Peptide Isoelectric Point Research Articles

Self-assembly and hydrogelation of a potential bioactive peptide derived from quinoa proteins

In this work the identification of peptides derived from quinoa proteins which could potentially self-assemble, and form hydrogels was carried out with TANGO, a statistical mechanical based algorithm that predicts β-aggregate propensity of peptides. Peptides with the highest aggregate propensity were subjected to gelling screening experiments from which the most promising bioactive peptide with sequence KIVLDSDDPLFGGF was selected. The self-assembling and hydrogelation properties of the C-terminal amidated peptide (KIVLDSDDPLFGGF-NH2) were studied. The effect of concentration, pH, and temperature on the secondary structure of the peptide were probed by circular dichroism (CD), while its nanostructure was studied by transmission electron microscopy (TEM) and small-angle neutron scattering (SANS). Results revealed the existence of random coil, α-helix, twisted β-sheet, and well-defined β-sheet secondary structures, with a range of nanostructures including elongated fibrils and bundles, whose proportion was dependant on the peptide concentration, pH, or temperature. The self-assembly of the peptide is demonstrated to follow established models of amyloid formation, which describe the unfolded peptide transiting from an α-helix-containing intermediate into β-sheet-rich protofibrils. The self-assembly is promoted at high concentrations, elevated temperatures, and pH values close to the peptide isoelectric point, and presumably mediated by hydrogen bond, hydrophobic and electrostatic interactions, and π-π interactions (from the F residue). At 15 mg/mL and pH 3.5, the peptide self-assembled and formed a self-supporting hydrogel exhibiting viscoelastic behaviour with G' (1 Hz) ~2300 Pa as determined by oscillatory rheology measurements. The study describes a straightforward method to monitor the self-assembly of plant protein derived peptides; further studies are needed to demonstrate the potential application of the formed hydrogels in food and biomedicine.

Optimization of conditions for single-step purification of recombinant hepatitis B surface antigen produced in Pichia pastoris using ion exchange chromatography

ABSTRACTThe adsorption and release of rHBsAg extracted from the final dosage form on various ion exchange resins and under different pH conditions were investigated after its peptide map and isoelectric point (PI) determination. Efficient antigen adsorption to the anion exchange resins occurred when the pH value of the protein buffer was adjusted to 5.0. In purification of rHBsAg derived from the yeast crude extract using Q Sepharose FF column, with adjusting the pH value of the crude extract to 5.0 (i.e., near to the target protein PI) and using 2M NaCl, rHBsAg with high purity (up to >95%) was obtained.Abbreviations: rHBsAg, recombinant hepatitis B surface antigen; Alhydrogel, aluminum hydroxide; IEF, isoelectric focusing; PI, isoelectric point; SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis; RP-HPLC, reversed-phase high-performance liquid chromatography; SE-HPLC, size-exclusion high-performance liquid chromatography; PBS, phosphate-buffered saline

LacSubPred: predicting subtypes of Laccases, an important lignin metabolism-related enzyme class, using in silico approaches.

BackgroundLaccases (E.C. 1.10.3.2) are multi-copper oxidases that have gained importance in many industries such as biofuels, pulp production, textile dye bleaching, bioremediation, and food production. Their usefulness stems from the ability to act on a diverse range of phenolic compounds such as o-/p-quinols, aminophenols, polyphenols, polyamines, aryl diamines, and aromatic thiols. Despite acting on a wide range of compounds as a family, individual Laccases often exhibit distinctive and varied substrate ranges. This is likely due to Laccases involvement in many metabolic roles across diverse taxa. Classification systems for multi-copper oxidases have been developed using multiple sequence alignments, however, these systems seem to largely follow species taxonomy rather than substrate ranges, enzyme properties, or specific function. It has been suggested that the roles and substrates of various Laccases are related to their optimal pH. This is consistent with the observation that fungal Laccases usually prefer acidic conditions, whereas plant and bacterial Laccases prefer basic conditions. Based on these observations, we hypothesize that a descriptor-based unsupervised learning system could generate homology independent classification system for better describing the functional properties of Laccases.ResultsIn this study, we first utilized unsupervised learning approach to develop a novel homology independent Laccase classification system. From the descriptors considered, physicochemical properties showed the best performance. Physicochemical properties divided the Laccases into twelve subtypes. Analysis of the clusters using a t-test revealed that the majority of the physicochemical descriptors had statistically significant differences between the classes. Feature selection identified the most important features as negatively charges residues, the peptide isoelectric point, and acidic or amidic residues. Secondly, to allow for classification of new Laccases, a supervised learning system was developed from the clusters. The models showed high performance with an overall accuracy of 99.03%, error of 0.49%, MCC of 0.9367, precision of 94.20%, sensitivity of 94.20%, and specificity of 99.47% in a 5-fold cross-validation test. In an independent test, our models still provide a high accuracy of 97.98%, error rate of 1.02%, MCC of 0.8678, precision of 87.88%, sensitivity of 87.88% and specificity of 98.90%.ConclusionThis study provides a useful classification system for better understanding of Laccases from their physicochemical properties perspective. We also developed a publically available web tool for the characterization of Laccase protein sequences (http://lacsubpred.bioinfo.ucr.edu/). Finally, the programs used in the study are made available for researchers interested in applying the system to other enzyme classes (https://github.com/tweirick/SubClPred).

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

We present a liquid chromatography-mass spectrometry (LC-MS)-based method permitting unbiased (gene prediction-independent) genome-wide discovery of protein-coding loci in higher eukaryotes. Using high-resolution isoelectric focusing (HiRIEF) at the peptide level in the 3.7-5.0 pH range and accurate peptide isoelectric point (pI) prediction, we probed the six-reading-frame translation of the human and mouse genomes and identified 98 and 52 previously undiscovered protein-coding loci, respectively. The method also enabled deep proteome coverage, identifying 13,078 human and 10,637 mouse proteins.

Membrane fractionation of a β-lactoglobulin tryptic digest: Effect of the pH

The tryptic digestion of β-lactoglobulin leads to the release of a large range of biologically active peptides. Ultrafiltration/nanofiltration technology can be used to fractionate protein hydrolysates in order to obtain permeate products with increased functionality and free from intact proteins and enzymes. The influence of the pH in the fractionation of the hydrolysate through a polyethersulfone membrane (MWCO 5kDa) was investigated in this work. In this case peptide transmission was mainly governed by charge mechanisms and reached its maximum value when the pH value is close to the peptide isoelectric point. Almost complete rejection of acidic peptides was achieved at basic pH values due to electrostatic repulsive forces with the negatively charged membrane and, in agreement with Donnan theory, positively charged peptides shown lower transmission than the neutral species. The highest peptide recovery and the best separation factor between bioactive and non-bioactive peptides were obtained following nanofiltration at pH 8.0.

Effect of electrostatics on aggregation of prion protein Sup35 peptide

Self-assembly of misfolded proteins into ordered fibrillar structures is a fundamental property of a wide range of proteins and peptides. This property is also linked with the development of various neurodegenerative diseases such as Alzheimer’s and Parkinson’s. Environmental conditions modulate the misfolding and aggregation processes. We used a peptide, CGNNQQNY, from yeast prion protein Sup35, as a model system to address effects of environmental conditions on aggregate formation. The GNNQQNY peptide self-assembles in fibrils with structural features that are similar to amyloidogenic proteins. Atomic force microscopy (AFM) and thioflavin T (ThT) fluorescence assay were employed to follow the aggregation process at various pHs and ionic strengths. We also used single molecule AFM force spectroscopy to probe interactions between the peptides under various conditions. The ThT fluorescence data showed that the peptide aggregates fast at pH values approaching the peptide isoelectric point (pI = 5.3) and the kinetics is 10 times slower at acidic pH (pH 2.0), suggesting that electrostatic interactions contribute to the peptide self-assembly into aggregates. This hypothesis was tested by experiments performed at low (11 mM) and high (150 mM) ionic strengths. Indeed, the aggregation lag time measured at pH 2 at low ionic strength (11 mM) is 195 h, whereas the lag time decreases ∼5 times when the ionic strength is increased to 150 mM. At conditions close to the pI value, pH 5.6, the aggregation lag time is 12 ± 6 h under low ionic strength, and there is minimal change to the lag time at 150 mM NaCl. The ionic strength also influences the morphology of aggregates visualized with AFM. In pH 2.0 and at high ionic strength, the aggregates are twofold taller than those formed at low ionic strength. In parallel, AFM force spectroscopy studies revealed minimal contribution of electrostatics to dissociation of transient peptide dimers.

Effects of Electrostatics on Interactions of Short Peptide from Yeast Prion Protein Sup35

Protein misfolding and subsequent aggregation are the first steps in a long, complex process central to prion diseases. Previous experiments show distinct growth patterns at different pH values, with the fastest kinetics observed at pH 5.6, which is in line with the AFM force spectroscopy studies revealing the strongest interactions at pH 5.6. Since this pH corresponds to the peptide isoelectric point, we hypothesize that the observed effects are due to electrostatic interactions.Here, we studied the effect of electrostatics on the aggregation and peptide-peptide interactions of a short fragment of the yeast prion protein, Sup35 (GNNQQNY), used as a model to describe protein misfolding. We characterized aggregate growth using AFM and Thioflavin T (ThT) fluorescence measurements in various pHs and ionic strengths. We used single molecule AFM force spectroscopy to characterize peptide-peptide interactions at different ionic strengths. The electrostatic effect should be the strongest at pH values far from the pI and the lowest at the isoelectric point. Indeed, the experiments showed that at pH 2.0, the aggregation lag time is 195 hours under low ionic strength (10 mM) whereas the lag time decreases to 42 hours when ionic strength at pH 2.0 increases to 150 mM. At pH 5.6, the aggregation lag time is 11 hours under low ionic strength, and there is minimal change to lag time when ionic strength is increased. In parallel, AFM force spectroscopy studies were performed. They revealed minimal contribution of electrostatics in the dissociation of transient dimers. Increasing ionic strength at pH 2.0 resulted in a significant increase in forces. Such an increase in the magnitudes of rupture forces indicates that ionic strength enhanced inter-peptide interactions at low pH. The effect was less noticeable near the isoelectric point.

Roles of Electrostatics and Conformation in Protein-Crystal Interactions

In vitro studies have shown that the phosphoprotein osteopontin (OPN) inhibits the nucleation and growth of hydroxyapatite (HA) and other biominerals. In vivo, OPN is believed to prevent the calcification of soft tissues. However, the nature of the interaction between OPN and HA is not understood. In the computational part of the present study, we used molecular dynamics simulations to predict the adsorption of 19 peptides, each 16 amino acids long and collectively covering the entire sequence of OPN, to the {100} face of HA. This analysis showed that there is an inverse relationship between predicted strength of adsorption and peptide isoelectric point (P<0.0001). Analysis of the OPN sequence by PONDR (Predictor of Naturally Disordered Regions) indicated that OPN sequences predicted to adsorb well to HA are highly disordered. In the experimental part of the study, we synthesized phosphorylated and non-phosphorylated peptides corresponding to OPN sequences 65–80 (pSHDHMDDDDDDDDDGD) and 220–235 (pSHEpSTEQSDAIDpSAEK). In agreement with the PONDR analysis, these were shown by circular dichroism spectroscopy to be largely disordered. A constant-composition/seeded growth assay was used to assess the HA-inhibiting potencies of the synthetic peptides. The phosphorylated versions of OPN65-80 (IC50 = 1.93 µg/ml) and OPN220-235 (IC50 = 1.48 µg/ml) are potent inhibitors of HA growth, as is the nonphosphorylated version of OPN65-80 (IC50 = 2.97 µg/ml); the nonphosphorylated version of OPN220-235 has no measurable inhibitory activity. These findings suggest that the adsorption of acidic proteins to Ca2+-rich crystal faces of biominerals is governed by electrostatics and is facilitated by conformational flexibility of the polypeptide chain.

Effects of single amino acid substitutions on peptide interaction with lipid membranes and bacteria–variants of GKE21, an internal sequence from human LL-37

Effects of helix destabilization on lipid membrane interaction, liposome rupture, and bacterial killing was investigated for variants of the antimicrobial peptide GKE21 (GKEFKRI VQRIKDFLRNL VPR), an internal sequence of human cathelicidin LL-37, by ellipsometry, circular dichroism, fluorescence spectroscopy, and bacterial radial diffusion assay. GKE21 displayed moderate helix induction in buffer, which increased on interaction with phospholipid membranes. Substituting either of the two valines (V) in GKE21 with either proline (P) or d-valine (dV) resulted in helix destabilization, while peptide isoelectric point, net charge at pH 7.4, and mean hydrophobicity remained unchanged. The decreased tendency for helix formation in GKE21 (V → P, V → dV) resulted in a lower induced (helix-related) amphiphilicity, and correlated to a lower peptide adsorption at supported phospholipid membranes, as well as to decreased peptide-induced liposome leakage, particularly at high electrolyte concentration where conformation-invariant electrostatic interactions are screened. In addition, bacterial killing was reduced for the substituted peptides, indicating that even minor changes in induced peptide amphiphilicity may be of relevance for the bactericidal properties of this type of antimicrobial peptides.

Cover Picture: Electrophoresis 13/2008

AbstractIssue 13 is a regular issue including an Emphasis Section offering a series of 10 papers on “Fundamentals and Methodologies”. These papers are related to peptide isoelectric point calculation, DNA separation by MEKC, modeling mobility of apothioneins, protein expression in osteoarthritis, capillary coating, preparative separation of proteins by dynamic field gradient focusing, determination of pKa, speciation analysis by CE‐inductively coupled plasma MS, etc.

Preparative Peptide Isoelectric Focusing as a Tool for Improving the Identification of Lysine-Acetylated Peptides from Complex Mixtures

Protein sequence database searching of tandem mass spectrometry data is commonly employed to identify post-translational modifications (PTMs) to peptides in global proteomic studies. In these studies, the accurate identification of these modified peptides relies on strategies to ensure high-confidence results from sequence database searching in which differential mass shift parameters are employed to identify PTMs to specific amino acids. Using lysine acetylation as an example PTM, we have observed that the inclusion of differential modification information in sequence database searching dramatically increases the potential for false-positive sequence matches to modified peptides, making the confident identification of true sequence matches difficult. In a proof-of-principle study of whole cell yeast lysates, we demonstrate the combination of preparative isoelectric focusing using free-flow electrophoresis, and an adjusted peptide isoelectric point prediction algorithm, as an effective means to increase the confidence of lysine-acetylated peptide identification. These results demonstrate the potential utility of this general strategy for improving the identification of PTMs which cause a shift to the intrinsic isoelectric point of peptides.

Trade-Off between High Sensitivity and Increased Potential for False Positive Peptide Sequence Matches Using a Two-Dimensional Linear Ion Trap for Tandem Mass Spectrometry-Based Proteomics

Two-dimensional linear ion trap mass spectrometers are rapidly becoming the new workhorse instruments for shotgun proteomic analysis of complex peptide mixtures. The objective of this study was to compare the potential for false positive peptide sequence matches between a two-dimensional ion trap instrument and a traditional, three-dimensional ion trap instrument. Through the comparative analysis of a complex protein sample, we found that in order to minimize false positive sequence matches, sequence match scoring criteria must be more stringent for data from the two-dimensional ion trap compared to the three-dimensional ion trap data. Given this increased potential for false positives, we also investigated two potential filtering strategies to reduce the false positive matches for data derived from the two-dimensional ion trap, including trypsin enzyme cleavage filtering, and the addition of peptide physicochemical information as a constraint, specifically peptide isoelectric point. The results described here provide a cautionary tale to researchers, demonstrating the need for careful analysis of MS/MS data from this new class of ion trap instruments, as well as the effectiveness of trypsin enzyme cleavage filtering and peptide pI information in maximizing high confidence protein identifications from this powerful proteomic instrumentation.

Evaluating Preparative Isoelectric Focusing of Complex Peptide Mixtures for Tandem Mass Spectrometry-Based Proteomics: A Case Study in Profiling Chromatin-Enriched Subcellular Fractions inSaccharomycescerevisiae

We have evaluated the use of free-flow electrophoresis, an emerging separation method for preparative isoelectric focusing of complex peptide mixtures, as a tool for high-throughput tandem mass spectrometry-based proteomic analysis. In this study, we investigated the ability of free-flow electrophoresis to resolve and fractionate complex peptide mixtures and also the effectiveness of using peptide isoelectric point in conjunction with peptide match probability scoring in sequence database searching. As a model system for this study, we analyzed a chromatin-enriched fraction from the yeast Saccharomyces cerevisiae. This mixture was fractionated using preparative isoelectric focusing by free-flow electrophoresis, followed by online capillary liquid chromatography electrospray tandem mass spectrometry and sequence database searching. Our results demonstrate that (1) FFE effectively resolves and fractionates complex peptide mixtures on the basis of peptide isoelectric point and (2) the introduction of peptide pI is effective in minimizing both false positive and false negative sequence matches in sequence database searching of tandem mass spectrometry data.

An alternative to tandem mass spectrometry: isoelectric point and accurate mass for the identification of peptides.

The traditional approach to the identification of peptides in complex biological samples integrally involves the use of tandem mass spectrometry to generate a unique fragmentation pattern in order to accurately assign its identity to a particular protein. In this article we describe the theoretical basis for a new paradigm for the identification of peptides and proteins. This methodology employs the use of accurate mass and peptide isoelectric point (pI) as identification criteria, and represents a change in focus from current tandem mass spectrometry-dominated approaches. A mathematical derivation of the false positive rate associated with accurate mass and pI measurements is presented to demonstrate the utility of the technique. The equations for calculation of the experimental false positive rate allow for the determination of the validity of the data. The false positive rate issue examined in detail here is not restricted to accurate mass-based approaches, but also has application to the tandem mass spectrometry community as well. The theoretical proteomes of Escherichia coli and Rattus norvegicus are used to evaluate the efficacy of this approach. The power of the technique is demonstrated by analyzing a series of peptides with the same monoisotopic masses but with differing isoelectric points. Finally, the speed of algorithm when combined with the experimental peptide analysis has the potential to rapidly accelerate the protein identification process.

Gel based isoelectric focusing of peptides and the utility of isoelectric point in protein identification.

Here we present the theoretical and experimental evaluation of peptide isoelectric point as a method to aid in the identification of peptides from complex mixtures. Predicted pI values were found to match closely the experimentally obtained data, resulting in the development of a unique filter that lowers the effective false positive rate for peptide identification. Due to the reduction of the false positive rate, the cross-correlation parameters Xcorr and deltaCn from the SEQUEST program can be lowered resulting in 25% more peptide identifications. This approach was successfully applied to analysis of the soluble fraction of the E. coli proteome, where 417 proteins were identified from 1022 peptides using just 20 microg of material.

Estimation of isoelectric points of human plasma proteins employing capillary isoelectric focusing and peptide isoelectric point markers.

Synthetic UV-detectable peptide pI markers were used to estimate isoelectric point (pI) values of proteins separated by capillary isoelectric focusing (CIEF) followed by cathodic mobilization in the absence of denaturing agents. The pI calculation and quantitative analysis of purified proteins showed the feasibility of these peptides as pI markers and internal standards in CIEF separation of proteins. Estimation of pI values of major proteins in human plasma was performed using the peptide pI markers, and the values were compared with those previously obtained by gel isoelectric focusing (IEF). Sera of immunoglobulin G (IgG) myeloma patients, which showed characteristic peaks of myeloma IgG in their CIEF patterns, were also subjected to the analysis and the pI values of the myeloma proteins have been estimated.

A Graphical Approach to Determine the Isoelectric Point and Charge of Small Peptides from pH 0 to 14

The knowledge of a peptide's isoelectric point (pI ) value and its charge value from pH 0 to 14 is of great importance in biology and medicine. Many separation and purification techniques and medic...

High-efficiency capillary isoelectric focusing of peptides.

Several approaches are presently being developed for global proteome characterization that are based upon the analysis of polypeptide mixtures resulting from digestion of (often complex) mixtures of proteins. Improved methods for peptide analysis are needed that provide for sample concentration, higher resolution separations, and direct compatibility with mass spectrometry. In this work, methods for the high-efficiency capillary isoelectric focusing (CIEF) separation of peptides have been developed that provide for simultaneous sample concentration and separation according to peptide isoelectric point. Under typical nondenaturing CIEF conditions, peptides are concentrated approximately 500-fold, and peptides present at < 1 ng/ microL were detectable using conventional UV detection. CIEF separations of peptides provided much faster measurements of isoelectric points compared with conventional isoelectric focusing in gels. Very small differences in peptide isoelectric points (deltapI approximately 0.01) could be resolved, High-efficiency CIEF separations for complex peptide mixtures from tryptic digestion of yeast cytosol fractions were obtained and showed significant improvement over those obtained using capillary zone electrophoresis and packed capillary reversed-phase liquid chromatography.

Micellar electrokinetic chromatographic study of the interaction between enkephalin peptide analogs and charged micelles.

The relative hydrophobicity/hydrophilicity of the pentapeptides leucine enkephalin (LE), methionine enkephalin (ME) and five analogs, differing in their uncharged side chain and/or chirality, was investigated by micellar electrokinetic capillary chromatography (MEKC) employing anionic and cationic surfactants. The effect of sodium dodecyl sulfate (SDS) concentration on peptide mobility was studied at pH 8.8, a value that is well above the peptide isoelectric point, to minimize electrostatic interaction with the anionic micelles. Similarly, the effect of cetyltrimethylammonium bromide (CTAB) cationic micelles on peptide migration was studied at pH 4.1. The migration order from MEKC experiments was compared to the peptide hydrophobicity calculated from reversed-phase HPLC-derived hydrophobicity coefficients. Although relative peptide hydrophobicity was, in general, positively correlated with effective electrophoretic mobility, a tryptophan-containing analog showed only weak interaction with micelles compared to the less hydrophobic peptides. The enkephalins studied were zwitterionic in character from pH 3 to 8, and their migration as a function of pH under MEKC conditions demonstrated that electrostatic forces were at least as important as hydrophobic interactions in pentapeptide-micelle complexation.