Peptides adsorption on TiO2 and Au: Molecular organization investigated by NEXAFS, XPS and IR

We present a spectroscopic study of the structure of two peptides deposited on Au and TiO₂:

- PeptA, (EAK16-RGD) bringing the adhesive RGD sequence linked to EAK16;

- PeptB, having RGD linked to a “scrambled” sequence of the EAK16 peptide.

Previously reported NEXAFS investigations on thin films of the self-assembling peptide EAK16 deposited on Au and TiO₂, revealed molecular order and orientation for both substrates.IR spectra show a β-sheet conformation for PeptA and a random structure for PeptB. Angular-dependent NEXAFS measurements reveal an ordered structure with preferential molecular orientation only for PeptA. XPS analysis indicates that PeptA is adsorbed on TiO₂ in a larger amount than PeptB.     

Ultraviolet resonance Raman spectroscopy of a β‐sheet peptide: a model for membrane protein folding

The partitioning of a hydrophobic hexapeptide, N‐acetyl‐tryptophan‐pentaleucine (AcWL5), into self‐associated β‐sheets within a vesicle membrane was studied as a model for integral membrane protein folding and insertion via vibrational and electronic spectroscopy. Ultraviolet resonance Raman spectroscopy allows selective examination of the structures of amino acid side chains and the peptide backbone and provides information about local environment and molecular conformation. The secondary structure of AcWL5 within a vesicle membrane was investigated using 207.5‐nm excitation and found to consist of β‐sheets, in agreement with previous studies. The β‐sheet peptide shows enhanced Raman scattering cross‐sections for all amide modes as well as extensive hydrogen‐bonding networks. Tryptophan vibrational structure was probed using 230‐nm excitation. Increases in Raman cross‐sections of tryptophan modes W1, W3, W7, W10, W16, W17, and W18 of membrane‐incorporated AcWL5 are primarily attributed to greater resonance enhancement with the B_b electronic transition. The W17 mode, however, undergoes a much greater enhancement than is expected for a simple resonance effect, and this observation is discussed in terms of hydrogen bonding of the indole ring in a hydrophobic environment. The observed tryptophan mode frequencies and intensities overall support a hydrophobic environment for the indole ring within a vesicle, and these results have implications for the location of tryptophan in membrane protein systems. Copyright © 2009 John Wiley & Sons, Ltd.     

Characterization of bioactive RGD peptide immobilized onto poly(acrylic acid) thin films by plasma polymerization

Plasma surface modification can be used to improve the surface properties of commercial pure Ti by creating functional groups to produce bioactive materials with different surface topography. In this study, a titanium surface was modified with acrylic acid (AA) using a plasma treatment and immobilized with bioactive arginine-glycine-aspartic acid (RGD) peptide, which may accelerate the tissue integration of bone implants. Both terminals containing the -NH₂ of RGD peptide sequence and -COOH of poly(acrylic acid) (PAA) thin film were combined with a covalent bond in the presence of 1-ethyl-3-3-dimethylaminopropyl carbodiimide (EDC). The chemical structure and morphology of AA film and RGD immobilized surface were investigated by X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FT-IR), atomic force microscopy (AFM), and scanning electron microscopy (SEM). All chemical analysis showed full coverage of the Ti substrate with the PAA thin film containing COOH groups and the RGD peptide. The MC3T3-E1 cells were cultured on each specimen, and the cell alkaline phosphatase (ALP) activity were examined. The surface-immobilized RGD peptide has a significantly increased the ALP activity of MC3T3-E1 cells. These results suggest that the RGD peptide immobilization on the titanium surface has an effect on osteoblastic differentiation of MC3T3-E1 cells and potential use in osteo-conductive bone implants.     

End-to-end Distance Distribution in Fluorescent Derivatives of Bradykinin in Interaction with Lipid Vesicles

Cellular membranes have relevant roles in processes related to proteases like human kallikreins and cathepsins. As enzyme and substrate may interact with cell membranes and associated co-factors, it is important to take into account the behavior of peptide substrates in the lipid environment. In this paper we report an study based on energy transfer in two bradykinin derived peptides labeled with the donor-acceptor pair Abz/Eddnp (ortho-aminobenzoic acid/N-[2,4-dinitrophenyl]-ethylenediamine). Time-resolved fluorescence experiments were performed in phosphate buffer and in the presence of large unilamelar vesicles of phospholipids, and of micelles of sodium dodecyl sulphate (SDS). The decay kinetics were analyzed using the program CONTIN to obtain end-to-end distance distribution functions f(r). Despite of the large difference in the number of residues the end-to-end distance of the longer peptide (9 amino acid residues) is only 20?% larger than the values obtained for the shorter peptide (5 amino acid residues). The proline residue, in position 4 of the bradykinin sequence promotes a turn in the longer peptide chain, shortening its end-to-end distance. The surfactant SDS has a strong disorganizing effect, substantially broadening the distance distributions, while temperature increase has mild effects in the flexibility of the chains, causing small increase in the distribution width. The interaction with phospholipid vesicles stabilizes more compact conformations, decreasing end-to-end distances in the peptides. Anisotropy experiments showed that rotational diffusion was not severely affected by the interaction with the vesicles, suggesting a location for the peptides in the surface region of the bilayer, a result consistent with small effect of lipid phase transition on the peptides conformations.     

An NMR Investigation of the Conformational Effect of Nitroxide Spin Labels on Ala-Rich Helical Peptides

Nitroxide spin labels, in conjunction with electron spin resonance (ESR) experiments, are extensively employed to probe the structure and dynamics of biomolecules. One of the most ubiquitous spin labeling reagents is the methanethiosulfonate spin label which attaches a spin label selectively to Cys residues via a disulfide bond (Cys-SL). However, the actual effect of the nitroxide spin label upon the conformation of the peptide or protein cannot be unambiguously determined by ESR. In this study, a series of 16-residue Ala-rich helical peptides was characterized by nuclear magnetic resonance techniques. The C_αH chemical shift analysis, NOEs, and³J_NHαcoupling constants for peptides with no Cys, free Cys, and Cys-SL (with the N–O group reduced) were compared. These results indicate that while replacement of an Ala with a Cys residue causes a loss of overall helical structure, the Cys-SL residue is helix supporting, as would be expected for a non-β-branched aliphatic amino acid. Thus, the Cys-SL residue does not perturb helical structure and, instead, exhibits helix-stabilizing characteristics similar to that found for Ala, Met, and Leu.     

Vibrational spectroscopy and DFT calculations of di‐amino acid peptides: α‐ and β‐N‐acetyl‐L‐Asp‐L‐Glu in the solid state

Experimental vibrational spectroscopic studies and density functional theory (DFT) calculations of the di‐amino acid peptide derivatives α‐ and β‐N‐acetyl‐L‐Asp‐L‐Glu have been undertaken. Raman and infrared spectra have been recorded for samples in the solid state. DFT simulations were conducted using the B3‐LYP correlation functional and the cc‐pVDZ basis set to determine energy minimized/geometry optimized structures (based on a single isolated molecule in the gaseous state). Normal coordinate calculations have provided vibrational assignments for fundamental modes, including their potential energy distributions. Significant differences are observed between α‐ and β‐N‐acetyl‐L‐Asp‐L‐Glu both in the computed structures and in the vibrational spectra. The combination of experimental and calculated spectra provide an insight into the structural and vibrational spectroscopic properties of di‐amino acid peptide derivatives. Copyright © 2009 John Wiley & Sons, Ltd.     

Characterization of peptide immobilization on an acetylene terminated surface via click chemistry

Peptide (A-A-A-A-G-G-G-E-R-G-D)¹ conjugated surfaces were prepared on silicon surfaces through click chemistry. The amino acid sequence RGD is the cellular attachment site of a large number of extracellular matrices such as blood and cell surface proteins. Recent research has focused on developing RGD peptides which mimic cell adhesion proteins and integrins [1], [2].The steps involved the formation of an alkyne-terminated monolayer on Si(111), followed by linking the peptide to 4-azidophenyl isothiocyanate via a specific and gentle reaction. This was followed by the attachment of the azido peptide to the surface-bound alkynes using the Cu (I)-catalyzed Huisgen 1,3-dipolar cycloaddition reaction. The surface structures of the alkyne terminated monolayer and the attached peptide were characterized using high resolution impedance spectroscopy (EIS), X-ray photoelectron spectroscopy (XPS) and Fourier Transform Infrared (ATR-FTIR) Spectroscopy. EIS characterization revealed the alkyne layer and the hydrophobic and polar regions of the attached peptide. XPS analysis showed a high surface coverage of the peptide on the silicon substrates and this was confirmed by FTIR.Our results confirmed a specific covalent attachment of the peptide on the silicon surfaces. This approach offers a versatile, experimentally simple, method for the specific attachment of peptide ligands. This approach would have applications for cell attachment and biosensors.     

Effect of core epitope modification on the antibody recognition of a MUC2 mucin peptide

Identification of protein epitopes via combinatorial chemistry was one of the most important discoveries of the past three decades. Mapping of linear antibody epitopes can be achieved rapidly and cost-effectively by the polymer pin-bound peptide approach. In this article, the determination of the fine epitope structure of MUC2 mucin glycoprotein is described by using specific monoclonal antibody. We have used positional scanning combinatorial approach, and also parallel synthesis. The residues within the MUC2 epitope ¹⁸PTGTQ²² of MAb 996 were replaced by all other proteinogenic amino acids on pin-bound peptide libraries, and their antibody binding was studied in modified ELISA. Thr¹⁹ was the least important of the residues in antibody recognition; most of the other amino acids could be replaced, except Pro. The other residues cannot be replaced without loss of antibody binding, where both the size and character of the amino acids were important. The significance of the non-chiral Gly²⁰ residue was further studied by competitive ELISA of parallelly synthesized soluble peptides containing l- or d-Ala instead of Gly residue. However, the d-Ala-containing oligopeptides showed no antibody binding; therefore, the backbone conformation is characteristic of that of l-amino acid containing peptides in this position as well. With the combinatorial approach we obtained relevant information about the contribution of individual amino acid side chains to the MAb 996 antibody binding within the PTGTQ predominant MUC2 mucin epitope. These results could be utilized for the design of synthetic antigens for detection of MUC2 protein core-specific antibodies related to carcinoma(s).     

An online nano-LC-ESI-FTICR-MS method for comprehensive characterization of endogenous fragments from amyloid β and amyloid precursor protein in human and cat cerebrospinal fluid

Amyloid precursor protein (APP) is the precursor protein to amyloid β (Aβ), the main constituent of senile plaques in Alzheimer's disease (AD). Endogenous Aβ peptides reflect the APP processing, and greater knowledge of different APP degradation pathways is important to understand the mechanism underlying AD pathology. When one analyzes longer Aβ peptides by low-energy collision-induced dissociation tandem mass spectrometry (MS/MS), mainly long b-fragments are observed, limiting the possibility to determine variations such as amino acid variants or post-translational modifications (PTMs) within the N-terminal half of the peptide. However, by using electron capture dissociation (ECD), we obtained a more comprehensive sequence coverage for several APP/Aβ peptide species, thus enabling a deeper characterization of possible variants and PTMs. Abnormal APP/Aβ processing has also been described in the lysosomal storage disease Niemann-Pick type C and the major large animal used for studying this disease is cat. By ECD MS/MS, a substitution of Asp7 → Glu in cat Aβ was identified. Further, sialylated core 1 like O-glycans at Tyr10, recently discovered in human Aβ (a previously unknown glycosylation type), were identified also in cat cerebrospinal fluid (CSF). It is therefore likely that this unusual type of glycosylation is common for (at least) species belonging to the magnorder Boreoeutheria. We here describe a detailed characterization of endogenous APP/Aβ peptide species in CSF by using an online top-down MS-based method.     

Study on the relationship between structure and taste activity of the umami peptide of Stropharia rugosoannulata prepared by ultrasound

Through virtual screening, electronic tongue verification, and molecular docking technology, the structure-taste activity relationship of 47 kinds of umami peptides (octapeptide - undecapeptide) from Stropharia rugosoannulata prepared by simultaneous ultrasonic-assisted directional enzymatic hydrolysis was analyzed. The umami peptides of S.rugosoannulata can form hydrogen bond interaction and electrostatic interaction with umami receptors T1R1/T1R3. The amino acid residues at the peptides' N-terminal and C-terminal play a vital role in binding with the receptors to form a stable complex. D, E, and R are the primary amino acids in the peptides that easily bind to T1R1/T1R3. The basic amino acid in the peptides is more easily bound to T1R1, and the acidic amino acid is more easily bound to T1R3. The active amino acid sites of the receptors to which the peptides bind account for 42%−65% of the total active amino acid residues in the receptors. ASP147 and ASP219 are the critical amino acid residues for T1R1 to recognize the umami peptides, and ARG64, GLU45, and GLU48 are the critical amino acid residues for T1R3 to recognize the umami peptides. The increase in the variety and quantity of umami peptides is the main reason for improving the umami taste of the substrate prepared by synchronous ultrasound-assisted directional enzymatic hydrolysis. This study provides a theoretical basis for understanding simultaneous ultrasound-assisted directional enzymatic hydrolysis for preparing umami peptides from S.rugosoannulata, enhancing the flavor of umami, and the relationship between peptide structure and taste activity.     

Local structural order in carbonic acid polymorphs: Raman and FT‐IR spectroscopy

Two different polymorphs of carbonic acid, α‐ and β‐H₂CO₃, were identified and characterized using infrared spectroscopy (FT‐IR) previously. Our attempts to determine the crystal structures of these two polymorphs using powder and thin‐film X‐ray diffraction techniques have failed so far. Here, we report the Raman spectrum of the α‐polymorph, compare it with its FT‐IR spectrum and present band assignments in line with our work on the β‐polymorph [Angew. Chem. Int. Ed. 48 (2009) 2690–2694]. The Raman spectra also contain information in the wavenumber range ∼90–400 cm⁻¹, which was not accessible by FT‐IR spectroscopy in the previous work. While the α‐polymorph shows Raman and IR bands at similar positions over the whole accessible range, the rule of mutual exclusion is obeyed for the β‐polymorph. This suggests that there is a center of inversion in the basic building block of β‐H₂CO₃ whereas there is none in α‐H₂CO₃. Thus, as the basic motif in the crystal structure we suggest the cyclic carbonic acid dimer containing a center of inversion in case of β‐H₂CO₃ and a catemer chain or a sheet‐like structure based on carbonic acid dimers not containing a center of inversion in case of α‐H₂CO₃. This hypothesis is strengthened when comparing Raman active lattice modes at < 400 cm⁻¹ with the calculated Raman spectra for different dimers. In particular, the intense band at 192 cm⁻¹ in β‐H₂CO₃ can be explained by the inter‐dimer stretching mode of the centrosymmetric RC(OHO)₂ CR entity with ROH. The same entity can be found in gas‐phase formic acid (RH) and in β‐oxalic acid (RCOOH) and produces an intense Raman active band at a very similar wavenumber. The absence of this band in α‐H₂CO₃ confirms that the difference to β‐H₂CO₃ is found in the local coordination environment and/or monomer conformation rather than on the long range. Copyright © 2011 John Wiley & Sons, Ltd.     

Enhanced spectral resolution in immobilized peptides and proteins by combining chemical shift sum and difference spectroscopy

A two-dimensional correlation experiment is introduced that records the sum and difference chemical shift of two scalar or dipolar coupled nuclei. Statistical results indicate that the suggested pulse scheme can significantly increase the possibility of separating chemical shift contributions due to residue type and backbone conformation in immobilized peptides and proteins. Experimental applications demonstrate the theoretical concept and lead to the predicted resolution enhancement between different amino acid types and among protein residues of different secondary structure.     

Use of peptide for selective and sensitive detection of an Anthrax biomarker via peptide recognition and surface‐enhanced Raman scattering

A short 16‐amino acid peptide has been used in place of an antibody to selectively detect the specific Anthrax biomarker, protective antigen (PA), using surface‐enhanced Raman scattering (SERS). Peptides are more stable than antibodies under various biological conditions and are easily synthesized for a specific target. A peptide that has high affinity to PA was conjugated onto gold nanoparticles along with a Raman reporter and then incubated in various concentrations of PA. Parallel studies in which the peptide sequence was replaced with an antibody were performed to compare the performance of the two methodologies. Both the peptide and antibody functionalized nanoparticles were able to specifically detect PA concentrations down to 6.1 fM . These results demonstrate that these short, robust peptides can be used in the place of traditional antibodies to specifically recognize target biomarkers in the field for the potential diagnosis of disease. Copyright © 2010 John Wiley & Sons, Ltd.     

Nanomechanics of single silkworm and spider fibres: a Raman and micro‐mechanical in situ study of the conformation change with stress

The combination of micro‐Raman spectroscopy and an advanced universal fibre tester (UFT) made it possible to probe at the nanoscale (through monitoring the modification of chemical bonds) the change in conformation (α‐helix, β‐sheet, etc.), macromolecular fibroin chain orientation and coupling during the application of stress, quantitatively. Different single fibres of silkworms (Bombyx mori, Gonometa rufobrunea, Gonometa postica) and a spider (Nephila madagascariensis) were tested in a dry environment and compared with the behaviour of keratin fibre. As observed previously for single keratin fibres, a direct relationship is observed between nano‐ and micro‐mechanical tensile behaviour. The phase transition plateau, well defined for some pristine B. mori fibres, disappears in degummed fibres, which indicates a structural modification and increasing disorder with chemical treatments. Stress‐controlled micro‐Raman analysis shows that a few modes involving CH₂ and/or amide groups of β‐conformation chains undergo a wavenumber softening during the elastic behaviour (∼0–3%), although most of the modes are not affected. A different behaviour is observed for modes associated with ‘ordered’ and ‘disordered’ β‐sheets and helical chains. Larger softening is observed for lattice modes with increasing stress/strain, as expected. Structural changes and relationships with mechanical behaviour are discussed. Copyright © 2008 John Wiley & Sons, Ltd.     

Vibrational spectroscopic studies of the structure of di‐amino acid peptides. Part II: cyclo(L‐Asp‐L‐Asp) in the solid state and in aqueous solution

Solid‐state protonated and N,O‐deuterated Fourier transform infrared (IR) and Raman scattering spectra together with the protonated and deuterated Raman spectra in aqueous solution of the cyclic di‐amino acid peptide cyclo(L ‐Asp‐L ‐Asp) are reported. Vibrational band assignments have been made on the basis of comparisons with previously cited literature values for diketopiperazine (DKP) derivatives and normal coordinate analyses for both the protonated and deuterated species based upon DFT calculations at the B3‐LYP/cc‐pVDZ level of the isolated molecule in the gas phase. The calculated minimum energy structure for cyclo(L ‐Asp‐L ‐Asp), assuming C₂ symmetry, predicts a boat conformation for the DKP ring with both the two L ‐aspartyl side chains being folded slightly above the ring. The CO stretching vibrations have been assigned for the side‐chain carboxylic acid group (e.g. at 1693 and 1670 cm⁻¹ in the Raman spectrum) and the cis amide I bands (e.g. at 1660 cm⁻¹ in the Raman spectrum). The presence of two bands for the carboxylic acid CO stretching modes in the solid‐state Raman spectrum can be accounted for by factor group splitting of the two nonequivalent molecules in a crystallographic unit cell. The cis amide II band is observed at 1489 cm⁻¹ in the solid‐state Raman spectrum, which is in agreement with results for cyclic di‐amino acid peptide molecules examined previously in the solid state, where the DKP ring adopts a boat conformation. Additionally, it also appears that as the molecular mass of the substituent on the C^α atom is increased, the amide II band wavenumber decreases to below 1500 cm⁻¹; this may be a consequence of increased strain on the DKP ring. The cis amide II Raman band is characterized by its relatively small deuterium shift (29 cm⁻¹), which indicates that this band has a smaller N H bending contribution than the trans amide II vibrational band observed for linear peptides. Copyright © 2009 John Wiley & Sons, Ltd.     

Electric dipole moments and conformations of isolated peptides

The electric dipole moments of the isolated amino acid tryptophan and small glycine-based peptides (WG_n, n = 1-5, W = tryptophan, G = glycine) have been measured by deflection of a molecular beam in an inhomogeneous electric field. The measurements are compared to the results of ab initio calculations and Monte-Carlo simulations. The conformation and the flexibility of the peptides, at different temperatures, are discussed. The WG_n peptides are much more floppy than an isolated tryptophan, even a single glycine is enough to make the peptide floppy on the timescale of the electric deflection measurements. Received 4 January 2002 Published online 13 September 2002     

Potential energy surface of alanine polypeptide chains

The multidimensional potential energy surfaces of the peptide chains consisting of three and six alanine (Ala) residues have been studied with respect to the degrees of freedom related to the twist of these molecules relative to the peptide backbone (these degrees of freedom are responsible for the folding of such peptide molecules and proteins). The potential energy surfaces have been calculated ab initio within the framework of the density functional theory taking into account all electrons in the system. The probabilities of transitions between various stable conformations of polypeptide molecules are evaluated. The results are compared to the data obtained by molecular dynamics simulations and to the available experimental data. The influence of the secondary structure of the polypeptide chain on its conformational properties with respect to rotations has been studied. It is shown that, in a chain of six amino acid (Ala) residues, the secondary structure type (helix or sheet conformation) influences the stable isomer states of the polypeptide.     

Structural characterization and angiotensin-converting enzyme (ACE) inhibitory mechanism of Stropharia rugosoannulata mushroom peptides prepared by ultrasound

To reveal the structural characteristics and angiotensin-converting enzyme (ACE) inhibition mechanism of Stropharia rugosoannulata mushroom peptides prepared by multifrequency ultrasound, the peptide distribution, amino acid sequence composition characteristics, formation pathway, and ACE inhibition mechanism of S. rugosoannulata mushroom peptides were studied. It was found that the peptides in S. rugosoannulata mushroom samples treated by multifrequency ultrasound (probe ultrasound and bath ultrasound mode) were mainly octapeptides, nonapeptides, and decapeptides. Hydrophobic amino acids were the primary amino acids in the peptides prepared by ultrasound, and the amino acid dissociation of the peptide bonds at the C-terminal under the action of ultrasound was performed mainly to produce hydrophobic amino acids. Pro and Val (PV), Arg and Pro (RP), Pro and Leu (PL), and Asp (D) combined with hydrophobic amino acids were the characteristic amino acid sequence basis of the active peptides of the S. rugosoannulata mushroom. The docking results of active peptides and ACE showed that hydrogen bond interaction remained the primary mode of interaction between ACE and peptides prepared by ultrasound. The peptides can bind to the amino acid residues in the ACE active pocket, zinc ions, or key amino acids in the domain, and this results in inhibition of ACE activity. Cation–pi interactions also played an important role in the binding of mushroom peptides to ACE. This study explains the structural characteristics and ACE inhibition mechanism used by S. rugosoannulata mushroom peptides prepared by ultrasound, and it will provide a reference for the development and application of S. rugosoannulata mushroom peptides.