Calcium-binding properties and molecular organization of bradykinin A solution 1H-NMR study

Comprehensive Analysis of Coupled Proline Cis-Trans States in Bradykinin Using ωBP-REMD Simulations

It is well-known that proline (Pro) cis-trans isomerization plays a decisive role in the folding and stabilization of proteins. The conformational coupling between isomerization states of different Pro residues in proteins during conformational adaptation processes is not well understood. In the present work, we investigate the coupled cis-trans isomerization of three Pro residues using bradykinin (BK), a partially unstructured nonapeptide hormone, as a model system. We use a recently developed enhanced-sampling molecular dynamics method (ω-bias potential replica exchange molecular dynamics; ωBP-REMD) that allows us to exhaustively sample all combinations of Pro isomer states and obtain converged probability densities of all eight state combinations within 885 ns ωBP-REMD simulations. In agreement with experiment, the all-trans state is seen to be the preferred isomer of zwitterionic aqueous BK. In about a third of its structures, this state presents the characteristic C-terminal β-turn conformation; however, other isomer combinations also contribute significantly to the structural ensemble. Unbiased probabilities can be projected onto the peptide bond dihedral angles of the three Pro residues. This unveils the interdependence of the individual Pro isomerization states, i.e., a possible coupling of the different Pro isomers. The cis/trans equilibrium of a Pro residue can change by up to 2.5 kcal·mol-1, depending on the isomerization state of other Pro residues. For example, for Pro7, the simulations indicate that its cis state becomes favored compared to its trans state when Pro2 is switched from the trans state to the cis state. Our findings demonstrate the efficiency of the ωBP-REMD methodology and suggest that the coupling of Pro isomerization states may play an even more decisive role in larger folded proteins subject to more conformational restraints.

Identification of Conformational Variants for Bradykinin Biomarker Peptides from a Biofluid Using a Nanopore and Machine Learning

There is a current need to develop methods for the sensitive detection of peptide biomarkers in complex mixtures of molecules, such as biofluids, to enable early disease detection. Moreover, to our knowledge, there is currently no detection method capable of identifying the different conformations of a peptide biomarker differing by a single amino acid. Single-molecule nanopore sensing promises to provide this level of resolution. In order to be able to identify these differences in a biofluid such as serum, it is necessary to carefully characterize electrical parameters to obtain specific signatures of each biomarker population observed. We are interested here in a family of peptide biomarkers, kinins such as bradykinin and des-Arg9 bradykinin, that are involved in many disabling pathologies (allergy, asthma, angioedema, sepsis, or cancer). We show the proof of concept for direct identification of these biomarkers in serum at the single-molecule level using a protein nanopore. Each peptide exhibits two unique electrical signatures attributed to specific conformations in bulk. The same signatures are found in serum, allowing their discrimination and identification in a complex mixture such as biofluid. To extend the utility of our experimental results, we developed a principal component analysis approach to define the most relevant electrical parameters for their identification. Finally, we used semisupervised classification to assign each event type to a specific biomarker at physiological serum concentration. In the future, single-molecule scale analysis of peptide biomarkers using a powerful nanopore coupled with machine learning will facilitate the identification and quantification of other clinically relevant biomarkers from biofluids.

Isolation, Purification and Structure Identification of a Calcium-Binding Peptide from Sheep Bone Protein Hydrolysate

To isolate a novel peptide with calcium-binding capacity, sheep bone protein was hydrolyzed sequentially using a dual-enzyme system (alcalase treatment following neutrase treatment) and investigated for its characteristics, separation, purification, and structure. The sheep bone protein hydrolysate (SBPH) was enriched in key amino acids such as Gly, Arg, Pro, Leu, Lys, Glu, Val, and Asp. The fluorescence spectra, circular dichroism spectra, and Fourier-transform infrared spectroscopy results showed that adding calcium ions decreased the α-helix and β-sheet content but significantly increased the random and β-turn content (p < 0.05). Carboxyl oxygen and amino nitrogen atoms of SBPH may participate in peptide−calcium binding. Scanning electron microscopy and energy dispersive spectrometry results showed that SBPH had strong calcium-chelating ability and that the peptide−calcium complex (SBPH−Ca) combined with calcium to form a spherical cluster structure. SBPH was separated and purified gradually by ultrafiltration, gel filtration chromatography, and reversed-phase high-performance liquid chromatography. Liquid chromatography-electrospray ionization/mass spectrometry identified the amino acid sequences as GPSGLPGERG (925.46 Da) and GAPGKDGVRG (912.48 Da), with calcium-binding capacities of 89.76 ± 0.19% and 88.26 ± 0.25%, respectively. The results of this study provide a scientific basis for the preparation of a new type of calcium supplement and high-value utilization of sheep bone.

Anti-osteoporosis effect and purification of peptides with high calcium-binding capacity from walnut protein hydrolysates

The walnut protein hydrolysate (WPH) was prepared via simulated gastrointestinal digestion. The degree of hydrolysis (DH), amino acid composition, and relative molecular weight distribution of WPH were analyzed. The results showed that the DH of WPH was 11.6%, WPH was rich in Glu and Pro, and the relative average molecular weight of 572 Da accounted for 59.78%. The effects of WPH on osteoporosis were evaluated using a model of retinoic acid-induced osteoporosis rat. Treatment with WPH effectively increased the serum calcium and phosphorus contents, alleviated calcium loss, and reduced tartrate-resistant acid phosphate and alkaline phosphatase activities and bone gla protein content. WPH treatment significantly improved the biomechanical properties of the bone and increased the value of bone mineral density. In addition, WPH treatment improved the bone microstructure. WPH was isolated and purified by Sephadex G-25 gel filtration chromatography and semi-preparative reversed-phase high-performance liquid chromatography. A fraction with high calcium-binding activity was obtained and 15 peptides were identified.

A novel calcium-binding peptide from Antarctic krill protein hydrolysates and identification of binding sites of calcium-peptide complex

Trypsin was used for preparing peptides with high calcium-binding capacity from Antarctic krill. Hydroxyapatite chromatography (HAC), size-exclusion chromatography (SEC), and reversed phase high performance liquid chromatography (RP-HPLC) were used to capture and purify calcium-binding peptides. The peptide sequence was determined to be VLGYIQIR (N- to C-terminal, MW = 960.58 Da), using LTQ Orbitrap XL. According to the results of FTIR and mass spectrometry, chelating site of calcium ions may possibly involve the carbonal or amino groups of Gln, Ile and Arg residues. Molecular dynamic simulation showed the conformation of peptide was markedly varied, and the distance between calcium ion and Gln and Ile residues was changing all the time. However, the distance between calcium ion and carboxyl oxygen of arginine residues was not changed significantly from 2 ns to 100 ns. Identified peptide can be used as a novel calcium supplement.

Spectroscopic studies of kinetically trapped conformations in the gas phase: the case of triply protonated bradykinin

We explore conformational space of triply protonated bradykinin. Three conformational families are mobility-separated and spectroscopically characterized. Kinetically trapped structures are identified via annealing.

Characterization of adsorption mode of new B2 bradykinin receptor antagonists onto colloidal Ag substrate

In this paper, the surface‐enhanced Raman scattering (SERS) spectra of the potent B2 bradykinin receptor antagonists, [D‐Arg0,Hyp3,Thi5,8,L‐Pip7]BK, Aaa[D‐Arg0,Hyp3,Thi5,8,L‐Pip7]BK, [D‐Arg0,Hyp3,Thi5,D‐Phe7,L‐Pip8]BK, and Aaa[D‐Arg0,Hyp3,Thi5,D‐Phe7,L‐Pip8]BK, were measured when immobilized onto a colloidal assembly of apparently randomly adhering Ag spheres with diameters of approximately 20 – 25 nm. The observed SERS bands corresponding to different vibrational modes of the molecule, attached to or near Ag, and the variations in these bands resulting from competitive interactions of the functional groups of the peptides with the SERS‐active Ag surfaces were analyzed in this study. Briefly, it was shown that Pip, in generally in vertical orientation, and Thi, in the edge‐on position, relative to the colloidal Ag surface interacted with this surface through their lone electron pairs on the nitrogen and sulfur atoms, respectively. The imide bond of the X‐Pro peptide linkage and the guanidine group of Arg were involved in the adsorption process. In addition, it was demonstrated that the specific differences in the amino acid sequences slightly influenced the mode of adsorption. For example, Aaa in Aaa[D‐Arg0,Hyp3,Thi5,8,L‐Pip7]BK and Aaa[D‐Arg0,Hyp3,Thi5,D‐Phe7,L‐Pip8]BK and D‐Phe (vertical with respect to the colloidal Ag surface) in [D‐Arg0,Hyp3,Thi5,D‐Phe7,L‐Pip8]BK, and Aaa[D‐Arg0,Hyp3,Thi5,D‐Phe7,L‐Pip8]BK assisted in the adsorption of these peptides onto the colloidal Ag particles. To discuss these spectral alterations due to the different surface adsorption mechanisms of these peptides, the spectral changes were analyzed according to the adsorption process and Fourier‐transform‐Raman spectra. Copyright © 2013 John Wiley & Sons, Ltd.

B2 bradykinin receptor antagonists: adsorption mechanism on electrochemically roughened Ag substrate

In this paper, the surface‐enhanced Raman scattering (SERS) spectra of the potent B2 bradykinin receptor antagonists, [D‐Arg0,Hyp3,Thi5,8,L‐Pip7]BK, Aaa[D‐Arg0,Hyp3,Thi5,8,L‐Pip7]BK, [D‐Arg0,Hyp3,Thi5,D‐Phe7,L‐Pip8]BK, and Aaa[D‐Arg0,Hyp3,Thi5,D‐Phe7,L‐Pip8]BK, were measured when immobilized onto a highly specific electrochemically roughened SERS‐active Ag substrate characterized by the formation of a 50 – 150 nm Ag islands on its surface. The observed SERS bands corresponding to different vibrational modes of the molecule, attached to or near Ag, and the variations in these bands resulting from competitive interactions of the functional groups of the peptides with the SERS‐active Ag surfaces and reorientation occurring over time of adsorption were analyzed in this study. Copyright © 2012 John Wiley & Sons, Ltd.

Flexibility in substrate recognition by thimet oligopeptidase as revealed by denaturation studies

Thimet oligopeptidase (TOP) is a soluble metalloendopeptidase belonging to a family of enzymes including neurolysin and neprilysin that utilize the HEXXH metal-binding motif. TOP is widely distributed among cell types and is able to cleave a number of structurally unrelated peptides. A recent focus of interest has been on structure-function relationships in substrate selectivity by TOP. The enzyme's structural fold comprises two domains that are linked at the bottom of a deep substrate-binding cleft via several flexible loop structures. In the present study, fluorescence spectroscopy has been used to probe structural changes in TOP induced by the chemical denaturant urea. Fluorescence emission, anisotropy and collisional quenching data support a two-step unfolding process for the enzyme in which complete loss of the tertiary structure occurs in the second step. Complete loss of activity and loss of catalytic Zn(II) from the active site, monitored by absorption changes of the metal chelator 4-(2-pyridylazo)-resorcinol, are also connected with the second step. In contrast, the first unfolding event, which is linked to changes in the non-catalytic domain, leads to a sharp increase in kcat towards a 9-residue substrate and a sharp decrease in kcat for a 5-residue substrate. Thus a conformational change in TOP has been directly correlated with a change in substrate selectivity. These results provide insight into how the enzyme can process the range of structurally unrelated peptides necessary for its many physiological roles.

Interaction and structural study of kinin peptide bradykinin and ganglioside monosialylated 1 micelle

Partitioning of small proteins and peptides from the aqueous to membrane phase is often coupled with folding. In this work we examine the binding and folding of the kinin peptide, bradykinin (BK), in the presence of the ganglioside monosialylated 1 (GM1) micelle. Using two-dimensional NMR techniques, we have shown that at low concentration, GM1 micelle is able to induce a turn conformation to BK. A pulsed-field gradient diffusion NMR study indicated that the peptide partitions into the GM1 micelle with a DeltaG(part) of -3.14 +/- 0.03 kcal/mol. A saturation transfer difference (STD) NMR study indicated that the binding is mostly through hydrophobic residues.

Modulation of agrin function by alternative splicing and Ca2+ binding

The aggregation of acetylcholine receptors on postsynaptic membranes is a key step in neuromuscular junction development. This process depends on alternatively spliced forms of the proteoglycan agrin with "B-inserts" of 8, 11, or 19 residues in the protein's globular C-terminal domain, G3. Structures of the neural B8 and B11 forms of agrin-G3 were determined by X-ray crystallography. The structure of G3-B0, which lacks inserts, was determined by NMR. The agrin-G3 domain adopts a beta jellyroll fold. The B insert site is flanked by four loops on one edge of the beta sandwich. The loops form a surface that corresponds to a versatile interaction interface in the family of structurally related LNS proteins. NMR and X-ray data indicate that this interaction interface is flexible in agrin-G3 and that flexibility is reduced by Ca(2+) binding. The plasticity of the interaction interface could enable different splice forms of agrin to select between multiple binding partners.

Conformational alteration of bradykinin in presence of GM1 micelle

We report here the interaction of bradykinin with ganglioside GM1 by circular dichroism, steady-state fluorescence, and one-dimensional 1H NMR spectroscopy. Circular dichroism spectroscopy is indicative of a turn formation of bradykinin backbone in the presence of GM1 micelle. The fluorescence quenching efficiencies of iodide and acrylamide are substantially reduced, indicating a shielding of phenylalanine residue of bradykinin from aqueous environment. Significant line broadening of NMR resonances of bradykinin, suggestive of motional restriction, is observed.

Conformational basis for the biological activity of TOAC-labeled angiotensin II and bradykinin: Electron paramagnetic resonance, circular dichroism, and fluorescence studies

N-Terminally and internally labeled analogues of the hormones angiotensin (AII, DRVYIHPF) and bradykinin (BK, RPPGFSPFR) were synthesized containing the paramagnetic amino acid 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). TOAC replaced Asp1 (TOAC1-AII) and Val3 (TOAC3-AII) in AII and was inserted prior to Arg1 (TOAC0-BK) and replacing Pro3 (TOAC3-BK) in BK. The peptide conformational properties were examined as a function of trifluoroethanol (TFE) content and pH. Electron paramagnetic resonance spectra were sensitive to both variables and showed that internally labeled analogues yielded rotational correlation times (tauC) considerably larger than N-terminally labeled ones, evincing the greater freedom of motion of the N-terminus. In TFE, tauC increased due to viscosity effects. Calculation of tau(Cpeptide)/tau(CTOAC) ratios indicated that the peptides acquired more folded conformations. Circular dichroism spectra showed that, except for TOAC1-AII in TFE, the N-terminally labeled analogues displayed a conformational behavior similar to that of the parent peptides. In contrast, under all conditions, the TOAC3 derivatives acquired more restricted conformations. Fluorescence spectra of AII and its derivatives were especially sensitive to the ionization of Tyr4. Fluorescence quenching by the nitroxide moiety was much more pronounced for TOAC3-AII. The conformational behavior of the TOAC derivatives bears excellent correlation with their biological activity, since, while the N-terminally labeled peptides were partially active, their internally labeled counterparts were inactive [Nakaie, C. R., et al., Peptides 2002, 23, 65-70]. The data demonstrate that insertion of TOAC in the middle of the peptide chain induces conformational restrictions that lead to loss of backbone flexibility, not allowing the peptides to acquire their receptor-bound conformation.

Is the C-terminal Region of Bradykinin the Binding Site of Polyphenols?

Bradykinin is a bioactive hormone involved in a variety of physiological processes. In various solvents, this peptide adopts beta-turn structures. The C-terminal turn is a structural feature for the receptor affinity of agonists and antagonists while the N-terminal turn might be important for antagonistic activities. Polyphenols like dimeric proanthocyanidin B3 interact with the peptide. Thus to investigate the effects of polyphenols on bradykinin activity and structure, we studied the interaction in the structuring solvent DMSO which can be a close mimic of aqueous physiological environments like receptor-binding sites. Bradykinin alone presented a folded structure with two turns. B3 interacted with the peptide C-terminus and involved the loss of the bend structure of this region, while the N-terminus turn was maintained. Numerous studies have shown that polyphenolic molecules can act upon various biological targets, and the formation of this type of complex might be one of the possible modes of action.

Structure-activity relationships of trout bradykinin ([Arg(0),Trp(5),Leu(8)]-bradykinin)

Trout bradykinin ([Arg(0),Trp(5),Leu(8)]-BK) produces sustained and concentration-dependent contractions of isolated longitudinal smooth muscle from trout stomach, although mammalian BK is without effect. Circular dichroism studies have demonstrated that trout BK, unlike mammalian BK, does not adopt a stable beta-turn conformation, even in the presence of sodium dodecyl sulfate (SDS) or trifluoroethanol. The myotropic actions of a series of analogs in which each amino acid in trout BK was replaced by either alanine or the corresponding D-isomer were investigated. The peptides with Ala(4), D-Pro(3), D-Trp(5), D-Ser(6), and D-Pro(7) substitutions were inactive and did not act as antagonists of trout BK. The analog with [Ala(5)] was a weak partial agonist. The substitution (Arg(0) --> Ala) led to >50-fold decrease in potency but, in contrast to the importance of Phe(8) in both BK and desArg(9)-BK in activating the mammalian B(2) and B(1) receptors respectively, substitutions at Leu(8) in trout BK had only a minor effect on potency. Antagonists to the mammalian B(2) receptor generally contain a D-aromatic amino acid at position 7 of BK but the analog [Arg(0),Trp(5),D-Phe(7),Leu(8)]-BK was a weak agonist at the trout receptor. Similarly, the potent nonpeptide mammalian B(2) receptor antagonist FR173657 was without effect on the action of trout BK. These data suggest the hypothesis that the receptor binding conformation of trout BK is defined by the central region (residues 3-7) of the peptide but is adopted only upon interaction with the receptor. The bioactive conformation is probably stabilized by an ionic interaction between Arg(0) in the peptide and an acidic residue in the receptor.

End-to-end distance distribution in bradykinin observed by Förster resonance energy transfer

Förster resonance energy transfer (FRET) was used to study the conformational dynamics of bradykinin related peptides. The fluorescent probe aminobenzoic acid (Abz) bound to the amino terminal of bradykinin maintained its fluorescence characteristics, like high quantum yield and excited state decay dominated by a lifetime of 8.3 ns. The binding of the acceptor group N-[2, 4-dinitrophenyl]-ethylenediamine (EDDnp) to the carboxy terminal of Abz labeled bradykinin resulted in a drastic decrease of the fluorescence intensity and in a fastening of the excited state decay. The change of the decay kinetics to an heterogeneous process, precludes the use of energy transfer models based on a single fixed distance between donor and acceptor. The computational package CONTIN was employed to the analysis of time-resolved fluorescence data, allowing the recovery of a distance distribution between donor and acceptor corresponding to the end-to-end distance of the labeled peptide. The distance distribution reflects the occurrence of distinct conformations for the peptide, that coexist in equilibrium during the fluorescence lifetime. We observed three distance populations for bradykinin in water, that merged to two populations when the solvent was trifluoroethanol (TFE). The results were consistent with those obtained from circular dichroism spectroscopy, that showed structural flexibility in water and the presence of more defined secondary structure in TFE. We also studied several peptides related to bradykinin, and the results emphasized the formation of turns involving the proline residues and the decrease of conformational flexibility induced by using TFE as the solvent.