Zwitterionic Peptide Research Articles

Action of an Antiparasitic Peptide Active against African Sleeping Sickness in Biomembrane Models

Peptides with trypanocidal activity are promising compounds for the treatment of African Sleeping Sickness, which have motivated the research into the ability of these compounds to disrupt the protozoan membrane. In this present study, we used the Langmuir monolayer technique to investigate the surface properties of an antiparasitic and zwitterionic peptide, namely S-(2,4-dinitrophenyl) glutathione di-2-propyl ester, and its interaction with a model membrane comprising a phospholipid monolayer, dipalmitoyl phosphatidyl choline (DPPC). The peptide formed a stable Langmuir monolayer, whose main feature of its surface pressure-area isotherm was the presence of a phase transition accompanied by a negative surface compressional modulus, which was attributed to the aggregation upon compression due to intermolecular bond associations of the molecules. This was inferred from surface pressure and surface potential isotherms, Brewster angle microscopy (BAM) images, Polarization modulation-infrared reflection-adsorption spectroscopy (PM-IRRAS), and dynamic elasticity measurements by the pendant drop technique. When co-spread with dipalmitoyl phosphatidyl choline (DPPC), the drug affected both the surface pressure and the monolayer morphology, even at high surface pressures and with low amounts of the drug. The results were interpreted by assuming a repulsive, cooperative interaction between the drug and DPPC molecules. Such repulsive interaction and the large changes in fluidity arising from drug aggregation may be related to the disruption of the membrane, which is key for the parasite killing property.

The interaction of an antiparasitic peptide active against African Sleeping Sickness with cell membrane models

Zwitterionic peptides with trypanocidal activity are promising lead compounds for the treatment of African Sleeping Sickness, and have motivated research into the design of compounds capable of disrupting the protozoan membrane. In this study, we use the Langmuir monolayer technique to investigate the surface properties of an antiparasitic peptide, namely S-(2,4-dinitrophenyl)glutathione di-2-propyl ester, and its interaction with a model membrane comprising a phospholipid monolayer. The drug formed stable Langmuir monolayers, whose main feature was a phase transition accompanied by a negative surface elasticity. This was attributed to aggregation upon compression due to intermolecular bond associations of the molecules, inferred from surface pressure and surface potential isotherms, Brewster angle microscopy (BAM) images, infrared spectroscopy and dynamic elasticity measurements. When co-spread with dipalmitoyl phosphatidyl choline (DPPC), the drug affected both the surface pressure and the monolayer morphology, even at high surface pressures and with low amounts of the drug. The results were interpreted by assuming a repulsive, cooperative interaction between the drug and DPPC molecules. Such repulsive interaction and the large changes in fluidity arising from drug aggregation may be related to the disruption of the membrane, which is key for the parasite killing property.

Mesoporous Calcite by Polymer Templating

Layered calcite crystals with internal 10−50 nm pores are precipitated from aqueous solution containing a polymer−peptide conjugate that aggregates into pore-forming templates. The zwitterionic peptide sequence behaves as the “binding block” of a double-hydrophilic block copolymer, facilitating templating, nucleation inhibition, and stabilization of amorphous precursor particles.

Protein electron transfer (mechanism and reproductive toxicity): Iminium, hydrogen bonding, homoconjugation, amino acid side chains (redox and charged), and cell signaling

This contribution presents novel biochemical perspectives of protein electron transfer (ET) with focus on the iminium nature of the peptide link, along with relationships to reproductive toxicity. The favorable influence of hydrogen bonding on protein ET has been widely documented. Hydrogen bonding of the zwitterionic peptide enhances iminium character. A wide array of such bonding agents is available in vivo, with many reports on the peptide link itself. ET proceeds along the backbone, due in part, to homoconjugation. Redox amino acids (AAs), mainly tyrosine (Tyr), tryptophan (Typ), histidine (His), cysteine (Cys), disulfide, and methionine (Met), are involved in the competing processes for radical formation: direct hydrogen atom abstraction versus electron and proton loss. It appears that the radical or radical cation generated during the redox process is capable of interacting with n-electrons of the backbone. Beneficial effects of cationic AAs impact the conduction process. A relationship apparently exists involving cell signaling, protein conduction, and radicals or electrons. In addition, the link between protein ET and reproductive toxicity is examined. A key element is the role of reactive oxygen species (ROS) generated by protein ET. There is extensive evidence for involvement of ROS in generation of birth defects. The radical species arise in protein mainly by ET transformations by enzymes, as illustrated in the case of alcoholism.

Charge Location Directs Electron Capture Dissociation of Peptide Dications

The effect of peptide dication charge location on electron capture dissociation (ECD) fragmentation pattern is investigated. ECD fragmentation patterns are compared for peptides with amide and free acid C-terminal groups. ECD of free acid compared with C-terminally amidated peptides with basic residues near the N-terminus demonstrates increased formation of a-type ions. Similarly, ECD of free acid compared with C-terminally amidated peptides with basic residues near the C-terminus exhibits increased formation of y-type ions. Alteration of the peptide sequence to inhibit the formation of charged side chains (i.e., amino acid substitution and acetylation) provides further evidence for charge location effect on ECD. We propose that formation of zwitterionic peptide structures increases the likelihood of amide nitrogen protonation (versus basic side chains), which is responsible for the increase in a- and y-type ion formation.

Performance Evaluation of the Three-Layer ONIOM Method: Case Study for a Zwitterionic Peptide.

The performance of the three-layer ONIOM method was systematically investigated by comparing the optimized geometries and calculated deprotonation energy of a zwitterionic peptide molecule, NH3(+)-CH(n)Bu-CO-NH-CH2-CO-NH-CH(n)Bu-COO(-), using all possible combinations of B3LYP/6-31G* as the high-level quantum (HQ), AM1 as the low-level quantum (LQ), and Amber as the MM method. Results show that the three-layer ONIOM(HQ:LQ:MM) method, which includes a medium-level quantum method in the middle system to take into account the electronic effects of the middle layer and to keep the problematic QM-MM boundary away from the action region, is more reliable and more stable than the QM:MM:MM or generic QM/MM method and is the best compromise between accuracy and computational cost.

Environment-Controlled Interchromophore Charge Transfer Transitions in Dipeptides Probed by UV Absorption and Electronic Circular Dichroism Spectroscopy

Charge transfer (CT) transitions between the C-terminal carboxylate and peptide group have been investigated for alanyl-X and X-alanine dipeptides by far-UV absorption and electronic circular dichroism (ECD) spectroscopy (where X represents different amino acid residues). The spectra used in the present study were obtained by subtracting the spectrum of the cationic species from that of the corresponding zwitterionic peptide spectrum. These spectra displayed three bands, e.g., band I between 44 and 50 kK (kK = 10(3) cm(-1)), band II at 53 kK, and band III above 55 kK, which were, respectively, assigned to a n(COO-) --> pi* CT transition, a pi(COO-) --> pi* CT transition, and a carboxylate pi --> pi* (NV1) transition, respectively By comparison of the intensity, bandwidth, and wavenumber position of band I of some of the investigated dipeptides, we found that positive charges on the N-terminal side chain (for X = K), and to a minor extent also the N-terminal proton, reduce its intensity. This can be understood in terms of attractive Coulomb interactions that stabilize the ground state over the charge transfer state. For alanylphenylalanine, we assigned band I to a n(COO-) --> pi* CT transition into the aromatic side chain, indicating that aromatic side chains interact electronically with the backbone. We also performed ECD measurements at different pH values (pH 1-6) for a selected subset of XA and AX peptides. By subtraction of the pH 1 spectrum from that observed at pH 6, the ECD spectrum of the CT transition was obtained. A titration curve of their spectra reveals a substantial dependence on the protonation state of the aspartic acid side chain of AD, which is absent in DA and AE. This most likely reflects a conformational transition of the C-terminus into a less extended state, though the involvement of a side chain --> peptide CT transition cannot be completely ruled out.

Effect of Charge and Molecular Weight on Transdermal Peptide Delivery by Iontophoresis

The study was conducted to investigate the impact of charge and molecular weight (MW) on the iontophoretic delivery of a series of dipeptides. Constant current iontophoresis of lysine and 10 variously charged lysine- and tyrosine-containing dipeptides was performed in vitro. Increasing MW was compensated by additional charge; for example, Lys (MW = 147 Da, +1) and H-Lys-Lys-OH (MW = 275 Da, +2) had equivalent steady-state fluxes of 225 +/- 48 and 218 +/- 40 nmol cm(-2) h(-1), respectively. For peptides with similar MW, e.g., H-Tyr-D-Arg-OH (MW = 337 Da, +1) and H-Tyr-D-Arg-NH(2) (MW = 336 Da, +2), the higher valence ion displayed greater flux (150 +/- 26 vs. 237 +/- 35 nmol cm(-2) h(-1)). Hydrolysis of dipeptides with unblocked N-terminal residues, after passage through the stratum corneum, suggested the involvement of aminopeptidases. The iontophoretic flux of zwitterionic dipeptides was less than that of acetaminophen and dependent on pH. For the series of dipeptides studied, flux is linearly correlated to the charge/MW ratio. Data for zwitterionic peptides indicate that they do not behave as neutral ("charge-less") molecules, but that their iontophoretic transport is dependent on the relative extents of ionization of the constituent ionizable groups, which may also be affected by neighboring amino acids.

MULTIPLE TRANSPORT SYSTEMS MEDIATE THE HEPATIC UPTAKE AND BILIARY EXCRETION OF THE METABOLICALLY STABLE OPIOID PEPTIDE [d-PENICILLAMINE2,5]ENKEPHALIN

Rapid and extensive biliary excretion of [D-penicillamine2,5]enkephalin (DPDPE) in rats as the unchanged peptide suggests that multiple transport proteins may be involved in the hepatobiliary disposition of this zwitterionic peptide. Although DPDPE is a P-glycoprotein substrate, the role of other transport proteins in the hepatic clearance of DPDPE has not been established. Furthermore, the ability of various experimental approaches to quantitate the contribution of a specific hepatic uptake or excretion process when multiple transport systems are involved has not been addressed. 3H-DPDPE uptake in suspended Wistar rat hepatocytes was primarily (>95%) due to temperature-dependent transport mechanisms; similar results were obtained in suspended hepatocytes from Mrp2-deficient (TR-) rats. Pharmacokinetic modeling revealed that saturable and linear processes were involved in 3H-DPDPE uptake in hepatocytes. The use of transport modulators suggested that hepatic uptake of 3H-DPDPE was mediated by Oatp1a1, Oatp1a4, and likely Oatp1b2. Accumulation of 3H-DPDPE in sandwich-cultured (SC) hepatocytes was rapid; uptake of 3H-DPDPE in SC rat hepatocytes from control and TR- rats was similar. However, the biliary excretion index and biliary clearance decreased by 83 and 85%, respectively, in TR- SC rat hepatocytes, indicating that DPDPE is an Mrp2 substrate. Rate constants for uptake and excretion of 3H-DPDPE in SC rat hepatocytes were determined by pharmacokinetic modeling; data were consistent with basolateral excretion of 3H-DPDPE from the hepatocyte. These results demonstrate the complexities of hepatobiliary disposition when multiple transport mechanisms are involved for a given substrate and emphasize the necessity of multi-experimental approaches for the comprehensive resolution of these processes.

All-Atom Numerical Studies of Self-Assembly of Zwitterionic Peptide Amphiphiles

We present an approach to study the self-assembly of organic macromolecules, based on all-atom empirical force field calculations. The approach is applied to self-assemblies of zwitterionic peptide amphiphiles possessing large dipoles in their hydrophilic headgroups. The assembly is built from the bottom up by first optimizing the diad amphiphile, which is then used as a basic unit to subsequently first build quartets, and then 4 × 4 supercells of molecules to be studied in periodic boundary conditions. Explicit water solvent is added to the surface of the periodic structures and molecular dynamics simulations are performed on them. The calculations reveal an interesting structure of the resulting assemblies: the dipoles in the upper parts of the headgroups are aligned in an antiparallel fashion with respect to each other and along one of the periodic axes, while hydrogen bonds in the lower, rigid parts of the headgroups form a parallel beta sheet along the same direction. It is shown that the structure ...

Dynamics of complex formation between biological and luminescent conjugated polyelectrolytes—a surface plasmon resonance study

A water-soluble polythiophene, POWT, with zwitterionic peptide like side chains possess good characteristics for biosensor applications. The zwitterionic side chains of the polymer can couple to biomolecules via electrostatic and hydrogen bonding. This creates possibilities to imprint biomolecules to spin-coated polymer films with maintained functionality, and use the resulting matrix as a biosensor. Polymer-biomolecular interaction studies done with surface plasmon resonance (SPR) reveal a well performing sensor matrix with high affinity for DNA hybridizations as well as for protein detection. The responses are distinct and very specific. A directional dependence of antibodies binding to POWT layer has also been observed. The polymer films have also been characterized by optical methods. Emission and absorption measurements in different buffer systems confirm that the polymer matrix can undergo structural and conformational changes on surfaces. The dielectric function in the interval 300–800 nm of POWT is reported, based on variable angle spectroscopic ellipsometry. This modeling reveals that a considerable amount of water is included in the material. The polymer layer possesses the characteristics needed for biochip applications and micro array techniques.

Ab initio study of (13)C(alpha) chemical shift anisotropy tensors in peptides.

This study reports magnitudes and the orientation of the (13)C(alpha) chemical shift anisotropy (CSA) tensors of peptides obtained using quantum chemical calculations. The dependency of the CSA tensor parameters on the energy optimization of hydrogen atom positions and hydrogen bonding effects and the use of zwitterionic peptides in the calculations are examined. Our results indicate that the energy optimization of the hydrogen atom positions in crystal structures is necessary to obtain accurate CSA tensors. The inclusion of intermolecular effects such as hydrogen bonding in the calculations provided better agreement between the calculated and experimental values; however, the use of zwitterionic peptides in calculations, with or without the inclusion of hydrogen bonding, did not improve the results. In addition, our calculated values are in good agreement with tensor values obtained from solid-state NMR experiments on glycine-containing tripeptides. In the case of peptides containing an aromatic residue, calculations on an isolated peptide yielded more accurate isotropic shift values than the calculations on extended structures of the peptide. The calculations also suggested that the presence of an aromatic ring in the extended crystal peptide structure influences the magnitude of the delta(22) which the present level of ab initio calculations are unable to reproduce.

A molecular dynamics study on the conformational stability of PrP 180–193 helix II prion fragment

Molecular dynamics of PrP 180–193 has allowed us to investigate the stability of the α-helical conformation of the zwitterionic peptide (L 1) and the neutralized (L 2). In water, the helical structure of L 1 is unstable; in L 2, the α-helix breaks up in the middle at Gln186, and the two resulting connected helices are stable. The hydrophobic enviroment decreases the stability of the helical structure of L 1, this effect is more evident for L 2 for which the unfolding of the C-terminus is followed by the formation of an intramolecular hydrogen bond connecting His 187 with Thr 191.

Conformer Profiles and Biological Activities of Peptides

Small, zwitterionic peptides (2-6 residues) are flexible molecules that occur in solution as an ensemble of conformational forms in dynamic equilibrium. They occur widely in Nature as components of the peptide pool produced by protein hydrolysis. Molecular modelling provides information on the conformations they adopt in aqueous solution. Contrary to expectations, they exist in a limited range of conformational forms that arise from particular combinations of backbone torsions. From the computed energies of the conformers, those with similar conformations can be aggregated and a profile of the conformer population displayed using a 3D pseudo- Ramachandran plot. Several different generic peptide transporters have evolved with complementary substrate specificities in response to these varied conformational forms. Molecular recognition templates (MRTs) define the stereo-electronic features of particular conformations that determine peptide recognition and binding by these transporters. The binding and transport of any peptide correlates with the proportion of its conformers that occur in a particular MRT. Specific con former binding appears generally to involve little or no ligand rearrangement, which minimises conformational entropy loss. Conformational analysis of peptide analogues, evaluation of their similarities to normal peptides and comparison of their conformer profiles with MRTs, allows estimates of their molecular recognition as putative bioactive ligands for such proteins, this is illustrated for a variety of pseudopeptides, isosteres and conformationally-constrained analogues. For peptide therapeutics, such as β-lactam antibiotics, inhibitors of angiotensin-converting enzyme, antiviral and chemotherapeutic agents, this approach can be used to evaluate in silico virtual libraries of drug analogues to estimate their potential for targeted delivery and oral availability. Keywords: Peptides, Molecule Parameters, dipeptide permease, binding protein, isothermal titration calorimetry, tripeptide permease, tripeptide torsional sector, virtual torsion, amino acid

New challenges in quantum chemistry: Quests for accurate calculations for large molecular systems.

As quantum chemistry plays a more and more central role in many complicated chemical problems, it has become necessary to obtain accurate results for large molecular systems. Conventional quantum chemistry methods are either too expensive to apply to large systems or too approximate for the results to be reliable, and they fail to satisfy this requirement. A variety of different approaches is being developed with the aim of achieving this goal: local correlation methods; divide-and-conquer methods; linear-scaling density functional methods based on the fast multipole and other approximations; effective potential methods; and hybrid methods. ONIOM (our N-layered integrated molecular orbital plus molecular mechanics method), developed by the authors, is a hybrid method in which a large molecular system is divided into onion-skin-like layers, and different quantum chemistry/molecular mechanics methods are used for different parts of the system; the results are combined to extrapolatively estimate the results of high-level calculation for the real system. Several applications of ONIOM will be discussed.

Preferential recognition of zwitterionic dipeptides as transportable substrates by the high-affinity peptide transporter PEPT2

We investigated the interaction of rat PEPT2, a high-affinity peptide transporter, with neutral, anionic, and cationic dipeptides using electrophysiological approaches as well as tracer uptake methods. d-Phe-L-Gln (neutral), d-Phe-L-Glu (anionic), and d-Phe-L-Lys (cationic) were used as representative, non-hydrolyzable, dipeptides. All three dipeptides induced H +-dependent inward currents in Xenopus laevis oocytes heterologously expressing rat PEPT2. The H +:peptide stoichiometry was 1:1 in each case. A simultaneous measurement of radiolabeled dipeptide influx and charge transfer in the same oocyte indicated a transfer of one net positive charge into the oocyte per transfer of one peptide molecule irrespective of the charged nature of the peptide. We conclude that the zwitterionic peptides are preferentially recognized by PEPT2 as transportable substrates and that the proton/peptide stoichiometry is 1 for the transport process.

Gene transfer with synthetic virus-like particles via the integrin-mediated endocytosis pathway.

The interaction between cationic DNA-containing particles and cell surface anionic proteoglycans is an efficient means of entering cultured cells. Therapeutic in vivo gene delivery levels, however, require binding to less ubiquitous molecules. In an effort to follow adenovirus, thiol-derivatized polyethylenimine (PEI) was conjugated to the integrin-binding peptide CYGGRGDTP via a disulfide bridge. The most extensively conjugated derivative (5.5% of the PEI amine functions) showed physical properties of interest for systemic gene delivery. In the presence of excess PEI-RGD, plasmid DNA was condensed into a rather homogeneous population of 30-100 nm toroidal particles as revealed by electron microscopy images in 150 mM salt. Their surface charge was close to neutrality as a consequence of the shielding effect of the prominent zwitterionic peptide residues. Transfection efficiency of integrin-expressing epithelial (HeLa) and fibroblast (MRC5) cells was increased by 10- to 100-fold as compared with PEI, even in serum. This large enhancement factor was lost when aspartic acid was replaced by glutamic acid in the targeted peptide sequence (RGD/RGE), confirming the involvement of integrins in transfection. PEI-RGD/DNA complexes thus share with adenovirus constitutive properties such as size and a centrally protected DNA core, and 'early' properties, i.e. cell entry mediated by integrins and acid-triggered endosome escape.

Delta-opiate DPDPE in magnetically oriented phospholipid micelles: binding and arrangement of aromatic pharmacophores

D-Penicillamine(2,5)-enkephalin (DPDPE) is a potent opioid peptide that exhibits a high selectivity for the delta-opiate receptors. This zwitterionic peptide has been shown, by pulsed-field gradient 1H NMR diffusion studies, to have significant affinity for a zwitterionic phospholipid bilayer. The bilayer lipid is in the form of micelles composed of dihexanoylphosphatidylcholine (DHPC) and dimyristoylphosphatidylcholine (DMPC) mixtures, where the DMPC forms the bilayer structure. At high lipid concentration (25% w/w) these micelles orient in the magnetic field of an NMR spectrometer. The resulting 1H-13C dipolar couplings and chemical shift changes in the natural abundance 13C resonances for the Tyr and Phe aromatic rings were used to characterize the orientations in the bilayer micelles of these two key pharmacophores.

Influence of sample pH on the conformational backbone dynamics of a pseudotripeptide (H‐Tyr‐TicΨ[CH2‐NH] Phe‐OH) incorporating a reduced peptide bond: An NMR investigation

In the present paper we investigate the influence of sample pH on the conformational and dynamical properties of the pseudotripeptide H-Tyr-Tic psi [CH2-NH]Phe-OH (TIP[psi]; Tic: 1,2,3,4,-tetrahydroisoquinoline-3-carboxylic acid) using various one- and two-dimensional nmr techniques in conjunction with molecular modeling. Studies were conducted at three different pH levels corresponding to the zwitterionic peptide containing a formal positive charge (pH 3.1), the deprotonated molecule (pH 9.1), and a situation at neutral pH (pH 7.2) involving both protonated and deprotonated states of the reduced peptide bond. Analysis of the one-dimensional1H-nmr spectra reveals that in solution TIP[psi] is in slow dynamic exchange between conformations containing cis and trans configurations of the Tyr-Tic bond. An nmr pH dependence study of the cis:trans ratio indicated that the exchange process was governed by the protonation state of the reduced bone amine. From the nmr data, reduced peptide bond pK alpha values of 6.5 and 7.5 were determined for the cis and trans conformers, respectively. It was concluded that conformations containing a trans Tyr-Tic bond are stabilized at low pH by an intramolecular hydrogen bond between the Tyr carbonyl and the reduced peptide bond protonated amine. This observation was corroborated by molecular mechanics investigations that revealed low energy trans structures compatible with nmr structural data, and furthermore, were consistently characterized by the existence of a strong N+ H ... O = C interaction closing a seven-membered cycle. The dynamics of cis-trans isomerization about the Tyr-Tic peptide bond were probed by nmr exchange experiments. The selective presaturation of exchanging resonances carried out at several temperatures between 50 and 70 degrees C allowed the determination of isomerization rate constants as well as thermodynamic activation parameters. delta G not equal to values were in close agreement with the cis-->trans energy barrier found in X-Pro peptide fragments (approximately 83 kJ/mol). A large entropic barrier determined for the trans-->cis conversion of TIP[psi] (5.7 JK-1 mol-1 at pH 3.1;6.5 J K-1 mol-1 at pH 9.1) is discussed in terms of decreased solvent molecular ordering around the conformers possessing a trans Tyr-Tic bond. Evidence that the neutral form of the reduced peptide bond gains rigidity upon protonation was obtained from relaxation measurements in the rotating frame. T1 rho measurements of several protons in the vicinity of the reduced peptide bond were made as a function of spin-lock field.(ABSTRACT TRUNCATED AT 400 WORDS)

The influence of peptide structure on transport across Caco-2 cells.

The relationship between structure and permeability of peptides across epithelial cells was studied. Using confluent monolayers of Caco-2 cells as a model of the intestinal epithelium, permeability coefficients were obtained from the steady-state flux of a series of neutral and zwitterionic peptides prepared from D-phenylalanine and glycine. Although these peptides ranged in lipophilicity (log octanol/water partition coefficient) from -2.2 to +2.8, no correlation was found between the observed flux and the apparent lipophilicity. However, a strong correlation was found for the flux of the neutral series and the total number of hydrogen bonds the peptide could potentially make with water. These results suggest that a major impediment to peptide passive absorption is the energy required to break water-peptide hydrogen bonds in order for the solute to enter the cell membrane. This energy appears not to be offset by the favorable introduction of lipophilic side chains in the amino acid residues.