A Model Study to Assess Fibrillation and Product Stability to Support Peptide Drug Design

The fibrillation of therapeutic peptides can present significant quality concerns and poses challenges for manufacturing and storage. A fundamental understanding of the mechanisms of fibrillation is critical for the rational design of fibrillation-resistant peptide drugs and can accelerate product development by guiding the selection of solution-stable candidates and formulations. The studies reported here investigated the effects of structural modifications on the fibrillation of a 29-residue peptide (PepA) and two sequence modified variants (PepB, PepC). The C-terminus of PepA was amidated, whereas both PepB and PepC retained the carboxylate, and Ser16 in PepA and PepB was substituted with a helix-stabilizing residue, α-aminoisobutyric acid (Aib), in PepC. In thermal denaturation studies by far-UV CD spectroscopy and fibrillation kinetic studies by fluorescence and turbidity measurements, PepA and PepB showed heat-induced conformational changes and were found to form fibrils, whereas PepC did not fibrillate and showed only minor changes in the CD signal. Pulsed hydrogen-deuterium exchange mass spectrometry (HDX-MS) showed a high degree of protection from HD exchange in mature PepA fibrils and its proteolytic fragments, indicating that most of the sequence had been incorporated into the fibril structure and occurred nearly simultaneously throughout the sequence. The effects of the net peptide charge and formulation pH on fibrillation kinetics were investigated. In real-time stability studies of two formulations of PepA at pH's 7.4 and 8.0, analytical methods detected significant changes in the stability of the formulations at different time points during the study, which were not observed during accelerated studies. Additionally, PepA samples were withdrawn from real-time stability and subjected to additional stress (40 °C, continuous shaking) to induce fibrillation; an approach that successfully amplified oligomers or prefibrillar species previously undetected in a thioflavin T assay. Taken together, these studies present an approach to differentiate and characterize fibrillation risk in structurally related peptides under accelerated and real-time conditions, providing a model for rapid, iterative structural design to optimize the stability of therapeutic peptides.

Molecular and Structural Mechanism of Pan-Genotypic HCV NS3/4A Protease Inhibition by Glecaprevir

Hepatitis C virus, causative agent of chronic viral hepatitis, infects 71 million people worldwide and is divided into seven genotypes and multiple subtypes with sequence identities between 68 to 82%. While older generation direct-acting antivirals had varying effectiveness against different genotypes, the newest NS3/4A protease inhibitors including glecaprevir (GLE) have pan-genotypic activity. The structural basis for pan-genotypic inhibition and effects of polymorphisms on inhibitor potency were not well-known due to lack of crystal structures of GLE-bound NS3/4A or genotypes other than 1. In this study, we determined the crystal structures of NS3/4A from genotypes 1a, 3a, 4a, and 5a in complex with GLE. Comparison with the highly similar grazoprevir indicated the mechanism of GLE's drastic improvement in potency. We found that, while GLE is highly potent against wild-type NS3/4A of all genotypes, specific resistance-associated substitutions (RASs) confer orders of magnitude loss in inhibition. Our crystal structures reveal molecular mechanisms behind pan-genotypic activity of GLE, including potency loss due to RASs at D168. Our structures permit for the first time analysis of changes due to polymorphisms among genotypes, providing insights into design principles that can aid future drug development and potentially can be extended to other proteins.

Evaluation of Aib and PEG-polymer insect kinin analogs on mosquito and tick GPCRs identifies potent new pest management tools with potentially enhanced biostability and bioavailability

Insect kinins modulate aspects of diuresis, digestion, development, and sugar taste perception in tarsi and labellar sensilla in mosquitoes. They are, however, subject to rapid biological degradation by endogenous invertebrate peptidases. A series of α-aminoisobutyric (Aib) acid-containing insect kinin analogs incorporating sequences native to the Aedes aegypti mosquito aedeskinins were evaluated on two recombinant kinin invertebrate receptors stably expressed in cell lines, discovering a number of highly potent and biostable insect kinin mimics. On the Ae. aegypti mosquito kinin receptor, three highly potent, biostable Aib analogs matched the activity of the Aib-containing biostable insect kinin analog 1728, which previously showed disruptive and/or aversive activity in aphid, mosquito and kissing bug. These three analogs are IK-Aib-19 ([Aib]FY[Aib]WGa, EC₅₀ = 18 nM), IK-Aib-12 (pQKFY[Aib]WGa, EC₅₀ = 23 nM) and IK-Aib-20 ([Aib]FH[Aib]WGa, EC₅₀ = 28 nM). On the Rhipicephalus (Boophilus) microplus tick receptor, IK-Aib-20 ([Aib]FH[Aib]WGa, EC₅₀ = 2 nM) is more potent than 1728 by a factor of 3. Seven other potentially biostable analogs exhibited an EC₅₀ range of 5-10 nM, all of which match the potency of 1728. Among the multi-Aib hexapeptide kinin analogs tested the tick receptor has a preference for the positively-charged, aromatic H over the aromatic residues Y and F in the X¹ variable position ([Aib]FX¹[Aib]WGa), whereas the mosquito receptor does not distinguish between them. In contrast, in a mono-Aib pentapeptide analog framework (FX¹[Aib]WGa), both receptors exhibit a preference for Y over H in the variable position. Among analogs incorporating polyethylene glycol (PEG) polymer attachments at the N-terminus that can confer enhanced bioavailability and biostability, three matched or surpassed the potency of a positive control peptide. On the tick receptor IK-PEG-9 (P₈-R[Aib]FF[Aib]WGa) was the most potent. Two others, IK-PEG-8 (P₈-RFFPWGa) and IK-PEG-6 (P₄-RFFPWGa), were most potent on the mosquito receptor, with the first surpassing the activity of the positive control peptide. These analogs and others in the IK-Aib series expand the toolbox of potent analogs accessible to invertebrate endocrinologists studying the structural requirements for bioactivity and the as yet unknown role of the insect kinins in ticks. They may contribute to the development of selective, environmentally friendly pest arthropod control agents.

Stapled truncated orexin peptides as orexin receptor agonists

The peptides orexin-A and -B, the endogenous agonists of the orexin receptors, have similar 19-amino-acid C-termini which retain full maximum response as truncated peptides with only marginally reduced potency, while further N-terminal truncations successively reduce the activity. The peptides have been suggested to bind in an α-helical conformation, and truncation beyond a certain critical length is likely to disrupt the overall helical structure. In this study, we set out to stabilize the α-helical conformation of orexin-A_15-33 via peptide stapling at four different sites. At a suggested hinge region, we varied the length of the cross-linker as well as replaced the staple with two α-aminoisobutyric acid residues. Modifications close to the peptide C-terminus, which is crucial for activity, were not allowed. However, central and N-terminal modifications yielded bioactive peptides, albeit with decreased potencies. This provides evidence that the orexin receptors can accommodate and be activated by α-helical peptides. The decrease in potency is likely linked to a stabilization of suboptimal peptide conformation or blocking of peptide backbone-receptor interactions at the hinge region by the helical stabilization or the modified amino acids.

Lipovelutibols A-D: Cytotoxic Lipopeptaibols from the Himalayan Cold Habitat Fungus Trichoderma velutinum

Four novel lipovelutibols A (1), B (2), C (3), and D (4) containing six amino acid residues with leucinol at the C-terminus and a fatty acyl moiety (n-octanoyl) at its N-terminus were isolated from the psychrotrophic fungus Trichoderma velutinum collected from the Himalayan cold habitat. The structures (1-4) were determined by NMR and MS/MS, and the stereochemistry of amino acids by Marfey's method. Lipopeptaibols 2 and 4 were found to contain d-isovaline, a nonproteinogenic amino acid, but lacked α-aminoisobutyric acid, characteristic of peptaibols. Cytotoxic activity of 2 and 4 was observed against HL-60, LS180, MDA-MB-231, and A549 cancer cell lines.

BAIBA attenuates insulin resistance and inflammation induced by palmitate or a high fat diet via an AMPK-PPARδ-dependent pathway in mice

AIMS/HYPOTHESIS

We explored the effects of β-aminoisobutyric acid (BAIBA) on hyperlipidaemic-condition-induced insulin resistance and inflammation as mediated through a signalling pathway involving AMP-activated protein kinase (AMPK) and peroxisome proliferator-activated receptor δ (PPARδ).

METHODS

Mouse skeletal muscle C2C12 cells and C57BL/6J mice were treated with palmitate or a high-fat diet (HFD) and BAIBA. Inflammation and the expression of genes associated with insulin signalling were determined by western blot and quantitative real-time PCR. Selected genes from candidate pathways were evaluated by small interfering (si)RNA knockdown and specific inhibitors.

RESULTS

BAIBA treatment ameliorated impairment of insulin receptor substrate (IRS)-1/Akt-mediated insulin signalling in palmitate-treated C2C12 myocytes and in skeletal muscle of HFD-fed mice. In addition, BAIBA treatment reversed HFD-induced increases in body weight and improved impaired glucose tolerance in mice. In vitro and in vivo, inhibitory κBα (IκBα) phosphorylation, nuclear factor κB (NFκB) nuclear translocation and downstream inflammatory cytokines were significantly suppressed by BAIBA. Furthermore, BAIBA treatment significantly induced AMPK phosphorylation and expression of PPARδ in C2C12 myocytes and in skeletal muscle of mice. Both compound C, an AMPK inhibitor, and Pparδ (also known as Ppard) siRNA abrogated the inhibitory effects of BAIBA on palmitate-induced inflammation and insulin resistance. BAIBA significantly induced the expression of genes associated with fatty acid oxidation, such as carnitine palmitoyltransferase 1 (Cpt1), acyl-CoA oxidase (Aco; also known as Acox1) and fatty acid binding protein 3 (Fabp3); this effect of BAIBA was significantly reduced by compound C and Pparδ siRNA.

CONCLUSIONS/INTERPRETATION

These results are the first to demonstrate that BAIBA attenuates insulin resistance, suppresses inflammation and induces fatty acid oxidation via the AMPK-PPARδ pathway in skeletal muscle.

Aib-containing peptide analogs: cellular uptake and utilization in oligonucleotide delivery

α-Aminoisobutyric acid (Aib)-containing peptide analogs derived from TV-XIIa, a cell-penetrating peptide (CPP), were synthesized to explore structure-activity relationships. The replacement of Aib at position 1, 5, or 9 in the TV-XIIa amino acid sequence with alanine (Ala) suppressed the cellular uptake,whereas the simultaneous substitution of the two proline (Pro) residues at positions 6 and 10 with Aib(P-IV) considerably increased the cellular uptake. In order to explore the potential use of the Aib-containing peptide analogs for the cellular delivery of oligonucleotides (ODNs), we synthesized a covalent conjugate (P-IV-AON) of a 15-mer antisense ODN, which is complementary to luciferase gene, with P-IV, and the antisense effect of the P-IV-AON conjugate on luciferase expression in A549 cells was examined. Luciferase expression was decreased in the presence of the conjugate upon treatment with the reaction buffer at the concentrations of 5 and 10 μM.

Multidimensional Langevin Modeling of Nonoverdamped Dynamics

Based on a given time series, data-driven Langevin modeling aims to construct a low-dimensional dynamical model of the underlying system. When dealing with physical data as provided by, e.g., all-atom molecular dynamics simulations, effects due to small damping may be important to correctly describe the statistics (e.g., the energy landscape) and the dynamics (e.g., transition times). To include these effects in a dynamical model, an algorithm that propagates a second-order Langevin scheme is derived, which facilitates the treatment of multidimensional data. Adopting extensive molecular dynamics simulations of a peptide helix, a five-dimensional model is constructed that successfully forecasts the complex structural dynamics of the system. Neglect of small damping effects, on the other hand, is shown to lead to significant errors and inconsistencies.

Recent data on obesity research: β-aminoisobutyric acid

The world-wide epidemic of obesity is now affecting up to a third of the adult population. Research attempting to contribute to management of this health scourge has been recently refocused on the essential role of physical activity. Muscle activity induces a dramatic increase in transcription of the peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α). This protein is a regulator of mitochondrial biogenesis and function. Very recently, in 2014 it was revealed that the mediator of this metabolic process is a low molecular myokine, the beta- aminoisobutyric acid (BAIBA). This compound with a simple molecular structure has a key metabolic role: it converts the cells of white adipose tissue into brown fat. The brown adipocytes contain a protein thermogenin. This substance turns off the energy stores, among others the adenosine triphosphate (ATP), thereby accelerating the breakdown of lipids into heat, water and CO2. We may be at the threshold of new and effective management of obesity. The world eagerly expects to see how the BAIBA will compare with other recently reported agents to fight the overweight (Fig. 2, Ref. 6).

Eight new peptaibols from sponge-associated Trichoderma atroviride

Eight new and four known peptaibols were isolated from a strain of the fungus, Trichoderma atroviride (NF16), which was cultured from an Axinellid sponge collected from the East Mediterranean coast of Israel. The structures of the pure compounds were determined using HRMS, MS/MS and one- and two-dimensional NMR measurements. The isolated compounds belong to the trichorzianines, a family of 19-residue linear hydrophobic peptides containing a high proportion of α-aminoisobutyric acid (Aib), an acetylated N-terminus and a C-terminal amino alcohol. These new peptaibols exhibited antimicrobial activity against environmental bacteria isolated from the Mediterranean coast of Israel.

Non-natural amino acids containing peptide-capped gold nanoparticles for drug delivery application

Peptide-based capping agents for gold nanoparticles (GNPs) are possible alternatives for capping and derivatizing GNPs, but suffer from a major disadvantage of sensitivity toward non specific proteases, which may limit their in vivo utility. Using non-natural analogs of natural α-amino acids offer an attractive alternate strategy to circumvent this potential bottleneck in realizing full potential of peptide based capping gents for GNPs for biological applications. Here, we have designed and developed pentapeptides containing non-natural amino acid (α,β-dehydrophenylalanine and α-aminoisobutyric acid) as capping agents for GNPs. All these peptides were able to efficiently cap GNPs and peptide induced aggregation was not observed. Peptide capped GNPs showed minimal cytotoxicity to mammalian cell lines (HeLa and L929) as well as mice spleenocytes. They encapsulated small drug like molecules and peptide capped GNPs entrapping drugs were more efficient in killing HeLa cells compared to the free drug. Therefore, these non-natural amino acid containing peptide-capped GNPs may be further developed as alternate drug delivery vehicles.

Conformationally constrained functional peptide monolayers for the controlled display of bioactive carbohydrate ligands

In this study, we employed thiolated peptides of the conformationally constrained, strongly helicogenic α-aminoisobutyric acid (Aib) residue to prepare self-assembled monolayers (SAMs) on gold surfaces. Electrochemistry and infrared reflection absorption spectroscopy support the formation of very well packed Aib-peptide SAMs. The immobilized peptides retain their helical structure, and the resulting SAMs are stabilized by a network of intermolecular H bonds involving the NH groups adjacent to the Au surface. Binary SAMs containing a synthetically defined glycosylated mannose-functionalized Aib-peptide as the second component display similar features, thereby providing reproducible substrates suitable for the controlled display of bioactive carbohydrate ligands. The efficiency of such Aib-based SAMs as a biomolecular recognition platform was evidenced by examining the mannose-concanavalin A interaction via surface plasmon resonance biosensing.

Normal coordinate analysis and vibrational spectroscopy (FT-IR and FT-Raman) studies of (2S)-2-amino-3-(3,4-dihydroxyphenyl)-2-methylpropanoic acid using ab initio HF and DFT method

The FT-IR and FT-Raman spectra of (2S)-2-amino-3-(3,4-dihydroxyphenyl)-2-methylpropanoic acid (2ADMA) were recorded in the region 4000-400 cm(-1) and 4000-100 cm(-1), respectively. The geometrical structure, harmonic vibrational frequency, infrared intensity, Raman activities and bonding features of this compound was carried out by ab initio HF and DFT methods with 6-31G (d,p) basis set. The complete vibrational frequency assignments were made by normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMF). The electric dipole moment (μ) and the first-order hyperpolarizability (β(0)) values have been the computed quantum mechanically. The calculated HOMO and LUMO energies show that, the charge transfer occurs within the molecule. The charge delocalizations of these molecules have been analyzed using NBO analysis. The solvent effects have been calculated using TD-DFT in combination with the polarized continuum model (PCM), and the results are in good agreement with experimental measurements. The other molecular properties like Mulliken population analysis, electrostatic potential (ESP) and thermodynamic properties of the title compound at the different temperatures have been calculated. Finally, the calculation results were applied to simulate infrared and Raman spectra of the title compound which shows good agreement with observed spectra.

Inhibition of caspase-9 by stabilized peptides targeting the dimerization interface

Caspases comprise a family of dimeric cysteine proteases that control apoptotic programmed cell death and are therefore critical in both organismal development and disease. Specific inhibition of individual caspases has been repeatedly attempted, but has not yet been attained. Caspase-9 is an upstream or initiator caspase that is regulated differently from all other caspases, as interaction with natural inhibitor X-linked inhibitor of apoptosis protein (XIAP)-baculovirus inhibitory repeat 3 (BIR3) occurs at the dimer interface maintaining caspase-9 in an inactive monomeric state. One route to caspase-9-specific inhibition is to mimic this interaction, which has been localized to the α5 helix of XIAP-BIR3. We have developed three types of stabilized peptides derived from the α5 helix, using incorporation of aminoisobutyric acid, the avian pancreatic polypeptide (aPP)-scaffold or aliphatic staples. The stabilized peptides are helical in solution and achieve up to 32 μM inhibition, indicating that this allosteric site at the caspase-9 dimerization interface is regulatable with low-molecular weight synthetic ligands and is thus a druggable site. The most potent peptides against caspase-9 activity are the aPP-scaffolded peptides. Other caspases, which are not regulated by dimerization, should not be inactivated by these peptides. Given that all of the peptides attain helical structures but cannot recapitulate the high-affinity inhibition of the intact BIR3 domain, it has become clear that interactions of caspase-9 with the BIR3 exosite are essential for high-affinity binding. These results explain why the full XIAP-BIR3 domain is required for maximal inhibition and suggest a path forward for achieving allosteric inhibition at the dimerization interface using peptides or small molecules.

Distribution and stable isotopic composition of amino acids from fungal peptaibiotics: assessing the potential for meteoritic contamination

The presence of nonprotein α-dialkyl-amino acids such as α-aminoisobutyric acid (α-AIB) and isovaline (Iva), which are considered to be relatively rare in the terrestrial biosphere, has long been used as an indication of the indigeneity of meteoritic amino acids. However, recent work showing the presence of α-AIB and Iva in peptides produced by a widespread group of filamentous fungi indicates the possibility of a terrestrial biotic source for the α-AIB observed in some meteorites. We measured the amino acid distribution and stable carbon and nitrogen isotopic composition of four α-AIB-containing fungal peptides and compared this data to similar meteoritic measurements. We show that the relatively simple distribution of the C(4) and C(5) amino acids in fungal peptides is distinct from the complex distribution observed in many carbonaceous chondrites. We also identify potentially diagnostic relationships between the stable isotopic compositions of pairs of amino acids from the fungal peptides that may aid in ruling out fungal contamination as a source of meteoritic amino acids.

Modifications on amphiphilicity and cationicity of unnatural amino acid containing peptides for the improvement of antimicrobial activity against pathogenic bacteria

The widespread natural sources-derived cationic peptides have been reported to reveal bacterial killing and/or growth-inhibiting properties. Correspondingly, a number of artificial peptides have been designed to understand antibacterial mechanism of the cationic peptides. These peptides are expected to be an alternative antibiotic against drug-resistant pathogenic bacteria because major antimicrobial mechanism of cationic peptides involves bacterial membrane disorder, although those availabilities have not been well evaluated. In this study, cationic peptides containing Aib were prepared to evaluate the availability as an antimicrobial agent, especially against representative pathogenic bacteria. Among them, BRBA20, consisting of five repeated Aib-Arg-Aib-Ala sequences, showed strong antibacterial activity against both Gram-negative and Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus. Additionally, growth of Serratia marcescens and multidrug-resistant Pseudomonas aeruginosa, known as proteases-secreting pathogenic bacteria, were also completely inhibited by BRBA20 under 20 µg/ml peptide concentrations. Our results suggested availabilities of Aib-derived amphiphilicity and protease resistance in the design of artificial antimicrobial peptides. Comparing BRBA20 with BKBA20, it was also concluded that Arg residue is the preferred cationic source than Lys for antimicrobial action of amphiphilic helices.

UVolution, a photochemistry experiment in low earth orbit: investigation of the photostability of carboxylic acids exposed to mars surface UV radiation conditions

The detection and identification of organic molecules on Mars are of prime importance to establish the existence of a possible ancient prebiotic chemistry or even a biological activity. To date, however, no complex organic compounds have been detected on Mars. The harsh environmental conditions at the surface of Mars are commonly advocated to explain this nondetection, but few studies have been implemented to test this hypothesis. To investigate the nature, abundance, and stability of organic molecules that could survive under such environmental conditions, we exposed, in low Earth orbit, organic molecules of martian astrobiological relevance to solar UV radiation (>200 nm). The experiment, called UVolution, was flown on board the Biopan ESA module, which was situated outside a Russian Foton automated capsule and exposed to space conditions for 12 days in September 2007. The targeted organic molecules [alpha-aminoisobutyric acid (AIB), mellitic acid, phthalic acid, and trimesic acid] were exposed with, and without, an analogous martian soil. Here, we present experimental results of the impact of solar UV radiation on the targeted molecules. Our results show that none of the organic molecules studied seemed to be radiotolerant to the solar UV radiation when directly exposed to it. Moreover, the presence of a mineral matrix seemed to increase the photodestruction rate. AIB, mellitic acid, phthalic acid, and trimesic acid should not be considered as primary targets for in situ molecular analyses during future surface missions if samples are only collected from the first centimeters of the top surface layer.

Analysis of the amide (15)N chemical shift tensor of the C(alpha) tetrasubstituted constituent of membrane-active peptaibols, the alpha-aminoisobutyric acid residue, compared to those of di- and tri-substituted proteinogenic amino acid residues

In protein NMR spectroscopy the chemical shift provides important information for the assignment of residues and a first structural evaluation of dihedral angles. Furthermore, angular restraints are obtained from oriented samples by solution and solid-state NMR spectroscopic approaches. Whereas the anisotropy of chemical shifts, quadrupolar couplings and dipolar interactions have been used to determine the structure, dynamics and topology of oriented membrane polypeptides using solid-state NMR spectroscopy similar concepts have been introduced to solution NMR through the measurements of residual dipolar couplings. The analysis of (15)N chemical shift spectra depends on the accuracy of the chemical shift tensors. When investigating alamethicin and other peptaibols, i.e. polypeptides rich in alpha-aminoisobutyric acid (Aib), the (15)N chemical shift tensor of this C(alpha)-tetrasubstituted amino acid exhibits pronounced differences when compared to glycine, alanine and other proteinogenic residues. Here we present an experimental investigation on the (15)N amide Aib tensor of N-acetyl-Aib-OH and for the Aib residues within peptaibols. Furthermore, a statistical analysis of the tensors published for di- (glycine) and tri-substituted residues has been performed, where for the first time the published data sets are compiled using a common reference. The size of the isotropic chemical shift and main tensor elements follows the order di- < tri- < tetra-substituted amino acids. A (15)N chemical shift-(1)H-(15)N dipolar coupling correlation NMR spectrum of alamethicin is used to evaluate the consequences of variations in the main tensor elements for the structural analysis of this membrane peptide.

Characterisation of the peptaibiome of the biocontrol fungus Trichoderma atroviride by liquid chromatography/tandem mass spectrometry

The present study describes the liquid chromatography/tandem mass spectrometry (LC/MS/MS)-based screening and characterisation of linear antibiotic alpha-aminoisobutyric acid (Aib)-containing non-ribosomal peptides (NRP) in culture samples of the filamentous fungus Trichoderma atroviride ATCC 74058. Fungal culture filtrates were enriched by solid-phase extraction (SPE) and separated by reversed-phase high-performance liquid chromatography (HPLC), prior to mass spectrometric (MS) and tandem mass spectrometric (MS/MS) analysis on a triple quadrupole-linear ion trap tandem mass spectrometer. A workflow consisting of two alternative screening strategies was applied to search for NRP. Various MS full scan and MS/MS measurement modes led to the identification of 16 trichorzianines and diagnostic in-source fragment ions of another four trichorzianines. Furthermore, we detected 15 novel Aib-containing peptides with putative molecular weights ranging from 951.7 to 1043.7 g/mol (monoisotopic masses), composed of up to 9 amino acids. While the amino acid sequences of the novel peptaibiotics showed typical microheterogeneity and consisted of the amino acids Leu/Ile, Aib, Ser, Val/Iva, Gly, Ac-Aib, Tyr and Phe, the mass increments at the C-termini of the peptides were not assignable to any residues described in the literature. The amino acid sequences were confirmed and structure proposals made for both molecule termini by high-resolution MS and MS/MS analysis. We propose the group name 'trichoatrokontins' for the newly identified peptaibiotics. As no other peptaibiotics were found in the culture samples, the peptaibiome of the investigated strain of T. atroviride consists of at least 20 trichorzianines and 15 trichoatrokontins.

Nonstereogenic alpha-aminoisobutyryl-glycyl dipeptidyl unit nucleates type I' beta-turn in linear peptides in aqueous solution

The use of alpha,alpha-disubstituted amino acids represents a valuable strategy to exercise conformational control in peptides. Incorporation of the nonstereogenic alpha-aminoisobutyryl-glycyl (Aib-Gly) dipeptidyl sequence into i+1 and i+2 positions of an acyclic peptide sequence, originally designed and investigated by Gellman and coworkers, [H-Arg-Tyr-Val-Glu-Val-Yyy-Xxx-Orn-Lys-Ile-Leu-Gln-NH2] nucleates a stable [2:4] left-handed type I' beta-turn in water. NMR spectra show that this newly designed beta-hairpin does not aggregate in water up to a concentration of approximately 1 mM, and that its backbone conformation is superimposable on corresponding hairpins containing the DPro-Gly (literature) and Aib-DAla (this work) sequences. The Aib-Gly turn-inducer sequence eliminates complications because of cis-trans isomerization of Zzz-Pro bonds, and constitutes an attractive alternative to the proteogenic Asn-Gly and nonproteogenic DPro-Gly motifs previously suggested as turn-inducer sequences. These design principles could be exploited to prepare water-soluble beta-hairpin peptides with robust structures and novel function.

Effect of aminoisobutyric acid (Aib) substitutions on the antimicrobial and cytolytic activities of the frog skin peptide, temporin-1DRa

Temporin-1DRa (HFLGTLVNLAKKIL.NH(2)), first isolated from the skin of the California red-legged frog Rana draytonii, shows broad-spectrum antimicrobial activity but its therapeutic potential is limited by its toxicity against mammalian cells. The cytolytic properties of cationic alpha-helical peptides are determined by a complex interaction between cationicity, hydrophobicity, conformation, and amphipathicity. This study has investigated the cytolytic properties of conformationally constrained analogs of temporin-1DRa containing alpha-aminoisobutyric acid (Aib) substitutions. Cytolytic activity was determined against the bacteria Escherichia coli and Staphylococcus aureus, the opportunistic yeast pathogen, Candida albicans, human erythrocytes, HepG2 hepatoma-derived cells, and L929 fibroblasts. Aib substitutions at Gly(4), Asn(8), and Ala(10) increased both % helicity, determined in methanol solution, and hydrophobicity resulting in increases in both antimicrobial potencies and toxicities against the mammalian cells. Substitution at Leu(6) resulted in an appreciable decrease in cytolytic activity against all cells whereas the substitutions at His(1), Phe(2), Leu(3), Thr(5), and Val(7) had only minor effects on activity. Substitutions at Leu(9), Ile(13), Leu(14) produced analogs with decreased helicity and hydrophobicity that retained activity against microorganisms but showed appreciably lower cytolytic activities against mammalian cells. In particular, the fourfold increase in therapeutic index [ratio of LC(50) against erythrocytes to minimum inhibitory concentration (MIC) against microorganisms] of [Aib(13)]temporin-1DRa identifies it as a compound with potential for development as a therapeutically valuable anti-infective agent.

Molecular design of histone deacetylase inhibitors by aromatic ring shifting in chlamydocin framework

Chlamydocin, a cyclic tetrapeptide containing aminoisobutyric acid (Aib), l-phenylalanine (l-Phe), d-proline (d-Pro), and a unique amino acid l-2-amino-8-oxo-9,10-epoxydecanoic acid, inhibits the histone deacetylases (HDACs), a class of enzymes, which play important roles in regulation of gene expression. Sulfur containing amino acids can also inhibit potently, so zinc ligand, such as sulfhydryl group connected with a linker to the so-called capping group, corresponding to cyclic tetrapeptide framework in case of chlamydocin is supposed to interact with the surface of HDAC molecule. Various changes in amino acid residues in chlamydocin may afford specific inhibitors toward HDAC paralogs. To find out specific inhibitors, we focused on benzene ring of l-Phe in chlamydocin framework to shift to various parts of cyclic tetrapeptide. We prepared and introduced several aromatic amino acids into the cyclic tetrapeptides. By evaluating inhibitory activity of these macrocyclic peptides against HDACs, we could find potent inhibitors by shifting the aromatic ring to the Aib site.

Molecular rectification of a helical peptide with a redox group in the metal-molecule-metal junction

A helical hexadecapeptide immobilized on gold via a thiophenyl group at the N-terminal was analyzed by scanning tunneling microscopy under ultrahigh vacuum to obtain the I-V response at a molecular level. The attenuation factor of the electron transfer through the hexadecapeptide was determined by applying the Simons model to the I-V response to show better molecular conductance of the hexadecapeptide than dodecanethiol. Chemical modification at the C-terminal of the hexadecapeptide with a ferrocene unit, on the other hand, brought about significant changes in the I-V response, where the helical peptide became more conductive at the negative bias voltage. The molecular rectification behavior is due to the ferrocene unit regulating the direction of the electron transfer at the metal-molecule junction.

Spectroscopic Evidence for the Formation of Helical Structures in Gas-Phase Short Peptide Chains

Aminoisobutyric acid (Aib) is a synthetic amino acid known to favor the formation of 3(10) helical structures in condensed phases, namely, crystals. The intrinsic character of these helicogenic properties has been investigated on the Ac-Aib-Phe-Aib-NH2 molecule under isolated conditions, namely, in the gas phase, both experimentally by double-resonance IR/UV spectroscopy and theoretically by quantum chemistry. A convergent set of evidence, based on energetic, IR, and UV spectroscopic data as well as on analogies with the similar peptide Ac-Ala-Phe-Ala-NH2 previously studied, enables us to conclude the formation of an incipient 310 helix in these isolated systems.

Copper (II) Complexes with Ac-HXH-NHMe (X=Gly, Ala and Aib) Peptide Motifs: Influence of Increasing CH3 Groups at C&#945; of Residue X on the Coordination in Solution

The interaction of Cu(II) ion with small peptides has been an interesting subject to clarify the role of copper in detail. As various Cu(II)-oligopeptide complexes can also be good models for the active centers of metalloenzymes, complexes of tripeptide and tetrapeptides are frequently investigated instead of the complexes of large peptides. The histidine side-chains of various metalloproteins frequently take part in the copper(II) coordination. Accordingly, we studied the coordination of Cu(II) to the N and C terminal protected tripeptide ligands L(A) (Ac-HisGlyHis-NHMe), L(B) (Ac-HisAlaHis-NHMe) and L(C) (Ac-HisAibHis-NHMe) in aqueous solution potentiometrially in order to determine the effect of C(alpha) methyl groups at middle residue acid on the ligation of the backbone NH and also on histidine's N(im) of coordination. Species distribution curves indicates that in acidic pH, all three peptides behave as bidentate ligands and a macrochelate forms on the metal coordination with the two histidine imidazolyl N. This coordination remains unaffected with the +I effect of increasing CH(3) groups at C(alpha) of middle residue. In the pH range 4-8, the tridentate coordination from the peptide is seen in ligand L(A) and L(B) while it is absent in L(C) due to +I effect of two C(alpha) methyl groups at middle residue as they makes N-terminal NH deprotonation difficult in this pH range and it takes place along with C terminal NH and only 4N coordinated species formed at higher pH. These 4N (N(im), N(-), N(-), N(im)) coordinated species are formed by all the three ligands at higher pH values.

Crystal-state 3D-structural characterization of novel, Aib-based, turn and helical peptides

The crystal-state conformations of the hexapeptide amide Pht-(Aib)(6)-NH-C(CH(3))(2)-O-OtBu (7), the hexapeptide Ac-L-aIle-(Aib)(5)-OtBu (6), the pentapeptide Z-(Aib)(3)-L-Glu(OtBu)-Aib-O-(CH(2))(2)-(1)Nap (5), the tetrapeptides Z-(Aib)(2)-L-His(N(tau)-Trt)-Aib-OMe (4 I) and Z-(Aib)(2)-L-Nva-Aib-OtBu (4 II), the tripeptide Pyr-(Aib)(3)-OtBu (3 I), the dipeptide amides Pyr-(Aib)(2)-(4)NH-TEMPO (3 II) and Piv-(Aib)(2)-NH-C(CH(3))(2)-O-OtBu (3 III), and the dipeptides Pht-Aib-betaAc(6)c-OtBu (2 I), Pht-Aib-NH-C(CH(3))(2)-O-OtBu (2 II) and Boc-gGly-mAib-OH (2 III) have been determined by X-ray diffraction analyses. All peptides investigated are characterized by one or more turn/helix forming Aib residues. Except the three short dipeptides, all are folded into C==O...H--N intramolecularly H-bonded 3(10)-helices, or into various types of beta-turns. In the structure of 6, two independent molecules of opposite screw sense were observed in the asymmetric unit, generating diastereomeric 3(10)-helices.

Design and synthesis of cationic Aib-containing antimicrobial peptides: conformational and biological studies

Development of antimicrobial peptides has attracted considerable attention in recent years due to the excessive use of antibiotics, which has led to multiresistant bacteria. Cationic amphiphilic Aib-containing peptide models Ac-(Aib-Arg-Aib-Leu)(n)-NH2, n = 1-4, and sequential cationic polypeptides (Arg-X-Gly)(n), X = Ala, Val, Leu, were prepared and studied for their antimicrobial and hemolytic activity, as well as for their proteolytic stability. Ac-(Aib-Arg-Aib-Leu)(n)-NH2, n = 2, 3 and the polypeptide (Arg-Leu-Gly)(n) exhibited significant antimicrobial activity, and they were nontoxic at their MIC values and resistant, in particular the Aib-peptide models, to enzymatic degradation. The conformational characteristics of the peptide models were studied by circular dichroism (CD). Structure-activity relationship studies revealed the importance of the amphipathic alpha-helical conformation of the reported peptides in inducing antimicrobial effects. It is concluded that peptide models comprising cationic amino acids (Arg), helicogenic and noncoding residues (Aib) and/or hydrophobic and helix-promoting components (Leu) may lead to the development of antimicrobial therapeutics.

Effect of peptide ligand dipole moments on the redox potentials of Au38 and Au140 nanoparticles

Phenylethanethiolate monolayer-protected Au38 and Au140 nanoclusters were modified by ligand place exchange with a series of thiolated peptides. The peptides were homooligomers based on the alpha-aminoisobutyiric acid unit. The effects of changing the peptide concentration and the peptide length in the capping monolayer were studied by differential pulse voltammetry. The results showed that the redox behavior of the nanoparticles can be affected very significantly by such modifications. For example, the first oxidation peak of Au38, a cluster displaying molecule-like behavior, could be shifted positively by as much as 0.7-0.8 V. Detectable redox shifts were noted even when one single oriented peptide was in the Au140 monolayer. These effects were attributed to the molecular dipole moments of the peptide ligands.

Peptide Folding Dynamics: A Time-Resolved Study from the Nanosecond to the Microsecond Time Regime

Time-resolved spectroscopies, spanning from the nanosecond to the microsecond time regime, coupled with molecular mechanics calculations, allowed us to assess the most populated conformations in solution of a series of analogues of trichogin GA IV, a natural undecapeptide showing significant antimicrobial activity. This peptide is characterized by a high content of the conformationally constrained alpha-aminoisobutyric acid and by a glycine-glycine motif in the central part of the sequence. Nanosecond time-resolved fluorescence experiments were performed to determine the conformational properties of the peptide analogues in solution, while transient absorption measurements allowed us to study the peptide dynamics on the microsecond time scale. Because the peptides examined were functionalized by a fluorescent probe at the N-terminus and a nitroxide quencher placed along the backbone at three different positions, the distance-dependent fluorophore-quencher interaction was exploited to obtain a deeper insight into their three-dimensional structural and dynamical properties. Further information on the conformational and dynamical features was obtained by photophysical experiments as a function of the viscosity and polarity of the medium. Taken together, the results revealed a transition from an elongated, helical conformation to a family of compact, folded structures mimicking a helix-turn-helix motif, which may represent a model of the early steps of the protein hydrophobic collapse.

Non-protein amino acids in the design of secondary structure scaffolds

The use of stereochemically constrained amino acids permits the design of short peptides as models for protein secondary structures. Amino acid residues that are restrained to a limited range of backbone torsion angles (phi-psi) may be used as folding nuclei in the design of helices and beta-hairpins. alpha-Amino-isobutyric acid (Aib) and related Calphaalpha dialkylated residues are strong promoters of helix formation, as exemplified by a large body of experimentally determined structures of helical peptides. DPro-Xxx sequences strongly favor type II' turn conformations, which serve to nucleate registered beta-hairpin formation. Appropriately positioned DPro-Xxx segments may be used to nucleate the formation of multistranded antiparallel beta-sheet structures. Mixed (alpha/beta) secondary structures can be generated by linking rigid modules of helices and beta-hairpins. The approach of using stereochemically constrained residues promotes folding by limiting the local structural space at specific residues. Several aspects of secondary structure design are outlined in this chapter, along with commonly used methods of spectroscopic characterization.

Chiral interaction in peptide molecules: Effects of chiral peptide species on helix-sense induction in an N-terminal-free achiral peptide

Noncovalent chiral domino effect (NCDE) has been proposed as terminal-specific interaction upon a 3(10)-helical peptide chain, of which the helix sense is manipulated by an external chiral stimulus (mainly amino acid derivatives) operating on the N-terminus (Inai, Y., et al. J Am Chem Soc 2000, 122, 11731-11732; ibid., 2002, 124, 2466-2473; ibid., 2003, 125, 8151-8162). We have investigated here a helix-sense induction in an optically inactive N-terminal-free nonapeptide (1) through the screening of several peptide species that differ in chiral sequence, chain length, and C-terminal group. Helix-sense induction in peptide 1 depends largely on both the C-terminal chirality and carboxyl group in the external peptide, in which N-carbonyl-blocked amino acids, "monopeptide acids," should be the minimum requirement for effective induction. N-Protected mono- to tetrapeptides of L-Leu residue commonly induce a right-handed helix. NMR study and theoretical computation reveal that the N-terminal segment of peptide 1 binds the N-protected dipeptide molecule through multipoint coordination to induce a right-handed helix preferentially. The present findings not only will improve our understanding of the chiral roles in peptide or protein helical termini, but also might demonstrate potential applications to chirality-responsive materials based on peptide helical fragments.

Designing amino acid residues with single-conformations

Drug design can benefit from the use of non-coded amino acids, such as alpha-amino isobutyric acids (Aib) or sarcosine (N-methyl-glycine). Non-coded amino acids can confer resistance to enzymatic degradation and increase the conformational stability of the peptides. We have simulated the conformational effects of combining N-methylation, bulky groups on the Calpha atom and/or thioamides using the class II CFF91 force field and our thioamide force field parameters. Although single amino acid substitutions (e.g. Aib) can restrict the available conformations, they do not necessarily lead to unique conformers, however, we predict that some of the amino acids described in this report will fold to a single phi, psi conformation (e.g. N-methylated and thioamide penicillamine). Several other amino acid/thiopeptide combinations were designed, which are predicted to prefer only two conformations. Novel amino acids of this type should prove useful for designing peptides with defined conformations.

Di- and tripeptide segments of zervamicin II-2: Z-Thr(OBn)-Aib-N(Me)Ph and Z-Val-Aib-Hyp(OBn)-OMe

The title compounds, O-benzyl-N-(benzyloxycarbonyl)threonyl-2,N-dimethylalaninanilide, C30H35N3O5, and methyl (4R)-4-benzyloxy-N-(benzyloxycarbonyl)valyl-2-(methylalanyl)prolinate, C30H39N3O7, were obtained from the ;azirine coupling' of the corresponding protected amino acids with 2,2,N-trimethyl-2H-azirin-3-amine and methyl (4R)-4-(benzyloxy)-N-(2,2-dimethyl-2H-azirin-2-yl)prolinate, respectively. The Aib unit in each molecule has the greatest turn- or helix-inducing effect on the molecular conformation. Intermolecular N-H...O interactions link the molecules of the tripeptide into sheets and those of the dipeptide into extended chains.

Mid-Infrared Spectroscopy of Protected Peptides in the Gas Phase: A Probe of the Backbone Conformation

Infrared/UV hole-burning spectroscopy is performed on individual conformers of the protected dipeptide Z-Aib-Pro-NHMe. The extended IR range probed in this study allows one to elucidate both the H-bonding motif (5-7 microm) as well as the backbone structure (7-10 microm). Comparison with DFT calculations shows that the backbone is locally constrained to an alpha-conformation by Aib and to a gamma-turn by Pro. The gamma-turn motif observed here is intriguing since the condensed phase structure is known to be a beta-turn. This is the first actual observation of such a discrepancy, and it emphasizes the subtle balance between intra- and intermolecular forces, which is responsible for the relative stability of the different secondary structure motifs.

Bombesin analogs containing α-amino-isobutyric acid with potent anticancer activity

Six octapeptide bombesin (BN) analogs were synthesized by substituting alpha-aminoisobutyric acid (Aib), in place of Ala9 or Gly11, or both, in the [D-Phe6, desMet14]-BN (6-14) sequence: D-Phe6-Gln7-Trp8-Ala9-Val10-Gly11-His12-Leu13-NH2 (P0). Additionally, Leu13 was replaced with isoleucine in two analogs and one of the analogs was butanoylated at the N-terminus. The antiproliferative activity of the analogs was tested in vitro on human pancreatic (MiaPaCa-2) and colon cancer (SW620, HT29 and PTC) cell lines using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The analogs demonstrated anticancer activity in the above cell lines at concentrations ranging from 0.01 nM to 1 microM. One of the analogs, P6, was evaluated for in vivo tumor regression in a xenograft model of human primary colon cancer in athymic nude mice and was found to cause significant reduction in tumor volume. NMR and molecular dynamics (MD) simulation studies for this analog revealed the presence of a mixed 3(10)/alpha-helical structure. This study demonstrates that the designed BN analogs retain their anticancer activity after the incorporation of the constrained amino acid, Aib, and are potential molecules for future use in cancer therapy and drug targeting.

Chiral interaction in Gly-capped N-terminal motif of 310-helix and domino-type induction in helix sense

Chiral interaction of helical peptide with chiral molecule, and concomitant induction in its helix sense have been demonstrated in optically inactive nonapeptide (1) possessing Gly at its N-terminus: H-Gly-(Delta(Z)Phe-Aib)(4)-OCH(3) (1: Delta(Z)Phe = Z-dehydrophenylalanine; Aib = alpha-aminoisobutyric acid). Spectroscopic measurements [mainly nuclear magnetic resonance (NMR) and circular diochroism (CD)] as well as theoretical simulation have been carried out for that purpose. Peptide 1 in the 3(10)-helix tends to adopt preferentially a right-handed screw sense by chiral Boc-L-amino acid (Boc: t-butoxycarbonyl). Induction in the helix sense through the noncovalent chiral domino effect should be derived primarily from the complex supported by the three-point coordination on the N-terminal sequence. Thus the 3(10)-helical terminus consisting of only alpha-amino acid residues enables chiral recognition of the Boc-amino acid molecule, leading to modulation of the original chain asymmetry. Dynamics in the helix-sense induction also have been discussed on the basis of a low-temperature NMR study. Furthermore, the inversion of induced helix sense has been achieved through solvent effects.

Gold Nanoclusters Protected by Conformationally Constrained Peptides

The preparation and properties of a series of gold nanoclusters protected by thiolated peptides based on the alpha-aminoisobutyric acid (Aib) unit are described. The peptides were devised to form 0-3 C=O...H-N intramolecular hydrogen bonds, as required by their 3(10)-helical structure. The monolayer-protected clusters (MPCs) were prepared, using a modified version of the two-phase Brust-Schiffrin preparation, and fully characterized with (1)H NMR spectrometry, IR and UV-vis absorption spectroscopies, transmission electron microscopy (TEM), thermogravimetric analysis (TGA), and X-ray photoelectron spectroscopy (XPS). The MPCs were obtained with core diameters in the range of 1.1-2.3 nm, depending on the reaction conditions. Structured peptides formed smaller clusters. The smallest MPC obtained is in agreement with the average formula Au(38)Pep(18). The results showed that the chemical integrity of the peptide is maintained upon monolayer formation and that the average number of peptide ligands per gold cluster is typically 75-85% the value calculated for alkanethiolate MPCs of similar sizes. The IR and NMR spectra indicated that in the monolayer the peptides are involved in both intra- and interligand C=O...H-N hydrogen bonds.

IR Study of Cross-Strand Coupling in a β-Hairpin Peptide Using Isotopic Labels

Model beta-hairpin peptides can be used to develop understanding of fundamental elements of beta-sheet secondary structure formation and stability. We have studied two 13C-labeled variants of a beta-hairpin peptide modified from a design originally proposed by Gellman: Arg-Tyr-Val-Glu-Val-Aib-Gly-Lys-Lys-Ile-Leu-Gln. (In this peptide, the two italicized residues form a beta-turn, while 13C-labels are on the amide C=O of Val3, Lys8 in HBG-L and Val3, Ile10 in HBG-S.) Both these peptides are labeled on opposite strands of the hairpin, but differ in the labeling pattern. One (HBG-L) forms a large (14-atom) H-bonded ring of labeled C=Os, while the other (HBG-S) forms a small (10-atom) H-bonded ring. These impact the amide I infrared spectra, with HBG-L having a 13C frequency and intensity higher than that of HBG-S, in good agreement with our spectral simulations based on quantum mechanically derived force fields. The thermal behavior of both peptides yields a broad thermal transition and lacks an isosbestic point. The 13C band for HBG-L has the largest intensity change with temperature, distinct from the 12C change and the HBG-S 13C change.

A new 2 methylalanine-PVC ESR dosimeter

The use of polyvinyl chloride (PVC) as a binder to 2-methylalanine (2MA) dosimeters was investigated. It was recently shown by Olsson et al. (Radiat. Res. 157 (2002) 113), that 2MA is approximately 70% more sensitive than L-alanine which makes this substance a good candidate to replace alanine in ESR dosimetry. PVC is a low yield material for free radical production by ionizing radiation and a good binding material easily processed and widely available. PVC can be prepared at room temperature and mixed up to 50% in weight with 2MA to produce a pellet stable in mass and physical dimensions, in large quantities and with low background signal. Pure PVC pellet irradiated at 50 Gy gave weaker ESR signals compared to 2MA at the region of spectral interest. Spectrometer settings such as microwave power, and modulation amplitude were optimized for the measurements. This dosimeter production scheme allows the addition of Mn2+ ions for an internal reference signal, leading to a self-calibrated dosimeter (J. Radional. Nucl. Chem. 240 (1999) 215).

β-Turn mimic in tripeptide with Phe(1)-Aib(2) as corner residues and β-strand structure in an isomeric tripeptide: an X-ray diffraction study

A single crystal X-ray diffraction study of the tripeptide Boc-Phe-Aib-Leu-OMe (Aib = alpha-aminoisobutyric acid) reveals that it forms structurally one of the best type II beta-turns so far reported in tripeptides, stabilized by 10 atom intramolecular hydrogen bonding. In contrast, the isomeric tripeptide Boc-Phe-Leu-Aib-OMe adopts a beta-strand like conformation. Interestingly, a previously reported structure of another isomeric tripeptide, Boc-Leu-Aib-Phe-OMe, shows a double bend conformation without any intramolecular hydrogen bonding. These results demonstrate an example of the creation of structural diversities in the backbone of small peptides depending upon the co-operative steric interactions amongst the amino acid residues.

Evidence Against the Hopping Mechanism as an Important Electron Transfer Pathway for Conformationally Constrained Oligopeptides

The rate constant of intramolecular electron transfer through oligopeptides based on the alpha-aminoisobutyric acid residue was determined as a function of the peptide length and found to depend weakly on the donor-acceptor separation. By measuring the electron-transfer activation energy and estimating the energy gap between donor and bridge, we were able to discard the electron hopping mechanism.

Efficient Photocurrent Generation by Self-Assembled Monolayers Composed of 310-Helical Peptides Carrying Linearly Spaced Naphthyl Groups at the Side Chains

Self-assembled monolayers (SAMs) were prepared on a gold substrate from a 310-helical peptide carrying three naphthyl groups at the side chain (SSN3B) or from the reference peptides carrying no or one naphthyl group. The 310-helical conformation of SSN3B in solution was confirmed by 1H NMR spectroscopy and geometry optimization. Cyclic voltammetry and infrared absorption-reflection spectroscopy showed vertical molecular orientation and a well-packed structure in the SSN3B SAM. Anodic photocurrent was successfully generated by the SSN3B SAM in the presence of triethanolamine, and the current intensity was found to be much larger than those by the other SAMs from peptides carrying one naphthyl group. It was therefore concluded that the linearly spaced naphthyl groups along the helical axis act as photosensitizer and electron-hopping site to promote photocurrent generation remarkably.

Conformational changes in alamethicin associated with substitution of its alpha-methylalanines with leucines: a FTIR spectroscopic analysis and correlation with channel kinetics

Alamethicin, a 20 residue-long peptaibol remains a favorite high voltage-dependent channel-forming peptide. However, the structural significance of its abundant noncoded residues (alpha-methylalanine or Aib) for its ion channel activity remains unknown, although a previous study showed that replacement of all Aib residues with leucines preserved the essential channel behavior except for much faster single-channel events. To correlate these functional properties with structural data, here we compare the secondary structures of an alamethicin derivative where all the eight Aibs were replaced by leucines and the native alamethicin. Fourier transform infrared (FTIR) spectra of these peptides were recorded in methanol and in aqueous phospholipid membranes. Results obtained show a significant conformational change in alamethicin upon substitution of its Aib residues with Leu. The amide I band occurs at a lower frequency for the Leu-derivative indicating that its alpha-helices are involved in stronger hydrogen-bonding. In addition, the structure of the Leu-derivative is quite sensitive to membrane fluidity changes. The amide I band shifts to higher frequencies when the lipids are in the fluid phase. This indicates either a decreased solvation due to a more complete peptide insertion or a peptide stretching to match the full thickness of the bilayer. These results contribute to explain the fast single-channel kinetics displayed by the Leu-derivative.

Conformational switching caused by biphenyl substitution at the Cαposition: ethyl 2-benzyl-2-(formylamino)-3-phenylpropionate and ethyl 3-(1,1′-biphenyl-4-yl)-2-(formylamino)-2-(4-phenylbenzyl)propionate

The title compounds, C19H21NO3 and C31H29NO3, are derivatives of alpha-aminoisobutyric acid, with benzyl and dibenzyl substitution. The pseudo-peptide formed by the N-formyl and ethyl ester substitution at the Calpha position switches from a trans-trans to a trans-cis configuration as a result of biphenyl substitution. The packing of the compounds is stabilized by N-H...O and C-H...O hydrogen bonds.

Synthesis and Characterization of a Series of Homooligopeptide Peroxyesters

A homologous series of stable N(alpha)-phthaloyl peptide peroxyesters based on alpha-aminoisobutyric acid residues was prepared. In each of the six oligomers synthesized, the chain of alpha-amino acids is separated from the peroxyester function by a beta-amino acid. [structure: see text]