measured in the organic non-polar environment of n-butanol. By combining the resulting hydrophobicity and helical propensity data, in conjunction with consideration of the 'threshold hydrophobicity' required for spontaneous membrane integration of protein segments, an approach was developed for prediction of TM segments wherein each must fulfill the dual requirements of hydrophobicity and helicity. Evaluated against the available high-resolution structural data on membrane proteins, the present combining method is shown to provide accurate predictions for the locations of TM helices. In contrast, no segment in soluble proteins was predicted as a 'TM helix'.

Uncoupling hydrophobicity and helicity in transmembrane segments. Alpha-helical propensities of the amino acids in non-polar environments

Although the chains of amino acids in proteins that span the membrane are demonstrably helical and hydrophobic, little attention has been paid toward addressing the range of helical propensities of individual amino acids in the non-polar environment of membranes. Because it is inappropriate to apply soluble protein-based structure prediction algorithms to membrane proteins, we have used de novo designed peptides (KKAAAXAAAAAXAAWAAXAAAKKKK-amide, where X indicates one of the 20 commonly occurring amino acids) that mimic a protein membrane-spanning domain to determine the alpha-helical proclivity of each residue in the isotropic non-polar environment of n-butanol. Peptide helicities measured by circular dichroism spectroscopy were found to range from theta222 = -17,000 degrees (Pro) to -38,800 degrees (Ile) in n-butanol. The relative helicity of each amino acid is shown to be well correlated with its occurrence frequency in natural transmembrane segments, indicating that the helical propensity of individual residues in concert with their hydrophobicity may be a key determinant of the conformations of protein segments in membranes.