Peptides In Aqueous Solution Research Articles

Infrared study of trifluoroacetic acid unpurified synthetic peptides in aqueous solution: Trifluoroacetic acid removal and band assignment

Synthetic peptide or protein samples are mostly unpurified with trifluoroacetic acid (TFA) used during the synthesis procedure, which strongly interferes with structure determination by infrared (IR) spectroscopy. The aim of this work was to propose a simple strategy to remove TFA contribution from attenuated total reflection (ATR)–IR spectra of the hexahistidine peptide (His6) in aqueous solution to study the conformation of this synthetic peptide without previous purification. Such a strategy is based on the subtraction mode widely employed to remove water contribution, and it is tested with TFA unpurified histidine as a model system. The subtraction is based on eliminating the strong TFA bands at 1147 and 1200 cm −1 by applying a scaling factor (as in buffer correction). The proposed modes represent excellent strategies that do not modify spectral features, and they provide reliable routines to obtain the synthetic peptide spectrum without TFA contribution. The conformational information from the corrected spectra at different pH values is deduced from semiempirical calculated IR spectra of different His6 conformers. The spectral features and the band positions of the corrected spectrum suggest that the peptide molecules mainly adopt an intermolecular β-sheet structure.

Unprecedented Molecular Architectures by the Controlled Self‐Assembly of a β‐Peptide Foldamer

Fighting against windmills: Highly homogeneous, well-defined, and finite “windmill”- and square-rod-shaped supramolecular architectures were formed by the self-assembly of a short helical β peptide in aqueous solution (see picture). The reproducible formation of the unprecedented 3D shapes could be controlled by the use of a surfactant of different concentrations. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Micelle-Like Architecture of the Monomer Ensemble of Alzheimer’s Amyloid-β Peptide in Aqueous Solution and Its Implications for Aβ Aggregation

Aggregation of amyloid-β (Aβ) peptide, a 39- to 43-residue fragment of the amyloid precursor protein, is associated with Alzheimer's disease, the most common form of dementia in the elderly population. Several experimental studies have tried to characterize the atomic details of amyloid fibrils, which are the final product of Aβ aggregation. Much less is known about species forming during the early stages of aggregation, in particular about the monomeric state of the Aβ peptide that may be viewed as the product of the very first step in the hypothesized amyloid cascade. Here, the equilibrium ensembles of monomeric Aβ alloforms Aβ1–40 and Aβ1–42 are investigated by Monte Carlo simulations using an atomistic force field and implicit solvent model that have been shown previously to correctly reproduce the ensemble properties of other intrinsically disordered polypeptides.Our simulation results indicate that at physiological temperatures, both alloforms of Aβ assume a largely collapsed globular structure. Conformations feature a fluid hydrophobic core formed, on average, by contacts both within and between the two segments comprising residues 12–21 and 24–40/42, respectively. Furthermore, the 11 N-terminal residues are completely unstructured, and all charged side chains, in particular those of Glu22 and Asp23, remain exposed to solvent. Taken together, these observations indicate a micelle-like††The terms “micelle-like architecture” and “micelle-like” used throughout this article refer to the average conformation of an individual polypeptide chain and do not imply the assembly of several molecules, unless otherwise noted. architecture at the monomer level whose implications for oligomerization, as well as fibril formation and elongation, are discussed. We establish quantitatively the intrinsic disorder of Aβ and find the propensity to form regular secondary structure to be low but sequence specific. In the presence of a global and unspecific bias for backbone conformations to populate the β-basin, the β-sheet propensity along the sequence is consistent with the arrangement of the monomer within the fibril, as derived from solid-state NMR data. These observations indicate that the primary sequence partially encodes fibril structure, but that fibril elongation must be thought of as a templated assembly step.

Polarization at metal–biomolecular interfaces in solution

Metal surfaces in contact with water, surfactants and biopolymers experience attractive polarization owing to induced charges. This fundamental physical interaction complements stronger epitaxial and covalent surface interactions and remains difficult to measure experimentally. We present a first step to quantify polarization on even gold (Au) surfaces in contact with water and with aqueous solutions of peptides of different charge state (A3 and Flg-Na3) by molecular dynamics simulation in all-atomic resolution and a posteriori computation of the image potential. Attractive polarization scales with the magnitude of atomic charges and with the length of multi-poles in the aqueous phase such as the distance between cationic and anionic groups. The polarization energy per surface area is similar on aqueous Au {1 1 1} and Au {1 0 0} interfaces of approximately -50 mJ m(-2) and decreases to -70 mJ m(-2) in the presence of charged peptides. In molecular terms, the polarization energy corresponds to -2.3 and -0.1 kJ mol(-1) for water in the first and second molecular layers on the metal surface, and to between -40 and 0 kJ mol(-1) for individual amino acids in the peptides depending on the charge state, multi-pole length and proximity to the surface. The net contribution of polarization to peptide adsorption on the metal surface is determined by the balance between polarization by the peptide and loss of polarization by replaced surface-bound water. On metal surfaces with significant epitaxial attraction of peptides such as Au {1 1 1}, polarization contributes only 10-20% to total adsorption related to similar polarity of water and of amino acids. On metal surfaces with weak epitaxial attraction of peptides such as Au {1 0 0}, polarization is a major contribution to adsorption, especially for charged peptides (-80 kJ mol(-1) for peptide Flg-Na(3)). A remaining water interlayer between the metal surface and the peptide then reduces losses in polarization energy by replaced surface-bound water. Computed polarization energies are sensitive to the precise location of the image plane (within tenths of Angstroms near the jellium edge). The computational method can be extended to complex nanometre and micrometer-size surface topologies.

Exploring the Surface Charge on Peptide−Gold Nanoparticle Conjugates by Force Spectroscopy

The conformation and charge exposure of peptides attached to colloidal gold nanoparticles (AuNPs) are critical for both the colloidal stability and for the recognition of biological targets in biomedical applications such as diagnostics and therapy. We prepared conjugates of AuNPs and three isomer peptides capable of recognizing toxic aggregates of the amyloid beta protein (Abeta) involved in Alzheimer's disease, namely, CLPFFD-CONH(2) (i0), CDLPFF-CONH(2) (i1), and CLPDFF-CONH(2) (i2), where D is the amino acid aspartic acid that is negatively charged at pH = 7.4. We then studied the effect of peptide sequence on the charge exposure through force spectroscopy measurements. The peptide-AuNPs conjugates were fixed on glass surfaces, and their interactions with peptide-functionalized tips were determined. Our results show a higher density of surface charge in the conjugates of the isomers i0 and i2 and a lower density in i1, which is due to the higher degree of functionalization in the first two compared with the third. However, the charge per molecule of the peptide is higher for i1 with respect to i0 and i2, which could be related to the local conformation that the peptides adopt on the surface. The acid-base behavior of the peptide anchored to the AuNPs is different than expected in aqueous solutions of free peptides, which could be related to the low accessibility of the NH(2)-terminal group belonging to the cysteine that is located near the AuNPs surface. In contrast with other techniques, the fixation of the peptide-AuNPs conjugates to a surface allows for characterization of the local charge exposure of peptides anchored to AuNPs over a wide range of pH.

Effect of Temperature on the Interactions of Glycyl Dipeptides with Sodium Dodecyl Sulfate in Aqueous Solution: A Volumetric, Conductometric, and Fluorescence Probe Study

The interactions of glycyl dipeptides (2-[(2-aminoacetyl)amino]acetic acid (commonly known as glycylglycine), 2-[(2-aminoacetyl)amino]-3-methylbutanoic acid (commonly known as glycyl-l-valine), and (2S)-2-[(2-aminoacetyl)amino]-4-methylpentanoic acid (commonly known as glycyl-l-leucine)) with sodium dodecyl sulfate (SDS) as a function of temperature in aqueous solution have been investigated by a combination of density, conductivity, and fluorescence methods. The standard partial molar volume (V2,ϕo), standard partial molar volumes of transfer for dipeptide from water to aqueous SDS solutions (ΔtVo), partial molar expansibility (Eϕo), and Hepler’s constant have been calculated from density data. Electrical conductivity was used to estimate the critical micellar concentration (cmc) and the thermodynamic parameters of micellization of SDS in aqueous peptide solutions. The change of micropolarity produced by the interaction was monitored by the measurement of emission intensity ratio between the first and th...

A Comparative Study of Two Different Force Fields on Structural and Thermodynamics Character of H1 Peptide via Molecular Dynamics Simulations

The dynamics and thermodynamics character of H1 peptide in aqueous solution has been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations using two different force fields (OPLS-AA and GROMOS 43A1). The two independent T-REMD simulations were completed starting from initial conformations a-helix and β-sheet, respectively. Each replica was run for 300 ns. The performance of each force field was assessed from the parameters such as the distributions of backbone dihedral angles, the number of native hydrogen bond, root mean square deviations (RMSD) of Ca atoms and all heavy atoms, formation of β-turn, the stability of folded β-hairpin structure and the favorite conformations of different force fields. The simulation using GROMOS 43A1 force field starting from a-helix structure sampled the conformation cluster which Ca RMSD was 0.05 nm from β-sheet structure and the cluster contains 39% of all conformations. The simulation using OPLS-AA force field produced more sampling in PII region than in GROMOS 43A1 force field. The both force field simulations produced some sampling in the a region, but the probabilities of the conformations including any helical content were only 1–2%. Under the both force fields, the β-turn structures exhibited higher stability than a-helix structures and the folded β-hairpin structures. In the GROMOS 43A1 force field, the free energy change from the unfolded state to the hairpin state was in good agreement with the results of several experiments about some β-peptides (not the H1 peptide) and the other molecular dynamics simulations of H1 peptide. However, the folded β-hairpin structure was more destabilized in the OPLS-AA force field than in the GROMOS 43A1 force field and experiments.

Helix-Hairpin Transitions of a Designed Peptide Studied by a Generalized-Ensemble Simulation

It was recently reported that the designed peptide, whose sequence is INYWLAHAKAGYIVHWTA, has both of the two structures, α-helix and β-hairpin, in aqueous solution. However, the detailed transformation between these two structures is still unclear. In order to study this transformation, we applied a generalized-ensemble simulation to the designed peptide in aqueous solution and deduced the pathways of the designed peptide between α-helix structures and β-hairpin structures.

Structure and water dynamics of aqueous peptide solutions in the presence of co-solvents

We perform neutron diffraction and quasi-elastic neutron scattering (QENS) to probe hydration water structure, and dynamics down to supercooled temperatures, of a concentrated amphiphilic peptide system with the co-solvents glycerol and dimethyl sulfoxide. We find that the kosmotropic co-solvent glycerol preserves the hydration structure near the peptide that is observed in the water solvent alone, that in turn preserves the dynamical temperature trends of two water relaxation processes--one corresponding to a localized relaxation process of the peptide bound surface water and a second relaxation process of the outer hydration layers. By contrast the chaotropic co-solvent, by disrupting the hydration layer near the peptide surface, eliminates the inner hydration layer relaxation process induced by the peptide, to show a single time scale for translational water dynamics.

Cross‐Reactive Sensor Arrays for the Detection of Peptides in Aqueous Solution by Fluorescence Spectroscopy

A simple but powerful method for the sensing of peptides in aqueous solution has been developed. The transition-metal complexes [PdCl(2)(en)], [{RhCl(2)Cp*}(2)], and [{RuCl(2)(p-cymene)}(2)] were combined with six different fluorescent dyes to build a cross-reactive sensor array. The fluorescence response of the individual sensor units was based on competitive complexation reactions between the peptide analytes and the fluorescent dyes. The collective response of the sensor array in a time-resolved fashion was used as an input for multivariate analyses. A sensor array comprised of only six metal-dye combinations was able to differentiate ten different dipeptides in buffered aqueous solution at a concentration of 50 muM. Furthermore, the cross-reactive sensor could be used to obtain information about the identity and the quantity of the pharmacologically interesting dipeptides carnosine and homocarnosine in a complex biological matrix, such as deproteinized human blood serum. The sensor array was also able to sense longer peptides, which was demonstrated by differentiating mixtures of the nonapeptide bradykinin and the decapeptide kallidin.

Molecular dynamics simulations of N-methylacetamide (NMA) in water by the ABEEM/MM model

The N-methylacetamide (NMA) is a very interesting kind of compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of peptides in aqueous solutions. We have carried out molecular dynamics (MD) simulations of a NMA molecule in water under 1 atm and 298 K. The simulations make use of the newly developed NMA–water fluctuating charge ABEEM/MM potential model ( Yang, Z. Z.; Qian, P. J. Chem. Phys. 2006, 125, 064311 ), which is based on the combination of the atom-bond electronegativity equalization method (ABEEM) and molecular mechanics (MM). This model has been successfully applied to NMA–water gas clusters, NMA(H2O)n (n = 1–6), and accurately reproduced many static properties. For the NMA–water ABEEM/MM potential model, two characters must be emphasized in the simulations. Firstly, the model allows the charges in system to fluctuate, responding to the ambient environment. Secondly, for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters klpO=,H and klpO–,HN–, respectively, which explicitly describe the short-range interaction of hydrogen bonds in the hydrogen bond interaction region. All sorts of properties have been studied in detail, such as, radial distribution function, energy distribution, ABEEM charge distribution and dipole moment, and so on. These simulation results show that the ABEEM/MM-based NMA–water potential model appears to be robust, giving the solution properties in excellent agreement with other dynamics simulations on similar systems.

Concentration and in Situ Detection of Peptides Using Liquid Matrix-Assisted Laser Desorption Ionization Matrixes

A ternary component system composed of alpha-cyano-4-hydroxycinnamic acid/3-aminoquinoline/quinoline (CHCA/3-AQ/Q; at a weight ratio of 1:4:4) was used as an extraction solvent as well as a liquid matrix for matrix-assisted laser desorption ionization (MALDI) mass spectrometry analysis. Peptides in aqueous solutions were extracted, concentrated, and prepared for MALDI analysis in one step. Extracting peptides in aqueous solutions was analogous to dispersive liquid-liquid microextraction and completed in less than 2 min because CHCA/3-AQ/Q was dispersed rapidly into the aqueous phase by ultrasonication during extraction. The detection limit for peptides in aqueous solutions was as low as 1.25 nM for angiotensin I. Protein digests obtained from conventional MALDI analysis and the proposed method were compared with respect to sequence coverage. The new approach was applied to sample cleanup, preconcentration, and in situ analysis of protein digests in signal suppressing agents such as Tris buffer and urea.

Chaperon-Mediated Single Molecular Approach Toward Modulating Aβ Peptide Aggregation

We report here a single molecular approach using chaperone-like molecular modulators for modulating the aggregation behavior of a vital analogue of beta-amyloid peptide (Abeta) by using scanning tunneling microscopy. The molecular structures of the beta-sheets for Abeta33-42 peptide are revealed, which are keen to the aggregation of Abeta42 relating to Alzheimer's disease. It was identified that the introduction of chaperone-like modulators could regulate the assembling behavior of the peptide at molecular level. Furthermore, the modulators could also significantly accelerate the aggregation of the peptide in aqueous solution as revealed by light scattering studies. These observations of the molecular modulator effect in peptide assemblies could provide a novel approach toward modulating Abeta peptide aggregations.

Quantum Mechanical and NMR Studies of Ring Puckering and cis/trans-Rotameric Interconversion in Prolines and Hydroxyprolines

Nuclear magnetic resonance (NMR) and quantum mechanical (QM) studies have been carried out for proline (Pro) containing peptides: N-acetyl-l-proline (AcProOH) and N-acetyl-4-hydroxy-l-proline (AcHypOH). Preliminary results of variable temperature NMR measurements for Gly-Pro-Gly-Gly (GPGG), Val-Ala-Pro-Gly (VAPG), and Ala-Pro-Gly-Trp amide acetate salt (APGW) are also reported. The effect of solvent (D(2)O, DMSO-d(6) and CD(3)CN) on the pyrrolidine ring conformation and cis/trans-rotamerisation along the amide bond preceding Pro was investigated by temperature dependent NMR followed by detailed transition state (TS) searches for both conformational equilibria using QM methods. The results revealed the energetic characteristics of the TS, which were in satisfactory agreement with NMR, and the corresponding TS geometries, which are not available from experiment. The most remarkable feature of the cis/trans-rotamerisation is that the amide nitrogen in AcProOH and AcHypOH adopts a tetrahedral geometry in the TS. Various HF, DFT, and MP2 calculations together with implicit solvation modeling were employed in order to identify the most suitable QM protocols for reliable predictions of the geometry and the relative energies of the conformations of Pro and Hyp containing peptides in aqueous solution. Solution NMR results were used for the verification of the reliability of the QM predictions. The results indicate that the MP2 calculations combined with implicit solvation models are reasonably accurate in reproducing NMR measured populations of four different conformations of either AcProOH or AcHypOH in different solvents, whereas HF and DFT B3LYP calculations were significantly less accurate.

Effect of trehalose on amyloid β (29–40)-membrane interaction

A growing body of experimental evidence indicates that the interaction between amyloid beta peptide and lipid bilayer membranes plays an important role in the development of Alzheimer disease. Recent experimental evidence also suggests that trehalose, a simple disaccharide, reduces the toxicity of amyloid beta peptide. Molecular simulations are used to examine the effect of trehalose on the conformational stability of amyloid beta peptide in aqueous solution and its effect on the interaction between amyloid beta peptide and a model phospholipid bilayer membrane. It is found that, in aqueous solution, the peptide exhibits a random coil conformation but, in the presence of trehalose, it adopts an alpha helical conformation. It is then shown that the insertion of amyloid beta peptide into a membrane is more favorable when the peptide is folded into an alpha-helix than in a random coil conformation, thereby suggesting that trehalose promotes the insertion of alpha-helical amyloid beta into biological membranes.

Photo-CIDNP Study of Transient Radicals of Met-Gly and Gly-Met Peptides in Aqueous Solution at Variable pH

Time-resolved chemically induced dynamic nuclear polarization (CIDNP) was applied to the investigation of the photo-oxidation of two sulfur containing peptides, glycylmethionine (Gly-Met) and methionylglycine (Met-Gly). It was established that the reaction of Gly-Met with a photosensitizer, triplet 4-carboxybenzophenone, occurs via electron transfer from the sulfur atom and also from the terminal amino group in its uncharged state. The latter process leads to the formation of nuclear polarization of the alpha-protons of the glycine residue. The sulfur-centered cation radical of Gly-Met formed as a result of triplet quenching participates in the degenerate electron exchange reaction with the parent molecule. The rate constant of this reaction obtained from a simulation of the CIDNP kinetics is 2x10(8) M(-1) s(-1). Two channels of triplet quenching were also found for the Met-Gly peptide at pH values above the pKa of the terminal amino group: electron transfer from the amino group and from the sulfur atom. On the basis of the analysis of the CIDNP spectra and kinetics, it was found that at pH below pKa of the terminal amino group photo-oxidation of Met-Gly leads to the formation of an open-chain S-centered cation radical, which releases a proton from its N-terminal amino group to form a five-membered cyclic radical structure with a three electron bond between the S and N atoms. The rate constant of deprotonation obtained to be 1.8x10(5) s(-1) is in agreement with the pKa=4.7 of the S-centered radical of Met-Gly determined from the pH dependence of nuclear polarization. At pH>pKa, the aminium radicals formed in both peptides as a result of electron transfer from the lone pair of N-terminal amino group undergo deprotonation to the neutral aminyl radical on the submicrosecond time scale. The involvement of the different radicals was confirmed by the dependence of CIDNP on the external magnetic field ranging from 0.1 T to 7 T.

Aggregation of Amyloidogenic Peptides near Hydrophobic and Hydrophilic Surfaces

The general effect of surface hydrophobicity/hydrophilicity on the aggregation of peptides is studied by simulations of oversaturated aqueous solutions of hydrophobic and hydrophilic amyloidogenic peptides. Peptide aggregation was studied in bulk solution, in solutions confined between hydrophobic boundaries (smooth planar paraffin-like surfaces and liquid-vapor interfaces) and in solutions confined between hydrophilic surfaces (smooth planar silica-like surfaces). Aggregation of hydrophobic peptides strongly enhances due to the confinement between hydrophobic surfaces with all peptides adsorbed at the boundaries and aligned predominantly parallel to them. In the other three cases considered, the peptides are repelled from the walls and do not reveal orientational ordering with respect to the surface. The degree of peptide aggregation in these cases is only slightly affected by the confinement (it is enhanced for hydrophobic peptides and decreased for hydrophilic peptides). Our results show that even a single environmental factor such as water-mediated peptide-surface interaction has a drastic effect on the degree and character of peptide aggregation. A wide diversity of possible scenarios can be expected when specific peptide-surface interactions are additionally taken into account.

Classical Simulation of Quantum Energy Flow in Biomolecules

Based on a comparison of classical and quantum-mechanical perturbation theory, the validity of classical nonequilibrium molecular dynamics simulations to describe vibrational energy redistribution in biomolecules is studied. Adopting a small model peptide in aqueous solution as an example, the theory correctly predicts quantum correction factors that need to be applied to the results of classical simulations in order to match the correct quantum results.

Modeling of Aqueous Biomolecules Using a New Free-Volume Group Contribution Model

In this article, a new group contribution model is suggested for obtaining the thermodynamic properties of biomolecules in aqueous solutions. Accordingly, a Freed-FV model has been applied for the combinatorial free-volume term. The activity coefficients, solubilities, densities, and vapor pressures of amino acids and simple peptides in aqueous solutions were correlated, using the proposed group contribution model. Group interaction parameters of the proposed model were obtained by use of experimental data from amino acids available in the literature. The results demonstrate that the group contribution model can accurately correlate activity coefficient, solubility, density, and vapor pressure data for aqueous amino acid and peptide solutions. Furthermore, the osmotic pressures of aqueous solutions containing lysozyme and ammonium sulfate were calculated at ionic strengths of 1 and 3 M and pH values of 4, 6, and 8. The results obtained from the suggested model were compared with those obtained from the virial osmotic model. Also, the model was coupled with the Debye−Hückel model to correlate partition coefficients of biomolecules in polymer−salt aqueous two-phase systems. The results showed that the new group contribution model can accurately correlate partition coefficients of biomolecules in polymer−salt aqueous two-phase systems.

Total chemical synthesis of proteins

This tutorial review outlines the modern ligation methods that enable the efficient total chemical synthesis of enzymes and other protein molecules. Key to this success is the chemoselective reaction of unprotected synthetic peptides ('chemical ligation'). Notably, native chemical ligation enables the reaction of two unprotected peptides in aqueous solution at neutral pH to form a single product in near quantitative yield. Full-length synthetic polypeptides are folded to form the defined tertiary structure of the target protein molecule, which is characterized by mass spectrometry, NMR, and X-ray crystallography, in addition to biochemical and/or biological activity.