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In this report, we describe the methodology for 96 parallel organic syntheses of peptides on Teflon-patterned paper assisted by heating with an infra-red lamp. SPOT synthesis is an important technology for production of peptide arrays on a paper-based support for rapid identification of peptide ligands, epitope mapping, and identification of bio-conjugation reactions. The major drawback of the SPOT synthesis methodology published to-date is suboptimal reaction conversion due to mass transport limitations in the unmixed reaction spot. The technology developed in this report overcomes these problems by changing the environment of the reaction from static to dynamic (flow-through), and further accelerating the reaction by selective heating of the reaction support in contact with activated amino acids. Patterning paper with Teflon allows for droplets of organic solvents to be confined in a zone on the paper array and flow through the paper at a well-defined rate and provide a convenient, power-free setup for flow-through solid-phase synthesis and efficient assembly of peptide arrays. We employed an infra-red (IR) lamp to locally heat the cellulosic support during the flow-through delivery of the reagents to each zone of the paper-based array. We demonstrate that IR-heating in solid phase peptide synthesis shortened the reaction time necessary for amide bond formation down to 3 minutes; in some couplings of alpha amino acids, conversion rates increased up to fifteen folds. The IR-heating improved the assembly of difficult sequences, such as homo-oligomers of all 20 natural amino acids.

Substitution of disulfide bonds with a diselenide bonds in peptides and proteins is an often-used strategy to increase the stability of naturally occurring peptides and proteins. In this paper, diselenide metathesis between model diselenide dimer peptides, as well as that in diselenide(s)-substituted biologically active peptides, were analyzed. Surprisingly, depending on the tertiary structure of the peptides, we observed that the metathesis reaction occurs under physiological conditions even in the absence of reducing agents, light and heating.

Murepavadin (POL7080) in phase III clinical trials, a backbone-cyclized polypeptide composed of 14 amino acids, has a novel mode of action and shows a specific and efficient bactericidal effect against multidrug-resistant Pseudomonas aeruginosa . It is a potential candidate to treat severe P. aeruginosa infections in the future and still has significant commercial value for further research and development. In this paper, we report a liquid-phase peptide synthetic route for this valuable candidate polypeptide assisted by hydrophobic-support materials (tags), which overcomes the difficulties of high cost and poor yield in the traditional solid-phase synthesis of macrocyclic peptides. Through the careful optimization of reaction conditions and the innovative strategy of synthetic post-treatment, we established a simple and efficient liquid-phase synthetic route suitable for POL7080 and other similar structures, with satisfactory yield, high purity and a production process not being controlled by scale.

Sequential peptide coupling plays a central role in chemical protein synthesis. This paper describes a new peptide derivative, peptide-aminothiazoline (At), whereof the C-terminus is functionalized with 2-aminothiazoline. Peptide-At streamlined the sequential peptide ligation in a one-pot manner and demonstrated the convergent synthesis of a circular protein and homogeneous glycoproteins.

In this paper, we show that a hierarchical approach for the construction of nanofibrils based on α,β-peptide foldamers is a rational method for the design of novel self-assembled nanomaterials based on peptides. Incorporation of a trans -(1 S ,2 S )-2-aminocyclopentanecarboxylic acid residue into the outer positions of the model coiled-coil peptide led to the formation of helical foldamers, which was determined by circular dichroism (CD) and vibrational spectroscopy. The oligomerization state of the obtained peptides in water was established by analytical ultracentrifugation (AUC). The thioflavin T assay and Congo red methods showed that the obtained α,β-peptides possess a strong tendency to aggregate, leading to the formation of self-assembled nanostructures, which were assessed by microscopic techniques. The location of the β-amino acid in the heptad repeat of the coiled-coil structure proved to have an influence on the secondary structure of the obtained peptides and on the morphology of the self-assembled nanostructures.

This paper is the first report of a non-competitive fluorescence polarization immunoassay (NC-FPIA) using a peptide as a tracer. The NC-FPIA can easily and quickly quantify the target after simply mixing them together. This feature is desirable for point-of-need applications such as clinical diagnostics, infectious disease screening, on-site analysis for food safety, etc. In this study, the NC-FPIA was applied to detect CD9, which is one of the exosome markers. We succeeded in detecting not only CD9 but also CD9 expressing exosomes derived from HeLa cells. This method can be applied to various targets if a tracer for the target can be prepared, and expectations are high for its future uses.

This paper focused on the mechanism of Ser-Ala-Gly-Pro-Ala-Phe (SAGPAF) treatment to improve gastric mucosal injury in mice. A gastric mucosa injury model induced by ethanol was established, and the superoxide dismutase (SOD) activity, malondialdehyde (MDA) content, nitric oxide (NO) content and myeloperoxidase (MPO) level were determined. We performed macroscopic and histopathological evaluation of the gastric organs. Moreover, we analyzed the mechanism of SAGPAF treatment by western blotting. Compared with the model group, the SOD activity and NO content in the medium-dose and high-dose SAGPAF groups of treated with 10 kV cm -1 field intensity were significantly increased. The MDA content and MPO level were decreased significantly. They significantly reduced the gastric mucosal injury induced by ethanol (21.17 ± 3.51% and 13.99 ± 2.00%) and the histopathological scores (3.83 ± 0.40 and 4.33 ± 0.37) ( P < 0.05). Western blotting analysis showed that SAGPAF after pulsed electric field (PEF) treatment improved gastric injury by reducing protein phosphorylation. These findings provided strong evidence that PEF-treated SAGPAF enhanced the gastric mucosal barrier function by inhibiting the activation of the mitogen-activated protein kinase (MAPK) and nuclear factor kappa-B (NF-κB) signaling pathways, reducing the ethanol-induced inflammatory response and oxidative stress.

In this paper, we report the preparation of paclitaxel-terminated peptide brush polymers wherein cell uptake and toxicity are tunable based on peptide sequence. Synthesis was enabled using a new paclitaxel-containing chain termination agent for ring-opening metathesis polymerization (ROMP). Critically, reverse phase HPLC could be used to efficiently separate peptide brush polymers consisting of one fluorophore and one terminal paclitaxel from crude polymer mixtures. These purified terminally-modified polymers showed greater potency than the original mixtures. Drug-terminated peptide brush polymers carrying positive charges exhibited enhanced cell uptake and cytotoxicity as compared to their neutral and negatively charged analogues.

Hydrophobic membrane peptides/proteins having low water solubility are often difficult to prepare. To overcome this issue, temporal introduction of solubilizing tags has been demonstrated to be beneficial. Following our recent work on the solubilization of a difficult target by using a hydrophilic oligo-Lys tag bearing a trityl linker (Trt-K method), this paper describes a comparative study of the solubilizing abilities of several peptidic trityl tags containing Lys, Arg, Glu, Asn, N ε -tri-Me-Lys or Cys-sulfonate using two hydrophobic model peptides. Among the tags evaluated, that containing N ε -tri-Me-Lys exhibits superior solubilizing ability.

Recently, due to their properties of high surface-to-volume ratio, easy penetration of the blood-brain barrier and easily modified surfaces, nanoparticles (NPs) have been recognized as promising inhibitors for Alzheimer's disease (AD) diagnosis and therapy. However, to achieve clinical application, the design and synthesis of specific NPs with good biocompatibility and degradability still are the main focus of research. In this paper, EGCG-Fe(iii)/PVP (EFPP) NPs with ultra-small size and good biocompatibility were first fabricated by the coordination reaction between Fe 3+ , EGCG and PVP. The obtained EFPP NPs exhibited effective influence on the inhibition of Aβ40 fibrillation and disaggregation of existing Aβ40 fibrils. The inhibitory effect was mainly derived from the synergistic effect of the weak hydrophobicity from PVP and antioxidant activity of EGCG. With the advantages of easy synthesis, high stability in simulated body fluid, high performance towards the antifibrillation of Aβ40 and biodegradability, it is reasonable to consider that the as-prepared EFPP NPs have good application prospects in the treatment of AD.

Chymotrypsin inhibitor 2 (CI2) is a special serine protease inhibitor which can resist hydrolysis for several days with a rapid equilibrium between the Michaelis complex and acyl-enzyme intermediate. The energies and conformational changes for subtilisin-catalyzed proteolysis of CI2 were examined in this paper for the first time by employing pseudo bond ab initio QM/MM MD simulations. In the acylation reaction, a low-barrier hydrogen bond between His64 and Asp32 in the transition state together with the lack of covalent backbone constraints makes the peptide bonds of CI2 break more easily than in other serine protease inhibitors. After acyl-enzyme formation, molecular dynamics simulations showed that the access of hydrolytic water to the active site requires partial dissociation of the leaving group. However, retention of the leaving group mainly by the intra- and inter-molecular H-bonding networks hinders the access of water and retards the deacylation reaction. Instead of the dissociation constant of inhibitors, we suggest employing the free energy at the acyl-enzyme state to predict the relative hydrolysis rates of CI2 mutants, which are testified by the experimental relative hydrolysis rates.

The role of copper in cancer progression has been established since decades. Additionally, copper is able to stimulate angiogenesis through the control of VEGF expression and activity in endothelial cells. In this paper a tetrapeptide, belonging to the histidine-proline-rich glycoprotein (HPRG) and encompassing four repeats of the sequence GHHPH (named TetraHPRG), was synthesized and its copper(ii) complex species were characterized by means of potentiometry, UV-vis, circular dichroism (CD), electron paramagnetic resonance (EPR) and electron spray ionization mass spectrometry (ESI-MS). Moreover, a peptide covalently bound through an amidic bond to trehalose (TH-TetraHPRG) was designed and synthesized as a prodrug system. The activity of both TetraHPRG and TH-TetraHPRG molecules on copper and VEGF induced angiogenic responses in endothelial cells was assessed. The two peptides show a similar and effective anti-angiogenic activity on both molecular and cellular responses. Since the trehalose derivative has a higher resistance to enzymatic degradation, it can be further exploited as a potential drug delivery system with anti-angiogenic activity.

Milk and milk-derived products are a relevant source of bioactive peptides, which are also potential components of functional foods. Bioactive peptides exert multiple actions including an antioxidant role. In the present paper, four synthetic peptides (NPYVPR, AVPYPQR, KVLPVPEK, and ARHPHPHLSFM), corresponding to milk-derived peptides were studied. Although with different features, as revealed by RP-HPLC chromatography and MS analysis, the obtained peptides were shown to be taken up by Caco-2 cells arranged in an epithelial monolayer formation. The four peptides were all able to preserve cell viability against induced oxidative stress indicating that they might have a role in the control of oxidative stress. Therefore, an estimation of total thiols and glutathione content was performed after cell treatment with oxidants like hydrogen peroxide (H 2 O 2 ) or tert-butyl hydroperoxide (TbOOH). The peptides were able to prevent the decrease of both total thiols and glutathione induced by H 2 O 2 or TbOOH, and, in addition, they showed a protective effect on the thiol-related antioxidant enzymes thioredoxin reductase and glutathione reductase. Finally, they caused a decrease of ROS production induced by TbOOH in Caco-2 cells. The reported results highlight the relevant antioxidant role played by bioactive peptides in cells, which adds to other previously known properties.

In this paper, we developed a tandem of two carbon-carbon bond-forming reactions to chemically diversify the libraries of peptides displayed on a bacteriophage. The Wittig reaction of a biotin-ester from a stabilized phosphorane ylide with model peptides containing N-terminal glyoxal exhibits reaction rates of 0.07 to 5 M -1 s -1 in water at pH 6.5-8. The log(k) scaled linearly with pH from pH 6 to 8; above pH 9 the reaction is accompanied by the hydrolysis of the ester functionality. Capture of the phage displaying the biotinylated product by streptavidin beads confirmed the rate of this reaction in a library of 10 8 peptides (k = 0.23 M -1 s -1 at pH = 6.5) and also confirmed the regioselectivity of this modification. Olefins introduced into the Wittig reaction can act as Michael acceptors: addition of glutathione, cysteamine, and DYKDDDDKC ("FLAG-Cys") peptide occurs with k = 0.12-4.1 M -1 s -1 at pH 7.8. Analogous reactions with the DYKDDDDKC peptide take place on phage-displayed peptides modified via the Wittig reaction. This reaction is manifested as a progressive emergence of a FLAG-epitope on the phage and detected by the capture of this phage using an anti-FLAG antibody. Olefins introduced into the Wittig reaction also act as dienophiles in the Diels-Alder reaction with cyclopentadiene. The conversion of the dienophile to norbornene-like adducts on the phage was observed by monitoring the disappearance of the thiol-reactive olefin on the phage. This report broadens the reaction scope of genetically-encoded peptide libraries displayed on the phage, expanding the structural diversity of these platforms and increasing their potential to be used in screening against important protein targets. The possibility of monitoring tandem reactions by the use of different labels illustrates the feasibility of obtaining highly functionalized peptides with chemical motifs impossible to achieve using conventional translational machinery.

In this paper, we report a theoretical investigation of the catalytic mechanism of peptide amidases that involve a Ser-(cis)Ser-Lys catalytic triad. Previous suggestions propose that these enzymes should follow a distinct catalytic mechanism from the one that is present in the classic Ser-His-Asp catalytic triad. The theoretical and computational results obtained in this work indicate the opposite idea, showing that both mechanisms are very similar and only few differences are observed between both reactions. The results reveal that the different alignment of the Ser-(cis)Ser-Lys catalytic triad in relation to the classical Ser-His-Asp triad may provide a better stabilisation of the reaction intermediates, and therefore make these enzymes catalytically more efficient. The catalytic mechanism has been determined at the M06-2X/6-311++G**//B3LYP/6-31G* level of theory and requires five sequential steps instead of the two that are generally proposed: (i) nucleophilic attack of serine on the carbonyl group of the substrate, forming the first tetrahedral intermediate, (ii) formation of an acyl-enzyme complex, (ii) release of an ammonia product, (iv) nucleophilic attack of a water molecule forming the second tetrahedral intermediate, and (iv) the release of the product of the reaction, the carboxylic acid. The computational results suggest that the rate-limiting step is the first one that requires an activation free energy of 15.93 kcal mol -1 . This result agrees very well with the available experimental data that predict a reaction rate of 2200 s -1 , which corresponds to a free energy barrier of 14 kcal mol -1 .

The folding/unfolding equilibrium of proteins in aqueous medium can be altered by adding small organic molecules generally termed as co-solvents. Denaturants such as urea are instrumental in the unfolding of proteins while protecting osmolytes favour the folded ensemble. Recently, room temperature ionic liquids (ILs) have been shown to counteract the deleterious effect of urea on proteins. In this paper, using atomistic molecular dynamics we show that a ternary mixture containing a particular ammonium-based IL, triethylammonium acetate (TEAA), and urea (in 1 : 5 molar ratio) helps a small 15-residue S-peptide analogue regain most of its native structure, whereas a binary aqueous mixture containing a large amount of urea alone completely distorts it. Our simulations show that the denaturant urea directly interacts with the peptide backbone in the binary mixture while for the ternary mixture both urea as well as the IL are preferentially excluded from the peptide surface.

In this paper, we presented a new design strategy for a peptide-based chiral supramolecular assembly. A series of aryl linked peptides 1a-1f were designed and synthesized. The bis-urea peptides 1a-1c self-assembled into a helical supramolecular arrangement resembling Trp zipper (Trpzip) structures present in proteins. Interestingly, a dihydrogenphosphate anion, upon binding to the assembly, could invert the chirality of the supramolecular assembly which could be reverted to the original by the addition of water. This chiroptical behavior can be repeated several times. Microscopy analysis showed that the supramolecular helices were assembled to form spheres. In addition to that, we also found that the handedness of supramolecular chirality is dependent on the position of Trp residues on the aromatic scaffold. Both left and right handed helical supramolecular arrangements were obtained by placing l-Trp residues at different positions on the aromatic core. The unprecedented Trpzip in these designed small peptidomimetics will stimulate more work in the area of peptide-based assemblies.

In this paper, we present a coarse replica exchange molecular dynamics (REMD) approach, based on kinetic Monte Carlo (kMC). The new development significantly can reduce the amount of replicas and the computational cost needed to enhance sampling in protein simulations. We introduce 2 different methods which primarily differ in the exchange scheme between the parallel ensembles. We apply this approach on folding of 2 different β-stranded peptides: the C-terminal β-hairpin fragment of GB1 and TrpZip4. Additionally, we use the new simulation technique to study the folding of TrpCage, a small fast folding α-helical peptide. Subsequently, we apply the new methodology on conformation changes in signaling of the light-oxygen voltage (LOV) sensitive domain from Avena sativa (AsLOV2). Our results agree well with data reported in the literature. In simulations of dialanine, we compare the statistical sampling of the 2 techniques with conventional REMD and analyze their performance. The new techniques can reduce the computational cost of REMD significantly and can be used in enhanced sampling simulations of biomolecules.

The adsorption and fusion of small unilamellar lipid vesicles on silica-based substrates such as glass is a common method used to fabricate supported lipid bilayers. Successful bilayer formation depends on a number of experimental conditions as well as on the quality of the vesicle preparation. Inevitably, a small fraction of unruptured vesicles always remains in a supported bilayer, and this kind of defect can have devastating influences on the morphological and electrical properties of the supported bilayer when used as a biosensing platform. In this paper, a simple method is reported to improve the completeness of supported bilayers by adding a vesicle rupturing peptide as a final step in the fabrication process. Peptide treatment reduces the fraction of unruptured vesicles to less than 1%, as determined by epifluorescence microscopy and quartz crystal microbalance-dissipation experiments. This step can easily be incorporated into existing procedures for preparing high-quality supported lipid bilayers.

Intrinsically disordered proteins/peptides play a crucial role in many physiological and pathological events and may assume a precise conformation upon binding to a specific target. Recently, we have described the conformational and functional properties of two linear ester peptides provided with the following sequences: Y-G-E-C-P-C-K-OAllyl (PepK) and Y-G-E-C-P-C-E-OAllyl (PepE). Both peptides are characterized by the presence of the "CPC" motif together with a few amino acids able to promote disorder. The CPC sequence is a binding motif for the CXCR4 receptor that represents a well-known target for cancer therapies. In this paper, we report on synthetic amphiphilic peptides that consist of lipophilic derivatives of PepE and PepK bearing two stearic alkyl chains and/or an ethoxylic spacer. These peptide amphiphiles form stable supramolecular aggregates; they present conformational features that are typical of intrinsically disordered molecules as shown by CD spectroscopy. Solution fluorescence and DLS studies have been performed to evaluate Critical Micellar Concentrations and the dimension of supramolecular aggregates. Moreover, preliminary in vitro cell-based assays have been conducted to investigate the molecular recognition processes involving the CXCR4 receptor. In the end, the results obtained have been compared with the previous data generated by the corresponding non-amphiphilic peptides (PepE and PepK).

Peptides from scorpion venom represent one of the most promising drug sources for drug discovery for some specific diseases. Current challenges in their separation include high complexity, high homologies and the huge range of peptides. In this paper, a modified strong cation exchange material, named MEX, was utilised for the two-dimensional separation of peptides from complex scorpion venom. The silica-based MEX column was bonded with two functional groups; benzenesulfonic acid and cyanopropyl. To better understand its separation mechanisms, seven standard peptides with different properties were employed in an evaluation study, the results of which showed that two interactions were involved in the MEX column: electrostatic interactions based on benzenesulfonic acid groups dominated the separation of peptides; weak hydrophobic interactions introduced by cyanopropyl groups increased the column's selectivity for peptides with the same charge. This characteristic allowed the MEX column to overcome some of the drawbacks of traditional strong cation exchange (SCX) columns. Furthermore, the study showed the great effects of the acetonitrile (ACN) content, the sodium perchlorate (NaClO4) concentration and the buffer pH in the mobile phase on the peptides' retention and separation selectivity on the MEX column. Subsequently, the MEX column was combined with a C18 column to establish an off-line 2D-MEX × C18 system to separate peptides from scorpion Buthus martensi Karsch (BmK) venom. Due to complementary separation mechanisms in each dimension, a high orthogonality of 47.62% was achieved. Moreover, a good loading capacity, excellent stability and repeatability were exhibited by the MEX column, which are beneficial for its use in future preparation experiments. Therefore, the MEX column could be an alternative to the traditional SCX columns for the separation of peptides from scorpion venom.

In this paper the reactivity of K15H[Zr(α2-P2W17O61)2]·25H2O (1), a Zr(IV)-substituted Wells-Dawson polyoxometalate, is examined towards a series of Gly-Aa, Aa-Gly or Aa-Ser dipeptides, in which the nature and the size of the Aa amino acid side chain were varied. The rate of peptide bond hydrolysis, determined by (1)H NMR experiments, in Gly-Aa dipeptides is strongly dependent on the molecular volume and the chemical structure of the Aa side chain. When the volume of the aliphatic side chain of the Aa residue in Gly-Aa increased, a clear decrease in the hydrolysis rate was observed. Replacing one α-H in the C-terminal Gly residue of Gly-Gly by a methyl group (Gly-Ala) resulted in a 6-fold reactivity decrease, pointing towards the importance of steric factors for efficient peptide bond hydrolysis. The rate constants for peptide bond hydrolysis in Gly-Aa dipeptides at pD 5.0 and 60 °C ranged from 208.0 ± 15.6 × 10(-6) min(-1) for Gly-Ser to 5.0 ± 1.0 × 10(-6) min(-1) for Gly-Glu, reflecting the influence of the different nature of the amino acid side chains on the hydrolysis rate. Faster hydrolysis was observed for peptides containing Ser and Thr since the hydroxyl group in their side chain is able to facilitate amide bond hydrolysis by promoting an N→O acyl rearrangement. Peptides containing positively charged side chains at pD 5.0 show enhanced hydrolysis rates as a result of the secondary electrostatic interactions with the negatively charged surface of the polyoxometalate, which stabilize the peptide-polyoxometalate complex. A slow hydrolysis rate was observed for Gly-Glu, because of the preferential coordination of the carboxylate group in the side chain of Glu to Zr(IV), which prevents coordination of the peptide carbonyl group and its activation towards hydrolysis.

In this paper we describe a solution phase peptide synthesis strategy using the 4-nitrobenzenesulfonamido/N-methyl-4-nitrobenzenesulfonamido group as a protecting/activating system of the carboxyl function. The 4-nitrobenzenesulfonamido group is stable during peptide chain elongation (Fmoc chemistry). The N-aminoacyl or N-dipeptidyl-4-nitrobenzensulfonamides, when activated by methylation, can be easily coupled with another amino acid or reconverted into the free-carboxyl function amino acids or peptides. This activatable protecting group allows both the C → N and the N → C direction solution phase peptide synthesis. We also verified that the absolute configuration at the chiral centers does not change during the coupling reactions.

The photofragmentation pathways at 263 nm of several small peptides containing tyrosine as the UV chromophore have been characterized using a multi-coincidence technique. A detailed study of the fragmentation dynamics of protonated Glycine-Tyrosine (GYH(+)), Tyrosine-Glycine (YGH(+)), Glycine-Tyrosine-Glycine (GYGH(+)), Alanine-Tyrosine (AYH(+)) and Tyrosine-Alanine (YAH(+)) is presented in this paper. Fragmentations occurring or initiated in an excited state are distinguished from those occurring after internal conversion to the ground electronic state by their rapid fragmentation times and binary nature. For the studied systems, it is shown that fragmentations occurring after internal conversion to the ground state are the dominant processes compared to fragmentations occurring in the excited state. The low abundances associated with the observed UV photospecific channels, i.e. Cα-Cβ bond breakage in YGH(+) and YAH(+) and direct z-type bond breakage in GYGH(+), respectively, can be rationalized upon consideration of charge transfer states accessible after absorption of one UV photon. Indeed, excited state calculations performed at the RI-CC2 level of theory indicate that charge transfer on the active CO group is a prerequisite for photospecific bond ruptures. The fragmentation mechanisms and the localization of the charge on the side chain after fragmentation are discussed in terms of ionization energies of the fragments.

This paper describes a sensitive, non-destructive displacement assay, using a fluorescent peptide indicator, for real-time monitoring of the interactions between RNA and RNA binding proteins (RBPs). The developed fluorescent peptide indicators, each containing a mid-sequence fluorophore unit, allowed sensing of target RNA and RNA-RBP interactions through changes in fluorescence intensity. We anticipate that this assay will open up new possibilities for meaningful studies of RNA-RBP interactions.

Synthetic light-driven molecular motors are molecular machines capable of rotation under photo-irradiation. In this paper, we report the synthesis of peptide-conjugated molecular motors and evaluate their DNA-binding properties.

In this paper, we report on the functionalization of silicon nanostructured (NanoSi) surface with an organic layer of nitrilotriacetic acid (NTA) and its subsequent use as an affinity surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) interface for histidine-tagged peptide enrichment and mass spectrometry analysis. The NTA terminal groups are immobilized onto the NanoSi surface via very stable Si-C covalent bonds. The NTA-modified NanoSi (NTA-NanoSi) interface was characterized by contact angle measurements, Fourier transform infrared (FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS). The NTA-NanoSi interface has shown a good selectivity toward His-tagged peptide and permits its enrichment from an artificial mixture of both tagged and untagged peptides and its subsequent mass spectrometry detection with good signal/noise ratio.

Backbone-fluorinated amino acids exhibit unique conformational behaviour, and have potential utility as components of bioactive shape-controlled peptides. However, methods for the elaboration of backbone-fluorinated amino acids have thus far been limited to solution phase peptide coupling reactions. In this paper, protocols are developed that allow the successful manipulation of backbone-fluorinated amino acids using Fmoc-strategy solid phase peptide synthesis. To exemplify this strategy, several fluorinated RGD peptide analogues were synthesised in moderate to good overall yields.

In this paper we present the formation of mono- and binuclear complexes by the octapeptide (c(HKHPHKHP)) with copper(II) ions. The ligand was synthesized manually by the solid-phase method. Its characteristic cyclic structure significantly influences the coordination abilities. The studied peptide has two Pro amino acid residues in the sequence. This causes the formation of two independent centres able to undertake metal ion binding. The potentiometric and spectroscopic (UV-vis, CD and EPR) studies were carried out in aqueous solutions in the pH range 2.5-11.0 at 298 K, HNO(3) was used as the solvent with KNO(3), where the ionic strength was 0.1 M. The analysis of the potentiometric together with spectroscopic studies have shown that the investigated peptide forms only mono-nuclear complexes when the metal-to-ligand molar ratio is 1 : 1. When the concentration of Cu(ii) ions increases and the ligand-to-metal molar ratio is 1 : 2 the formation of binuclear complexes is preferred in the system.

The emerging "bottom-up" nanotechnology reveals a new field of bioinspired nanomaterials composed of chemically synthesized biomolecules. They are formed from elementary constituents in supramolecular structures by the use of a developed nature self-assembly mechanism. The focus of this perspective paper is on intrinsic fundamental physical properties of bioinspired peptide nanostructures and their small building units linked by weak noncovalent bonds. The observed exceptional optical properties indicate a phenomenon of quantum confinement in these supramolecular structures, which originates from nanoscale size of their elementary building blocks. The dimensionality of the confinement gives insight into intrinsic packing of peptide supramolecular nanomaterials. QC regions, revealed in bioinspired nanostructures, were found by us in amyloid fibrils formed from insulin protein. We describe ferroelectric and related properties found at the nanoscale based on original crystalline asymmetry of the nanoscale building blocks, packing these structures. In this context, we reveal a classic solid state physics phenomenon such as reconstructive phase transition observed in bioorganic peptide nanotubes. This irreversible phase transformation leads to drastic reshaping of their quantum structure from quantum dots to quantum wells, which is followed by variation of their space group symmetry from asymmetric to symmetric. We show that the supramolecular origin of these bioinspired nanomaterials provides them a unique chance to be disassembled into elementary building block peptide nanodots of 1-2 nm size possessing unique electronic, optical and ferroelectric properties. These multifunctional nanounits could lead to a new future step in nanotechnology and nanoscale advanced devices in the fields of nanophotonics, nanobiomedicine, nanobiopiezotronics, etc., (This journal is © the Owner Societies 2012)

This paper presents a novel sensor to detect proteolytically active prostate-specific antigen (PSA) by assembling a purpose-designed FITC-labeled peptide with graphene oxide (GO). The fluorescence of the dye-labeled peptide was quenched in the presence of GO. Reaction of the sensor with PSA cleaves the peptide, leading to the release of the dye moiety and a great increase in fluorescence intensity in a dose- and time-dependent manner, and PSA can be quantified accordingly. This approach is simple compared to existing methods since the GO-peptide-based sensor is easily assembled and detection can be achieved without the involvement of complicated procedures. Moreover, the applicability of the method has been demonstrated by detecting PSA in spiked urine samples.

High blood pressure is considered as a significant health problem worldwide. In addition to numerous preventive and therapeutic drug treatments, important advances have been achieved in the identification of dietary compounds that may contribute to cardiovascular health. Among these compounds, peptides with antihypertensive properties received special attention in the past 15 years. Although milk proteins are still the main source of antihypertensive peptides, recently a remarkable increase has been noticed in the report of antihypertensive peptides released from other dietary sources. Most of these peptides have demonstrated their properties by in vitro assays. However, the evidence for their beneficial antihypertensive effects has to be based on animal experiments and clinical trials. This paper reviews the current data of the blood pressure-lowering activity of food-derived peptides demonstrated in vivo (animal models and humans). Other aspects, such as the mechanism of action and bioavailability of these peptides which play a key role in their antihypertensive effects are also summarized in this review., (This journal is © The Royal Society of Chemistry 2012)

Assembly of proteins or peptides into fibrils is an important subject of study in various research fields. In the field of food research, the protein fibrils are interesting candidates as functional ingredients. It is essential to understand the formation and properties of the fibrils for successful application of the fibrils in food products. This paper describes the impact of recent research on the general view of the process of fibril formation from β-lg and the properties of the fibrils that are formed, leading to better control of applications for the fibrils. There is a need for a better understanding of the behavior of fibrils in more complex food systems.

The paper reports on a novel localized surface plasmon resonance (LSPR) substrate architecture for the immobilization and detection of histidine-tagged peptides. The LSPR interface consists of an ITO (indium tin oxide) substrate coated with gold nanostructures. The latter are obtained by thermal deposition of a thin (2 nm thick) gold film followed by post-annealing at 500 °C. The LSPR interface was coated with poly[3-(pyrrolyl)carboxylic acid] thin films using electrochemical means. The ability of the LSPR interfaces coated with poly[3-(pyrrolyl)carboxylic acid] to chelate copper ions was investigated. Once loaded with metal ions, the modified LSPR interface was able to bind specifically to histidine-tagged peptides. The binding process was followed using LSPR.

An efficient approach for the synthesis of a series of S-acyl peptides containing internal cysteine residues has been developed and the chemical long-range ligation of these S-acyl peptides via 5-, 8-, 11- and 14-membered cyclic transition states has been investigated. Our results include the first examples of successful isopeptide ligations starting from S-acyl peptides containing non-terminal cysteine residues and indicate that the cyclic transition states studied in this present paper are decreasingly favored in the order of their sizes 5≫14>11≫8.

Zinc porphyrin functionalized with double long-chain alkylated L-glutamide (GTPP-Zn) was synthesized for the first time, and its self-assembling behaviour was investigated in nonpolar organic solvents. The uniqueness of this functionalized porphyrin is characterized by its drastic colour change from dark green to purple via the formation of chirally stacked structures through selective axial coordination on zinc with pyridine derivatives. In this paper, we report the versatility of the GTPP-Zn assembly process as a stimuli-responsive chiroptical switching system and describe the remarkable ligand-specific induction of secondary chirality accompanied by aggregation morphological change.

This paper describes a methodology that correlates experimental chemical shifts (at the alpha proton) of proteins with their geometrical data (both dihedral angles and distances) obtained from 13 representative proteins, which are taken from the Protein Data Bank (PDB) and the BioMagRes Data Bank (BMRB). To this end, the experimentally measured proton chemical shifts of simple amides have been correlated with DFT-based calculated structures, at the B3PW91/6-31G* level. This results in a series of mathematical relationships, which are extrapolated to the above-mentioned proteins giving rise to a modified equation for such skeleta. It is relevant to note that the equation is also supported by a clear comparison with NMR data of a protein beyond the chosen set, such as insulin, even with lower errors. The model also relates the dependence of chemical shifts on hydrophobic and anisotropic effects at the amino acid residues.

We have previously reported that a double-chain anionic amphiphile capable of intermolecular triple hydrogen bonds could form extremely hydrophobic sites in water and specifically incorporated stilbazolium-based compact hemicyanine dyes as monomeric species, resulting in induction of intense fluorescence emission in the dyes. In this paper, the structural requirements of the intense fluorescence-inducing amphiphiles were investigated. It is noted that the introduction of beta-Ala residues into two long-chain alkyl group moieties was most effective for the amphiphiles derived from L-glutamic acid with relatively shorter side-chain methylenes. The dye specificity in terms of induction of the intense fluorescence was also investigated using hemicyanines (stilbazolium etc.), cyanine, carbocyanine, thiacarbocyanines, and azo dye. The amphiphile with the shortest octanoyl-beta-alanyl double-chain alkyl groups, longer side-chain, and shorter spacer was found to show increased sensitivity to alkali metal ions, especially Li(+). This could be a potential OFF-ON type fluorescence sensor for Li(+).

This paper describes the host-guest interaction between nonionic peptide lipids and solvatochromic dipolar betaine dyes in nonpolar aprotic organic solvent. We have serendipitously found that the colour of Reichardt's Dye (referred to as ET(30) hereafter, although the term ET(30) has been used as a polarity parameter) in chlorobenzene unusually blue-shifted in the presence of L-glutamic acid-derived peptide lipid 1 with a benzyloxycarbonylated Gly headgroup. Since it is widely accepted that ET(30) shows negative solvatochromism, i.e., the visible absorption band of this dye blue-shifts as the solvent polarity increases, the blue-shift indicates that ET(30) was in contact with the more polar microenvironment produced by the peptide lipid 1 rather than chlorobenzene under aggregate-free conditions. The binding site was assumed to be N-H(delta+) and CO(delta-) attached to both sides of the Gly residue, respectively, i.e., the O- and N+ of ET(30) complementarily bound to N-H(delta+) and CO(delta-) through hydrogen bonding and ion-dipole interaction, respectively. Since ET(30) is practically non-fluorescent, it was not feasible to use fluorescence spectrometry, which is a powerful method for the study of host-guest interactions, in order to specify the binding mode of ET(30). Therefore, a synthetic approach, although very laborious but reliable, has been used in conjunction with solvatochromic probing using visible absorption spectroscopy to specify the binding site on peptide lipid 1. The binding site has been found to be located on two dipoles, i.e., N-H(delta+) and CO(delta-) attached to both sides of the Gly residue, respectively, because introducing steric hindrance into the Gly moiety using several L-alpha-amino acids with bulky -substituents interfered with the binding of ET(30). Similar specific binding behaviour of ET(30) was observed by replacing the Gly residue of the lipid 1 with sarcosine (Sar). It was found that self-assembly of the peptide lipid was necessary for effective capture of ET(30). The molecular structural requirements of the peptide lipids that form such specific polar microenvironments complementary to dipolar betaine dyes have also been investigated.

This paper describes a new fluorescent chemosensor for phosphorylated peptide, which comprises a rigid trans-4,4'-diazastilbene and two Zn(II)-Dpa (2,2'-dipicolylamine) units; this chemosensor sequence-selectively binds to a (i, i + 1) bis-phosphorylated peptide and displays a dual-emission fluorescence change.

The binding of zinc (Zn) ions to proteins is important for many cellular events. The theoretical and computational description of this binding (as well as that of other transition metals) is a challenging task. In this paper the binding of the Zn ion to four cysteine residues in the structural site of horse liver alcohol dehydrogenase (HLADH) is studied using a synthetic peptide mimic of this site. The study includes experimental measurements of binding constants, classical free energy calculations from molecular dynamics (MD) simulations and quantum mechanical (QM) electron structure calculations. The classical MD results account for interactions at the molecular level and reproduce the absolute binding energy and the hydration free energy of the Zn ion with an accuracy of about 10%. This is insufficient to obtain correct free energy differences. QM correction terms were calculated from density functional theory (DFT) on small clusters of atoms to include electronic polarisation of the closest waters and covalent contributions to the Zn-S coordination bond. This results in reasonably good agreement with the experimentally measured binding constants and Zn ion hydration free energies in agreement with published experimental values. The study also includes the replacement of one cysteine residue to an alanine. Simulations as well as experiments showed only a small effect of this upon the binding free energy. A detailed analysis indicate that the sulfur is replaced by three water molecules, thereby changing the coordination number of Zn from four (as in the original peptide) to six (as in water).

Substances that mediate the import of proteins into cells, "carriers", have many potential applications. The most potentially useful carriers do not have to be covalently linked to their protein cargoes. However, a common problem with all carrier molecules is that they tend to deposit the cargo proteins into endosomes; diffuse distribution in the cytosol is the desired outcome. This paper describes the import of four different labeled (Alexa Fluor 488) proteins (avidin, recombinant streptavidin, bovine serum albumin, and beta-galactosidase), with the well-known non-covalent carrier called pep-1 (also known as Chariot), with R(8) (a molecule that is not widely appreciated to import protein cargoes via a non-covalent mode of action), and with a new molecule called azo-R(8). The data collected from fluorescence microscopy and flow cytometry indicate that all three non-covalent carriers can facilitate transport. At 37 degrees C, import into endocytic compartments dominates, but at 4 degrees C weak, diffuse fluorescence is observed in the cytosol, indicative of a favorable mode of action.

The detection of peptides with mass spectrometry from volume-limited biological samples is a challenging task due to low sample volume, a broad range of peptide concentrations down to trace levels, endogenous high proteins and salt levels. Previously, a microspotting method was presented for trace-level peptide detection with MALDI-MS from sub-microlitre samples with biological salt levels. However, in the presence of proteins, peptide signals are significantly reduced. This paper presents a novel dialysis device for removal of proteins from sub-microlitre samples using a semipermeable hollow fiber membrane to enhance peptide detection. A dialysis device was constructed to perform sub-microlitre dialysis to remove proteins from complex samples. Angiotensin I was used as a model peptide in the presence of 350 mg L(-1) BSA prepared in physiological saline to mimic biological samples. In the absence of BSA, clear angiotensin I peaks were seen at 250 pM, yet in the presence of the BSA, 10 nM angiotensin I was barely detected. After dialysis, peak detection was improved to a 500 pM level. Protein removal and peptide recovery (approximately 66%) were determined using CE-LIF. Clinical vitreous samples as low as 200 nL were successfully dialyzed in 30 min and a 3-fold increase in peptide peaks were detected with greatly improved signals. This method is simple and can be a useful technique for trace level peptide detection from volume-limited biological samples.

Determining the structure and dynamics of large biologically relevant molecules is one of the key challenges facing biology. Although X-ray crystallography (XRD) and nuclear magnetic resonance (NMR) yield accurate structural information, they are of limited use when sample quantities are low. Mass spectrometry (MS) on the other hand has been very successful in analyzing biological molecules down to atto-mole quantities and has hence begun to challenge XRD and NMR as the key technology in the life sciences. This trend has been further assisted by the development of MS techniques that yield structural information on biomolecules. Of these techniques, collision-induced dissociation (CID) and hydrogen/deuterium exchange (HDX) are among the most popular. Despite advances in applying these techniques, little direct experimental evidence had been available until recently to verify their proposed underlying reaction mechanisms. The possibility to record infrared spectra of mass-selected molecular ions has opened up a novel avenue in the structural characterization of ions and their reaction products. On account of its high pulse energies and wide wavelength tunability, the free electron laser for infrared experiments (FELIX) at FOM Rijnhuizen has been shown to be ideally suited to study trapped molecular ions with infrared photo-dissociation spectroscopy. In this paper, we review recent experiments in our laboratory on the infrared spectroscopic characterization of reaction products from CID and HDX, thereby corroborating some of the reaction mechanisms that have been proposed. In particular, it is shown that CID gives rise to linear fragment ion structures which have been proposed for some time, but also yields fully cyclical ring structures. These latter structures present a possible challenge for using tandem MS in the sequencing of peptides/proteins, as they can lead to a scrambling of the amino acid sequence information. In gas-phase HDX of an amino acid it is shown that the structure can be changed from a charge solvated to a zwitterionic structure, thereby demonstrating that HDX can be an invasive technique, in fact changing the structure of the analyte. These results emphasize that more fundamental work is required in order to understand the underlying mechanisms in two of the most important structural techniques in MS.

An ageing society faces an increasing number of neurodegenerative diseases such as Alzheimer's, Parkinson's, and Creutzfeld-Jacob disease. The deposition of amyloid fibrils is a pathogenic factor causing the destruction of neuronal tissue. Amyloid-forming proteins are mainly alpha-helical in their native conformation, but undergo an alpha-helix to beta-strand conversion before or during fibril formation. Partially unfolded or misfolded beta-sheet fragments are discussed as direct precursors of amyloids. To potentially cure neurodegenerative diseases we need to understand the complex folding mechanisms that shift the equilibrium from the functional to the pathological isoform of the proteins involved. This paper describes a novel approach that allows us to study the interplay between peptide primary structure and environmental conditions for peptide and protein folding in its whole complexity on a molecular level. This de novo designed peptide system may achieve selective inhibition of fibril formation.

The delta-conotoxin EVIA from the Conus ermineus venom, a recently characterized toxin, exhibits cis-trans isomerism of the Leu12-Pro13 bond associated with the triggering of its biological activity. In this paper we use the pseudoproline concept to target the presumed bioactive cis conformation. We report the design and the synthesis of loop 2 analogs from residue 8 to 18 containing either the cis-inducing Cys(PsiMe,MePro)13 unit or the natural proline residue. NMR studies in water and molecular modeling allowed us to identify the amide bond "locked" in a cis conformation for as in the suggested bioactive form of the natural toxin., (Copyright 2004 The Royal Society of Chemistry)

This paper presents a highly efficient sample preparation technique for matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The purpose of the research is to use a conventional MALDI support to directly and conveniently detect sub-nM levels of peptides from volume-limited samples with physiological salt levels. In this new method, highly uniform matrix-nitrocellulose spots with a 500 microm diameter were conveniently generated by direct contact of a capillary tip to a stainless steel MALDI plate. An array of 50 microspots can be blotted from 1 microL matrix-nitrocellulose solution within 1 min. It was found that the addition of high concentration nitrocellulose to the alpha-cyano-4-hydroxycinnamic acid (CHCA) matrix solution is critical for the formation of microspots. Samples are deposited on top of those microspots and incubated for 3 min. The CHCA-nitrocellulose surface shows a significant peptide binding capability for sub-nM levels of peptide. Restricting the matrix spot diameter to 500 microm gives an analyte enrichment effect because the peptides are confined to a small solid-phase surface area. Selective peptide binding is seen even with >0.15 M salt levels. Loading small aliquots of samples with multiple applications allows low level peptide detection down to 100 pM. Push-pull perfusates collected from the rat striatum were successfully analyzed with the microspot method., (Copyright 2004 The Royal Society of Chemistry)

This paper reports the syntheses of individual dendritic branches based on L-lysine and functionalised with either Boc or Bz surface groups. Convergent and divergent synthetic approaches were employed and the preservation of stereochemistry during the syntheses was monitored using polarmetry, NMR and HPLC. In addition, racemic dendritic branches based on D,L-lysine were synthesised for comparative purposes. It was observed that the preservation of stereochemistry in the dendritic peptide was dependent on the method of synthesis, with divergent methodology being preferred. The results are discussed in terms of the known stereochemical outcomes of traditional peptide coupling processes, and are generalised to the synthesis of other dendritic peptides. Such observations about the chirality of dendritic peptides are of relevance to chemists developing dendritic systems for applications where single enantiomer dendrimers would clearly be preferred, such as enantioselective catalysis or pharmaceutical chemistry.