Expanding the conformational pool of cis-beta-sugar amino acid: accommodation of beta-hGly motif in robust 14-helix

Tendencies of forming stable helices of heterooligomers composed of alternating rigid cis-beta-sugar amino acid and flexible beta-hGly motifs have been investigated, using a combination of molecular mechanics, CD, FT-IR, and NMR techniques. The results show that the solution structures of these oligomers exist as robust right-handed 14-helices. Here, we examine the role of conformationally rigid cis-beta-sugar amino acid in preorganizing the conformation of beta-hGly to form the 14-helix. Our findings also show that a right-handed 14-helix can be formed with as few as four properly sequenced heterogeneous residues. These results represent the expansion of the conformational pool of sugar amino acid in the design of well-folded 14-helices, which can be used to develop beta-peptides endowed with biological activity.     

Crystallographic characterization of helical secondary structures in alpha/beta-peptides with 1:1 residue alternation

Oligomers that contain both alpha- and beta-amino acid residues in a 1:1 alternating pattern have recently been shown by several groups to adopt helical secondary structures in solution. The beta-residue substitution pattern has a profound effect on the type of helix formed and the stability of the helical conformation. On the basis of two-dimensional NMR data, we have previously proposed that beta-residues with a five-membered ring constraint promote two different types of alpha/beta-peptide helix. The "11-helix" contains i, i+3 CO...H-N hydrogen bonds between backbone amide groups; these hydrogen bonds occur in 11-atom rings. The alpha/beta-peptide "14/15-helix" contains i, i+4 CO...H-N hydrogen bonds, which occur in alternating 14- and 15-atom rings. Here we provide crystallographic data for 14 alpha/beta-peptides that form the 11-helix and/or the 14/15-helix. These results were obtained for a series of oligomers containing beta-residues derived from ( S,S)- trans-2-aminocyclopentanecarboxylic acid (ACPC) and alpha-residues derived from alpha-aminoisobutyric acid (Aib) or l-alanine (Ala). The crystallized alpha/beta-peptides range in length from 4 to 10 residues. Nine of the alpha/beta-peptides display the 11-helix in the solid state, three display the 14/15-helix, and two display conformations that contain both i, i+3 and i, i+4 CO...H-N hydrogen bonds, but not bifurcated hydrogen bonds. Only 3 of the 14 crystal structures presented here have been previously described. These results suggest that longer alpha/beta-peptides prefer the 14/15-helix over the 11-helix, a conclusion that is consistent with previously reported NMR data obtained in solution.     

Positional screening and NMR structure determination of side-chain-to-side-chain cyclized β3-peptides

Many β-peptides fold in a 14-helical secondary structure in organic solvents, but similar 14-helix formation in water requires additional stabilizing elements. Especially the 14-helix stabilization of short β-peptides in aqueous solution is critical, due to the limited freedom for incorporating stabilizing elements. Here we show how a single lactam bridge, connecting two β-amino acid side-chains, can lead to high 14-helix character in short β(3)-peptides in water. A comparative study, using CD and NMR spectroscopy and structure calculations, revealed the strong 14-helix inducing power of a side-chain-to-side-chain cyclization and its optimal position on the β(3)-peptide scaffold with respect to pH and ionic strength effects. The lactam bridge is ideally incorporated in the N-terminal region of the β(3)-peptide, where it limits the conformational flexibility of the peptide backbone. The lactam bridge induces a 14-helical conformation in methanol and water to a similar extent. Based on the presented first high resolution NMR 3D structure of a lactam bridged β(3)-peptide, the fold shows a large degree of high order, both in the backbone and in the side-chains, leading to a highly compact and stable folded structure.     

Chain-length-dependent helical motifs and self-association of beta-peptides with constrained side chains

Homo-oligomers constructed by using trans-2-aminocyclohexanecarboxylic acid monomers without protecting groups were studied. Both ab initio theory and NMR measurements showed that the tetramer tends to adopt a 10-helix motif, while the pentamer and hexamer form the known 14-helix. It was concluded that the conformationally constrained backbone is flexible enough to afford both 10-helical and 14-helical motifs, this observation in turn providing evidence of the true folding process. Self-association of the helical units was also detected, and the results of variable-temperature diffusion NMR measurements strongly suggested the presence of helical bundles in methanol solution.     

Three-dimensional organization of helices: design principles for nucleobase-functionalized beta-peptides

The construction and molecular recognition of various three-dimensional biomimetic structures is based on the predictable de novo design of artificial molecules. In this regard beta-peptides are especially interesting, since stable secondary structures are obtained already with short sequences; one of them is the 14-helix in which every third residue has the same orientation. The covalent functionalization of every third 14-helix side chain with nucleobases was used for a reversible organization of two helices based on nucleobase pairing. A series of beta-peptides with various nucleobase sequences was synthesized and the stability of double strand formation was investigated. As few as four nucleobases are sufficient for considerable duplex stability. The stability of base pairing was examined by temperature-dependent UV spectroscopy and the formation of the 14-helix was confirmed by circular dichroism (CD) spectroscopy. The preferred strand orientation of complementary-nucleobase-modified beta-peptide helices was investigated as well as the influence of helix content on the duplex stability. The preorganization of a 14-helix in regard to double-strand recognition was tuned by the sequential order of polar beta-amino acids or by the amount of 2-aminocyclohexanecarboxylic acid units incorporated, which are known to facilitate 14-helix formation, respectively.     

Relationship between side chain structure and 14-helix stability of beta3-peptides in water

Folded polymers are used in Nature for virtually every vital process. Nonnatural folded polymers, or foldamers, have the potential for similar versatility, and the design and refinement of such molecules is of considerable current interest. Here we report a complete and systematic analysis of the relationship between side chain structure and the 14-helicity of a well-studied class of foldamers, beta(3)-peptides, in water. Our experimental results (1) verify the importance of macrodipole stabilization for maintaining 14-helix structure, (2) provide comprehensive evidence that beta(3)-amino acids branched at the first side chain carbon are 14-helix-stabilizing, (3) suggest a novel role for side chain hydrogen bonding as an additional stabilizing force in beta(3)-peptides containing beta(3)-homoserine or beta(3)-homothreonine, and (4) demonstrate that diverse functionality can be incorporated into a stable 14-helix. Gas- and solution-phase calculations and Monte Carlo simulations recapitulate the experimental trends only in the context of oligomers, yielding insight into the mechanisms behind 14-helix folding. The 14-helix propensities of beta(3)-amino acids differ starkly from the alpha-helix propensities of analogous alpha-amino acids. This contrast informs current models for alpha-helix folding, and suggests that 14-helix folding is governed by different biophysical forces than is alpha-helix folding. The ability to modulate 14-helix structure through side chain choice will assist rational design of 14-helical beta-peptide ligands for macromolecular targets.     

Secondary Structure Characterization of Glucagon Products by Circular Dichroism and Nuclear Magnetic Resonance Spectroscopy

Glucagon, a 29-amino acid polypeptide hormone, is an essential therapeutic agent used in the emergency treatment of hypoglycemia. However, glucagon is inherently unstable in aqueous solution. While glucagon equilibrates between unordered and the secondary α-helix state in solution, it can quickly transform into a different secondary β-sheet-rich amyloid-like fibril/oligomer structure under various conditions. Since changes in the secondary structure of glucagon can cause significant impacts, structure analysis is necessary and essential to assess the safety of the product. This study analyzed the secondary structure of glucagon products at the release and at the expiry using circular dichroism spectroscopy (CD) and 2D Nuclear Overhauser effect spectroscopy (2D NOESY). In order to also determine if structural differences exist between glucagon produced through different manufacturing processes, synthetic and recombinant glucagon products were used and compared. The CD results indicated that for all release and expired glucagon products, the structure compositions were 14 to 16% α-helix, 17 to 19% β-strand, 14 to 15% Turn, and 53 to 54% Unordered. This was consistent with the 2D NOESY analysis which showed that both products had an approximate α-helix composition of 14 to 17%. Overall, there were no significant differences in terms of the secondary structure between synthetic and recombinant glucagon products both at the release and at the expiry.     

A systematic study of the solid state and solution phase conformational preferences of β-peptides derived from transpentacin

The solid state and solution phase conformational preferences of a homologous series of β-peptides derived from (S,S)-2-aminocyclopentanecarboxylic acid (transpentacin) have been investigated using a variety of spectroscopic and crystallographic techniques. These studies indicate that the hexamer and pentamer persist as a 12-helix in both the solid state and solution phase. Although the conformational traits of a 12-helix are exhibited by oligomers with as few as three residues in the solid state, in solution the trimer exists as an equilibrium of many alternative conformers whilst the tetramer has been shown to predominantly exist in either a 12-helix or a turn-type conformation.     

Substrate selectivity of the sublancin S-glycosyltransferase

SunS is a novel S-glycosyltransferase involved in the biosynthesis of the antimicrobial peptide sublancin. It selectively modifies Cys22 in a 56 amino acid peptide substrate SunA and can accept a variety of NDP sugars. This study reports the substrate selectivity with regard to the peptide substrate and the antimicrobial activity of the resulting sublancin analogues. The results suggest that SunS recognizes an α-helix N-terminal of the Cys to be glycosylated, which is present in a flexible linker. Interestingly, when Cys22 is mutated, sugar attachment is not required for sublancin antimicrobial activity. Furthermore, the sublancin-producing strain Bacillus subtilis 168 also becomes susceptible to such mutants. These data suggest that S-glycosylation may be important for self-resistance.     

Preparation of some carbon-14-labeled amino acids by radiophotosynthesis using sugar beet plant

Radiophotosynthesis has been applied as a means for preparing a number of carbon-14-labeled amino acids using sugar beet plants grown under controlled environmental conditions. The apparatus used, conditions of operation, isolation of products, and their analysis and radiometry have been discussed in detail. From the results obtained, it can be inferred that a number of labeled amino acids could be separated from the leaves of sugar beet including [¹⁴C]alanine, γ-[¹⁴C]aminobutyric acid, [¹⁴C]glutamic acid, [¹⁴C]aspartic acid, [¹⁴C]serine, [¹⁴C]valine, and [¹⁴C]aspargine with specific activities of several microcuries per millimole. The specific activities of the products could be significantly increased by increasing the specific activity of the radioactive carbonate initially used.     

Accommodation of alpha-substituted residues in the beta-peptide 12-helix: expanding the range of substitution patterns available to a foldamer scaffold

Beta-amino acid oligomers composed exclusively of homochiral trans-2-aminocyclopentanecarboxylic acid (ACPC) residues and/or related pyrrolidine-based residues are known to favor a specific helical secondary structure that is defined by 12-membered ring C=O(i)- -H-N(i+3) hydrogen bonds ("12-helix"). The 12-helix is structurally similar to the familiar alpha-helix and therefore represents a source of potential alpha-helix-mimics. The 12-helix will be most useful in this regard if this conformational scaffold can be employed to arrange specific sets of protein-like side chains in space. Here we examine whether the 12-helix tolerates insertion of acyclic beta-amino acid residues bearing a substituent in the alpha-position ("beta(2)-residues"). Seventeen homologous beta-peptide heptamers have been prepared in which one to four beta(2)-residues reside among ACPC and/or pyrrolidine residues. Circular dichroism comparisons suggest that beta(2)-residues have a lower 12-helical propensity than do residues preorganized by a five-membered ring, as expected, but that beta-peptides containing beta(2)-residues at one or two of the seven positions retain a significant preference for 12-helix formation. These results indicate that a limited number of beta(2)-residues can be used to introduce side chains at specific positions along the surface of a 12-helix.     

Synthesis and characterisation of helical beta-peptide architectures that contain (S)-beta3-HDOPA(Crown Ether) derivatives

A new set of beta-amino acids that carry various crown ether receptors on their side chains of the general formula (S)-beta(3)-HDOPA(crown ether) (HDOPA: homo-3,4-dihydroxyphenylalanine; (crown ether): [15]crown-5 ([15-C-5]), [18]crown-6 ([18-C-6]), [21]crown-7 ([21-C-7]), 1,2-Benzo-[24]crown-8 ([Benzo-24-C-8]) and (R)-Binol-[20]crown-6 ([(R)-Binol-20-C-6])) was prepared. Peptides that are based on these new crowned beta-amino acids combined with (1S,2S)-ACHC (2-aminocyclohexanecarboxylic acid), which is known to be a potent 3(14)-helix inducer, to the hexamer level, with two crowned residues at the i and i+3 positions of the main-chain, were synthesized in solution by stepwise coupling using Boc-N(alpha)-protection (Boc: tert-butoxycarbonyl) and the EDC/HOAt C-activation method. Their conformational analysis was performed by using FTIR absorption, NMR and CD spectroscopy techniques. Our results are in full agreement with a 3(14)-helix conformation.     

Specific inclusion mode of guest compounds in the amylose complex analyzed by solid state NMR spectroscopy

The inclusion compound formation between linear amylose of molecular weight 102500 (AS100) and p-aminobenzoic acid (PA) during the sealed-heating process was investigated by powder X-ray diffractometry, infrared spectroscopy and solid state NMR spectroscopy. Sealed-heating of AS100 and PA at 100 degrees C for 6 h provided an inclusion compound with 6(1)-helix structure, while a 7(1)-helix structure was found when sealed-heating was carried out at 150 degrees C for 1 h. The formation of an inclusion compound was not observed when sealed-heating was performed at 50 degrees C for 6 h. The 7(1)-helix inclusion compound maintained its structure even during storage at high temperature while the 6(1)-helix inclusion compound decomposed and returned to the original V(a)-amylose upon heating to 180 degrees C. Quantitative determination revealed that one PA molecule could be included per one helical turn of AS100 for both 6(1)-helix and 7(1)-helix inclusion compounds. Solid state NMR spectroscopy suggested that PA molecules were included in the amylose helix core in the 7(1)-helix inclusion compound, while in the case of 6(1)-helix inclusion compound, PA molecules were accommodated in the interstices between amylose helices. Moreover, the inclusion compound formation by sealed-heating of AS100 was also observed when using PA analogues as guest compounds. The binding ratio of AS100 and PA analogues varied depending on the size of guest molecules.     

Structure-activity studies of 14-helical antimicrobial beta-peptides: probing the relationship between conformational stability and antimicrobial potency

Antimicrobial alpha-helical alpha-peptides are part of the host-defense mechanism of multicellular organisms and could find therapeutic use against bacteria that are resistant to conventional antibiotics. Recent work from Hamuro et al. has shown that oligomers of beta-amino acids ("beta-peptides") that can adopt an amphiphilic helix defined by 14-membered ring hydrogen bonds ("14-helix") are active against Escherichia coli [Hamuro, Y.; Schneider, J. P.; DeGrado, W. F. J. Am. Chem. Soc. 1999, 121, 12200-12201]. We have created two series of cationic 9- and 10-residue amphiphilic beta-peptides to probe the effect of 14-helix stability on antimicrobial and hemolytic activity. 14-Helix stability within these series is modulated by varying the proportions of rigid trans-2-aminocyclohexanecarboxylic acid (ACHC) residues and flexible acyclic residues. We have previously shown that a high proportion of ACHC residues in short beta-peptides encourages 14-helical structure in aqueous solution [Appella, D. H.; Barchi, J. J.; Durell, S. R.; Gellman, S. H. J. Am. Chem. Soc. 1999, 121, 2309-2310]. Circular dichroism of the beta-peptides described here reveals a broad range of 14-helix population in aqueous buffer, but this variation in helical propensity does not lead to significant changes in antibiotic activity against a set of four bacteria. Several of the 9-mers display antibiotic activity comparable to that of a synthetic magainin derivative. Among these 9-mers, hemolytic activity increases slightly with increasing 14-helical propensity, but all of the 9-mers are less hemolytic than the magainin derivative. Previous studies with conventional peptides (alpha-amino acid residues) have provided conflicting evidence on the relationship between helical propensity and antimicrobial activity. This uncertainty has arisen because alpha-helix stability can be varied to only a limited extent among linear alpha-peptides without modifying parameters important for antimicrobial activity (e.g., net charge or hydrophobicity); a much greater range of helical stability is accessible with beta-peptides. For example, it is very rare for a linear alpha-peptide to display significant alpha-helix formation in aqueous solution and manifest antibacterial activity, while the linear beta-peptides described here range from fully unfolded to very highly folded in aqueous solution. This study shows that beta-peptides can be unique tools for analyzing relationships between conformational stability and biological activity.     

Relationship between salt-bridge identity and 14-helix stability of beta3-peptides in aqueous buffer

[STRUCTURE: SEE TEXT] We report a systematic analysis of the relationship between salt bridge composition and 14-helix structure within a family of model beta-peptides in aqueous buffer. We find an inverse relationship between side-chain length and the extent of 14-helix structure as judged by CD. Introduction of a stabilizing salt bridge pair within a previously reported beta-peptide ligand for hDM2 led to changes in structure that were detectable by NMR.     

Helix macrodipole control of beta 3 peptide 14-helix stability in water

beta-Peptides have attracted considerable attention by virtue of their ability to populate helical secondary structures in methanol, even in the absence of stabilizing tertiary interactions. Recent efforts in beta-peptide design have produced few beta3-peptides that form stable 14-helices in water; those that do require stabilizing intramolecular salt bridges on two of three helical faces and therefore possess limited utility as tools in biological research. Here we show that favorable interactions with the 14-helix macrodipole significantly stabilize the 14-helix in water, alleviating the need for multiple salt bridges on two of three helical faces. We also report the previously unrecognized stabilization of 14-helix structure by gamma-branched beta3-amino acids. The most structured molecules we describe are highly heterogeneous at the primary sequence level, containing seven different beta3-amino acids within an 11-residue sequence. These results represent the essential first step toward the design of well-folded 14-helices that explore the interactions between beta3-peptides and biological macromolecules in vitro and in vivo.     

Comparison of two force fields in MD-simulations of α-helical structures in keratins

Molecular dynamic (MD) simulations based on two different force fields, CVFF and CFF91, were carried out in order to check their feasibility for the structural investigation of the wool intermediate filament (IF) monomeric unit. Selecting an ideal α-helix as start conformation, all MD-simulations with CVFF in vaccum show the α-helix to be unstable. Independently of the amino acid sequence of the α-helix, a new helical structure with a larger diameter arises during the MD-simulation, due to a shift of the intrahelical hydrogen bonds. However in simulations with surrounding water the α-helix remains stable throughout the simulations with the CVFF force field. In contrast to this, MD-simulations in vaccume based on the CFF91 force field are able to determine different stabilities for the α-helical start conformation of various IF-segments, that agree well with secondary structure predictions. The simulation results obtained with CFF91 in vacuum can like wise be verified using an explicit water environment. We found that higher partial charges attributed to the atoms of the amide groups that form the intrahelical hydrogen bonds are the reason for the superiority of the CFF91 force field.     

Helical beta-peptide inhibitors of the p53-hDM2 interaction

hDM2 is recognized in vivo by a short alpha-helix within the p53 trans-activation domain (p53AD). Disruption of the p53.hDM2 interaction is an important goal for cancer therapy. A functional epitope comprised of three residues on one face of the p53AD helix (F19, W23, and L26) contributes heavily to the binding free energy. We hypothesized that the p53AD functional epitope would be recapitulated if the side chains of F19, W23, and L26 were presented at successive positions three residues apart on a stabilized beta3-peptide 14-helix. Here, we report a set of beta3-peptides that possess significant 14-helix structure in water; one recognizes a cleft on the surface of hDM2 with nanomolar affinity. The strategy for beta3-peptide design that we describe is general and may have advantages over one in which individual or multiple beta-amino acid substitutions are introduced into a functional alpha-peptide, because it is based on homology at the level of secondary structure, not primary sequence.     

Synthesis of new peptidic glycoclusters derived from beta-alanine. Part 2: optionally modulated distance between side-chain branched points

The synthesis of an asymmetric glycocluster 1 has been achieved using two glycocluster units 12 and 13, prepared by coupling the cluster chain unit 4 with each omega-amino acid (beta-alanine and 6-aminocapronic acid) trichloroethyl ester, and peptidic C-terminal block glycocluster 16, prepared by coupling the bifunctional linker 14 with sugar unit 9. This method facilitated the synthesis of the cluster optionally modulated the distance between the side-chain branched points by using various omega-amino acids. We also synthesized glycodendron 2 using the same intermediate.     

Application of microwave irradiation to the synthesis of 14-helical beta-peptides

[structure: see text] We have evaluated the effects of microwave irradiation on the solid-phase synthesis of beta-peptides. Sequences designed to adopt the 14-helix, especially those containing the structure-promoting residue trans-2-aminocyclohexanecarboxylic acid (ACHC), suffer from poor synthetic efficiency under standard SPPS conditions. A comparison of microwave and conventional heating shows that both provide excellent synthetic results for shorter sequences; however, we identify a clear benefit from microwave irradiation for longer beta-peptides.