Peptides In Aqueous Solution Research Articles

Proline Isomerization of Histone H3 Regulates Lysine Methylation and Gene Expression

The cis-trans isomerization of proline serves as a regulatory switch in signaling pathways. We identify the proline isomerase Fpr4, a member of the FK506 binding protein family in Saccharomyces cerevisiae, as an enzyme which binds the amino-terminal tail of histones H3 and H4 and catalyses the isomerization of H3 proline P30 and P38 in vitro. We show that P38 is necessary for methylation of K36 and that isomerization by Fpr4 inhibits the ability of Set2 to methylate H3 K36 in vitro. These results suggest that the conformational state of P38, controlled by Fpr4, is important for methylation of H3K36 by Set2. Consistent with such an antagonistic role, abrogation of Fpr4 catalytic activity in vivo results in increased levels of H3K36 methylation and delayed transcriptional induction kinetics of specific genes in yeast. These results identify proline isomerization as a novel noncovalent histone modification that regulates transcription and provides evidence for crosstalk between histone lysine methylation and proline isomerization.

A study of N-methylacetamide in water clusters: Based on atom-bond electronegativity equalization method fused into molecular mechanics

N-methylacetamide (NMA) is a very interesting 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 the peptides in aqueous solutions. Here we present NMA-water potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) that is to take ABEEM charges of all atoms, bonds, and lone-pair electrons of NMA and water molecules into the electrostatic interaction term in molecular mechanics. The model has the following characters: (1)it allows the charges in system to fluctuate responding to the ambient environment; (2) 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 k(lpO=, H) and k(lpO(-), HN(-)), respectively. The newly constructed potential model based on ABEEM/MM is first applied to amide-water clusters and reproduces gas-phase state properties of NMA(H(2)O)(n) (n=1-3) including optimal structures, dipole moments, ABEEM charge distributions, energy difference of the isolated trans- and cis-NMA, interaction energies, hydrogen bonding cooperative effects, and so on, whose results show the good agreement with those measured by available experiments and calculated by ab initio methods. In order to further test the reasonableness of this model and the correctness and transferability of the parameters, many static properties of the larger NMA-water complexes NMA(H(2)O)(n) (n=4-6) are also studied including optimal structures and interaction energies. The results also show fair consistency with those of our quantum chemistry calculations.

Contrast variation SANS for the solution structure of the β-amyloid peptide 1–40 influenced by SDS surfactants

Using small-angle neutron scattering (SANS), we have studied the suppression of fibril formation of β-amyloid peptide (A β ), a 1–40 amino acid peptide fragment derived from proteolytic cleavage of a large amyloid precursor protein, by an ionic surfactant, SDS. In comparison with the pure peptide in aqueous solutions which forms long and thin fibrils, A β forms smaller complex with SDS, which hinders partially the growth of long fibrils. With a selected deuteration of SDS for a contrast variation in SANS, we have extracted the structural information of the SDS/peptide complex, including a short rod-like shape, size, and an association ratio between SDS and the peptide.

Condensation of amino acids to form peptides in aqueous solution induced by the oxidation of sulfur(iv): An oxidative model for prebiotic peptide formation

Condensation of amino acids to peptides is an important step during the origin of life. However, up to now, successful explanations for plausible prebiotic peptide formation pathways have been limited. Here we report that the oxidation of sulfur (IV) can induce the condensation reaction of carboxylic acids and amines to form amides, and the condensation reaction of amino acids to form peptides. This might be a general reaction contributing to prebiotic peptide formation.

Raman optical activity of the hinge peptide

We report results of Raman optical activity investigation of the hinge peptide (a parallel dimer of the octapeptide H-Thr-Cys-Pro-Pro-Cys-Pro-Ala-Pro-OH with two disulphide bonds) derived from the sequence of human IgG1, its single thread model (a linear octapeptide H-Thr-Met-Pro-Pro-Met-Pro-Ala-Pro-OH), S–S bridged tetrapeptide (H-Gly-Cys-OH) 2 and poly- l-proline. The ROA spectra confirm PPII as a prevailing conformation of the double thread hinge peptide in aqueous solution while for its single thread Met analog PPII conformation as the only conformation. Diagnostic positive ROA band at 1320 cm −1 remains present even in proline-rich peptides and can serve as reliable PPII marker. Significant positive ROA signal related to C–S stretching vibration has been found but a clear ROA signature of S–S stretching mode still remains uncertain.

Isentropic and isothermal compressibilities of the backbone glycyl group of proteins in aqueous solution

The partial molar isentropic compressibilities at infinite dilution, K S,2 o, have been determined for the peptides serylglycine, serylglycylglycine and serylglycylglycylglycine in aqueous solution at 25 °C. The partial molar volumes at infinite dilution, V 2 o, have also been determined for these peptides in aqueous solution at the temperatures 15, 30 and 40 °C. These results, along with those obtained previously at 25 °C, were used to derive the partial molar exansibilities, E 2 o, of the peptides at 25 °C, which in turn were used to convert the isentropic compressibilities into the partial molar isothermal compressibilities at infinite dilution, K T,2 o. These K S,2 o and K T,2 o results were used to obtain the partial molar compressibilities of the glycyl group CH 2CONH at 25 °C. The results are compared with those obtained using data for other series of peptides of sequence ala(gly) n , n = 1–4, and (gly) n , n = 2–5.

Phase Behavior of Amino Acids and Peptides in Aqueous Solutions Using the Modified Wilson Model

Phase Behavior of Amino Acids and Peptides in Aqueous Solutions Using the Modified Wilson Model

Correlation of phase equilibria of amino acids and peptides in aqueous solution based on the perturbation theory of equation of state

In this paper, the activity coefficients of amino acids and simple peptides in aqueous solutions were correlated by using a three parameters model based on the perturbation theory. The adjustable parameters of this model were obtained from the experimental data and a relation for calculating the activity coefficient is derived. The calculated activity coefficients of amino acids and simple peptides obtained show that the equation of state based on the perturbation model can be used to correlate the activity coefficients of amino acids more accurately than the other models. A correlation for the solubility of amino acids in aqueous solutions is also derived. The results show that this correlation can accurately correlate the solubility of amino acids in aqueous solution over a wide range of temperatures (0–100 °C).

Probing the importance of lateral hydrophobic association in self-assembling peptide hydrogelators

A class of peptides has been designed whose ability to self-assemble into hydrogel is dependent on their conformationally folded state. Under unfolding conditions aqueous peptide solutions are freely flowing having the viscosity of water. When folding is triggered by external stimuli, peptides adopt a beta-hairpin conformation that self-assembles into a highly crosslinked network of fibrils affording mechanically rigid hydrogels. MAX 1, a 20 residue, amphiphilic hairpin self-assembles via a mechanism which entails both lateral and facial self-assembly events to form a network of fibrils whose local structure consists of a bilayer of hairpins hydrogen bonded in the direction of fibril growth. Lateral self-assembly along the long axis of the fibril is mainly facilitated by intermolecular hydrogen bonding between the strands of distinct hairpins and the formation of hydrophobic contacts between residue side chains of laterally associating hairpins. Facial assembly is driven by the hydrophobic collapse of the valine-rich faces of the amphiphilic hairpins affording a bilayer laminate. The importance of forming lateral hydrophobic contacts during hairpin self-assembly and the relative contribution these interactions have towards nano-scale morphology and material rigidity is probed via the study of: MAX1, a hairpin designed to exploit lateral hydrophobic interactions; MAX 4, a peptide with reduced ability to form these interactions; and MAX5, a control peptide. CD spectroscopy and rheological experiments suggest that the formation of lateral hydrophobic interactions aids the kinetics of assembly and contributes to the mechanical rigidity of the hydrogel. Transmission electron microscopy (TEM) shows that these interactions play an essential role in the self-assembly process leading to distinct nano-scale morphologies.

Interfacing liquid chromatography with atmospheric pressure MALDI-MS

Two different strategies for coupling liquid chromatography with atmospheric pressure matrix assisted laser desorption/ionization (AP MALDI) are presented. The first method is flow-injection liquid AP UV-MALDI. Compared with previous similar research, the detection limit was improved 10 times to 8.3 fmol using a solution of 50 nM peptide with 25 mM alpha-cyano-4-hydroxycinnamic acid. The applicability of this method to measure oligosaccharides, actinomycin antibiotics, antibiotics, phosphopeptides, and proteins is demonstrated. The upper mass limit achieved with the current instrumentation is 6,500 Da (doubly charged cytochrome c). The feasibility of a second strategy based on single-droplet IR AP MALDI is demonstrated here. Aqueous peptide solutions were successfully measured by this method.

Peptides analysis in blood plasma using on-line system of supported liquid membrane and high-performance liquid chromatography

The potential of using supported liquid membrane (SLM) technique, combined with reversed-phase high-performance liquid chromatography (RP-HPLC) has been investigated for the determination of peptides in human blood plasma. The peptides studied were DLLeu DLPhe, MetLeuPhe, GlyLeuTyr and ValGluProIleProTyr. The carrier (Aliquat 336) was incorporated in membrane phase in order to facilitate the transport of investigated peptides. After extraction, the analyte-enriched acceptor phase was directly injected into an HPLC system for analysis. With SLM, high selectivity and efficiency were achieved for extraction of peptides in aqueous solutions. Lower extraction efficiency was obtained in plasma sample. The limiting factors were the presence of salts and proteins in blood plasma. The necessary of ultrafiltration application before the SLM was required in order to improve its stability. The minimum quantifiable concentration was 90–130 ng/ml of the investigated peptides based on 0.5 ml plasma. The standard curve was linear over the concentration range of 0.05–10 μg/ml.

A structural study of model peptides derived from HIV‐1 integrase central domain

The HIV-1 integrase (IN) catalyzes the integration of viral DNA in the human genome. In vitro the enzyme displays an equilibrium of monomers, dimers, tetramers and larger oligomers. However, its functional oligomeric form in vivo is not known. We report a study of the auto-associative properties of three peptides denoted K156, E156 and E159. These derive from the alpha4 helix of the IN catalytic core. The alpha4 helix is an amphipatic helix exposed at the surface of the protein and could be involved in the oligomerization process through its hydrophobic face. The peptides were obtained from the replacement of several amino acid residues by more helicogenic ones in the alpha4 helix peptide. K156 carries the basic residues Lys156 and Lys159, which have been shown important for the binding of IN to viral DNA. In E156 and E159 they are replaced with the acidic residue Glu. A fourth peptide K(E)156 obtained from the replacement of hydrophobic residues with Glu in K156 in order to abolish the auto-associative properties is used as a negative control. The capacity shown by peptides for alpha-helical formation is demonstrated by circular dichroism (CD) analysis performed in aqueous solution and in aqueous trifluoroethanol (TFE) mixtures. Both electrospray ionization mass spectrometry (ESI-MS) and glutaraldehyde chemical cross-linking show that peptides adopt different solvent-dependent equilibriums of monomers, dimers, trimers and tetramers. Oligomerization of peptides in aqueous solution is related to their ability to form helical structures. Addition of a small amount of TFE (<10%) stimulates helix stabilization and the interhelical hydrophobic contacts. Higher amounts of TFE alter the hydrophobic contacts and disrupt the oligomeric species. In addition to hydrophobic interactions, the patterns indicate that the biologically important Lys156 and Lys159 residues also participate in helix association. K(E)156 despite its ability to adopt a helical structure is unable to associate into oligomers, demonstrating the importance of hydrophobic contacts for oligomerization. Thus, the designed peptides provide us information on the functional properties of the alpha4 IN that seems to hold a dual role in DNA recognition and protein oligomerization.

Molecular-Dynamics Simulations of C- and N-Terminal Peptide Derivatives of GCN4-p1 in Aqueous Solution

We report the investigation of two 16-residue peptides in aqueous solution by means of molecular-dynamics simulations. The peptides constitute the C- and N-terminal halves of the 33-residue monomer whose dimer constitutes the leucine zipper of the yeast transcriptional activator, denoted GCN4-p1. To examine a hypothesis about coiled-coil formation, in which the C-terminal half contains a helix-formation trigger site absent in the N-terminal half, experimental studies of the two peptides have determined their helix propensities under several conditions of temperature, pH, and salt concentration with circular dichroism. An NMR experiment provides additional evidence. At temperatures of 278 and 325 K and pH 7.5, mixtures of alpha- and pi-helical secondary structure constitute the most probable conformations in both C- and N-terminal halves. A bifurcated salt bridge between Arg25 and Glu22/20 correlates with the structural fluctuations of the C-terminal half. It also exhibits a persistent loop at the N-terminal end involving the side chains of His18 and Glu22, which is reminiscent of helix-capping boxes. Nonreversible unfolding appears to occur abruptly in the Arg25 mutant, suggesting a cooperative event. Analysis does not indicate that the N-terminal half is less stable than the C-terminal half, indicating that 100 ns is too short a period to observe complete unfolding.

Theoretical study of volume changes associated with the helix–coil transition of an alanine‐rich peptide in aqueous solution

The changes in the partial molar volume (PMV) associated with the conformational transition of an alanine-rich peptide AK16 from the alpha-helix structure to various random coil structures are calculated by the three-dimensional interaction site model (3D-RISM) theory coupled with the Kirkwood-Buff theory. The volume change is analyzed by decomposing it into contributions from geometry and hydration: the changes in the van der Waals, void, thermal, and interaction volume. The total change in the PMV is positive. This is primarily due to the growth of void space within the peptide, which is canceled in part by the volume reduction resulting from the increase in the electrostatic interaction between the peptide and water molecules. The changes in the void and thermal volume of the coil structures are widely distributed and tend to compensate each other. Additionally, the relations between the hydration volume components and the surface properties are investigated. We categorize coil structures into extended coils with the PMV smaller than helix and general coils with the PMV larger than helix. The pressure therefore can both stabilize and destabilize the coil structures. The latter seems to be a more proper model of random coil structures of the peptide.

SWET for Secure Water Suppression on Probes with High Quality Factor

Water suppression by selective preirradiation is increasingly difficult to achieve on probeheads with high quality factor because of the opposing forces of radiation damping. Here we show that a simple modification to the WET scheme provides reliable water suppression in aqueous solutions of proteins and peptides with minimal saturation of the H(alpha) protons. The scheme is shown to work also with dilute peptide solutions. It is recommended to maintain the water suppression during the evolution time of COSY experiments by weak selective irradiation that causes only minimal Bloch-Siegert shifts. The new water-suppression scheme suppresses the water magnetization by spatial scrambling. Traditional water suppression by preirradiation is similarly based more on water scrambling due to the radiofrequency inhomogeneity than on relaxation effects.

Cross-Linking between Thymine and Indolyl Radical: Possible Mechanisms for Cross-Linking of DNA and Tryptophan-Containing Peptides

As experimentally observed in gamma-irradiated aqueous solutions of tryptophan-containing peptides in the presence of DNA, a fast electron (or hydrogen atom) transfer from the DNA restores an intact tryptophan residue at the expense of the DNA integrity. Alternatively, addition of the deprotonated electron-deficient indolyl radical to the DNA, followed by subsequent rearrangement, may lead toward DNA/tryptophan-containing peptide cross-linking. Herein, possible reaction mechanisms for thymine-indolyl radical cross-linking are proposed. The consistent use of the contact spin density distribution is the key virtue of this work. The Becke 3, Lee, Yang, and Parr (B3LYP) density functional theory (DFT) method is employed to investigate the feasibility of the proposed cross-linking mechanisms. A possible complete reaction mechanism consists of a combination of the C(5)-hydroxylated thymine and indolyl radicals forming the initial cross-linked product, a hydrogen transfer within the initial cross-linked product by use of a bridging water molecule, and a dehydration step. The overall thermodynamics of the free energy profiles at 0 and 298 K are similar and display differences of magnitude for the hydrogen-transfer reaction. Temperature may be a key factor influencing the overall mechanism. The skeletal structures and contact spin densities on the heavy atoms of the tryptophan side chain and indolyl radicals are essentially equal. Hence, it is believed that a direct combination of the C(5)-hydroxylated thymine and tryptophan radicals should form the initial cross-linked product, as far as addition of the tryptophan radical to the DNA is concerned.

Conformational and Electronic Properties of a Microperoxidase in Aqueous Solution: A Computational Study

A theoretical study of the conformational properties of a small heme peptide in aqueous solution is carried out by classical, long-timescale molecular dynamics simulations. The electronic properties of this species, that is, the relative energies of its excited electronic states and the redox potential, are reproduced and related to the conformational behavior using the perturbed matrix method and basic statistical mechanics. Our results show an interesting coupling between the conformational transitions and the electronic properties. These investigations, beyond the biophysically relevant results addressing the long-standing question of the actual role of the enzyme structure on the enzyme activity, are also of some methodological interest since they offer a further computational perspective for including the electronic degrees of freedom into the modeling of rather complex molecular systems.

1H NMR studies of natural and synthetic immunostimulating peptides in aqueous solution.

The peptides LAla-DGlu (L-alanyl-D-glutamic acid), LAla-DGlu[LLA2pm(Gly)]NH2, i.e. N2-(L-alanyl-D-gamma-isoglutaminyl)-N6-glycyl-LL-2,6-diaminopimelic acid, and LAla-DGlu[LLA2pm(Gly)-D-Ala], i.e. N2-(L-alanyl-D-gamma-glutamyl)-N6-glycyl-LL-alpha-2,6-diaminopimelyl-D-alanine, extracted from a Streptomyces strain and their immunostimulating synthetic lauroyl derivatives were studied by 1H NMR spectroscopy at 270 MHz. The chemical shift analysis confirms (a) the sequence of these compounds, (b) the occurrence of a gamma bond between Glu (or GluNH2) and A2pm, (c) the presence of a carboxamide group on the backbone of the tetrapeptide LAla-DGlu[LLA2pm(Gly)]. Temperature and pH studies strongly suggest that the tetrapeptide and pentapeptide exist under several folded conformations characterized by a proximity between the NH3 group of Gly and the Glu (or GluNH2) residue. THe similarity between the chemical shifts of the corresponding protons in LAla-DGlu, lauroly-LAla-DGlu and muramyl-L:Ala-DGluNH2 shows that the coupling of the dipeptide with a lauroyl or a muramyl group does not induce significant changes in the structure of the peptide moiety. In the lipopeptide series the presence of the lauroyl chain leads to amphipathic substances which form, micelles in aqueous solution as shown by the large increase of the proton linewidths. The immunostimulating properties of this kind of peptide manifest themselves at very low concentration and only after their coupling with a sugar or lipid moiety. These features can be interpreted by the formation of mixed complexes between the immunoadjuvants and cell membrane constituents.

A Luminescent Receptor with Affinity for N-Terminal Histidine in Peptides in Aqueous Solution

Crown ethers of suitable size are the perfect artificial host compounds for ammonium ion binding, but the rather low affinity in aqueous solution prevents their use at physiological conditions. We report here the synthesis and properties of a luminescent benzo crown ether with a pendant copper imidodiacetic acid complex, which coordinates with high affinity to histidine. The emission intensity of the benzo crown ether increases significantly in the presence of ammonium ions in methanol. At physiological conditions in buffered water at pH 7.5 these interactions are too weak to be detected. If an ammonium ion and an imidazole moiety are present in the analyte, such as in His-Lys-OMe or His-OMe, high binding affinity in aqueous solution is restored. The binding event is signaled by an increase in emission intensity, which can even be observed with the naked eye. This allows the selective detection of small peptides containing N-terminal histidine or histidine among all other amino acids at physiological conditions.

Fluorescence probes for thiol-containing amino acids and peptides in aqueous solution

A new fluorescence probe is described using the "chemosensing ensemble" method. The probe shows high selectivity and sensitivity for thiol-containing amino acids and peptides, and can detect cysteine and homocysteine from healthy to abnormal levels under physiologically-relevant conditions.