Hydrophobic high-performance liquid chromatography of hormonal polypeptides and proteins on alkylsilane-bonded silica

Peptide retention prediction using hydrophilic interaction liquid chromatography coupled to mass spectrometry

A model that predicts retention for peptides using a HALO® penta-HILIC column and gradient elution was created. Coefficients for each amino acid were derived using linear regression analysis and these coefficients can be summed to predict the retention of peptides. This model has a high correlation between experimental and predicted retention times (0.946), which is on par with previous RP and HILIC models. External validation of the model was performed using a set of H. pylori samples on the same LC-MS system used to create the model, and the deviation from actual to predicted times was low. Apart from amino acid composition, length and location of amino acid residues on a peptide were examined and two site-specific corrections for hydrophobic residues at the N-terminus as well as hydrophobic residues one spot over from the N-terminus were created.

Influence of degree of hydrolysis on functional properties and angiotensin I-converting enzyme-inhibitory activity of protein hydrolysates from cuttlefish (Sepia officinalis) by-products

BACKGROUND

In Tunisia the cuttlefish-processing industry generates large amounts of solid wastes. These wastes, which may represent 35% of the original material and constitute an important source of proteins, are discarded without any attempt at recovery. This paper describes some functional properties and the angiotensin I-converting enzyme (ACE)-inhibitory activity of protein hydrolysates prepared by hydrolysis of cuttlefish (Sepia officinalis) by-products with crude enzyme extract from Bacillus licheniformis NH1.

RESULTS

Cuttlefish by-product protein hydrolysates (CPHs) with different degrees of hydrolysis (DH 5, 10 and 13.5%) were prepared. All CPHs contained 750-790 g kg(-1) proteins. Solubility, emulsifying capacity and water-holding capacity increased while fat absorption and foaming capacity decreased with increasing DH. All hydrolysates showed greater fat absorption than the water-soluble fraction from undigested cuttlefish by-product proteins and casein. CPHs were also analysed for their ACE-inhibitory activity. CPH3 (DH 13.5%) displayed the highest ACE inhibition (79%), with an IC(50) value of 1 mg mL(-1).

CONCLUSION

Hydrolysis of cuttlefish by-product proteins with alkaline proteases from B. licheniformis resulted in a product with excellent solubility over a wide pH range and high ACE-inhibitory activity. This study suggests that CPHs could be utilised to develop functional foods for prevention of hypertension.

Informatics for peptide retention properties in proteomic LC-MS

Retention times in HPLC yield valuable information for the identification of various analytes and the prediction of peptide retention is useful for the identification of peptides/proteins in LC-MS-based proteomics. Informatics methods such as artificial neural networks and support vector machines capable of solving nonlinear problems made possible the accurate modeling of quantitative structure-retention relationships of peptides (including large polymers) up to 5 kDa to which classical linear models cannot be applied, as well as the proteome-wide prediction of peptide retention. Proteome-wide retention prediction and accurate mass-information facilitate the identification of peptides in complex proteomic samples. In this review, we address recent developments in solid informatics methods and their application to peptide-retention properties in 'bottom-up' shotgun proteomics. We also describe future prospects for the standardization and application of retention times.

Elution mechanism of polypeptides in reversed-phase liquid chromatography based on the critical threshold of organic solvent to induce abrupt change in adsorption capacity to the column packing

Adsorption capacity of polypeptides to the column packing in a solution containing multiple organic solvents was found to be expressed by means of an fn value, which is the sum of the ratios of the content of each organic solvent in the solution to the critical content of each organic solvent to cause abrupt change in the adsorption capacity, and to change abruptly at the point where the fn value becomes 1. Additionally, our results indicate that each polypeptide is eluted by the eluent containing a specific organic solvent content regardless of gradient elution rate in reversed-phase liquid chromatography, and that total organic solvent content in the eluent containing polypeptides is equal to the critical content. Considering the power law relationship between the retention times and the gradient elution rates, our results suggest that the elution of each polypeptide in reversed-phase liquid chromatography is mainly controlled by abrupt change in the adsorption capacity induced by change in the organic solvent content of the eluent during a gradient elution process, and that the abrupt change repeats across the critical threshold while a polypeptide moves through the column, and as a result, each polypeptide is concentrated in the eluent with the critical threshold.

Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information

We describe an improved artificial neural network (ANN)-based method for predicting peptide retention times in reversed-phase liquid chromatography. In addition to the peptide amino acid composition, this study investigated several other peptide descriptors to improve the predictive capability, such as peptide length, sequence, hydrophobicity and hydrophobic moment, and nearest-neighbor amino acid, as well as peptide predicted structural configurations (i.e., helix, sheet, coil). An ANN architecture that consisted of 1052 input nodes, 24 hidden nodes, and 1 output node was used to fully consider the amino acid residue sequence in each peptide. The network was trained using approximately 345,000 nonredundant peptides identified from a total of 12,059 LC-MS/MS analyses of more than 20 different organisms, and the predictive capability of the model was tested using 1303 confidently identified peptides that were not included in the training set. The model demonstrated an average elution time precision of approximately 1.5% and was able to distinguish among isomeric peptides based upon the inclusion of peptide sequence information. The prediction power represents a significant improvement over our earlier report (Petritis, K.; Kangas, L. J.; Ferguson, P. L.; Anderson, G. A.; Pasa-Tolic, L.; Lipton, M. S.; Auberry, K. J.; Strittmatter, E. F.; Shen, Y.; Zhao, R.; Smith, R. D. Anal. Chem. 2003, 75, 1039-1048) and other previously reported models.

Proteomics based on high-efficiency capillary separations

Identifying and quantifying in a high throughput manner the proteins expressed by cells, tissues or an organism provides the basis for understanding the functions of its constituents at a "systems" level. As a result, proteome analysis has increasingly become the focus of significant interest and research over the past decade. This is especially true following the recent stunning achievements in genomics analyses. However, unlike the static genome, the complexities and dynamism of the proteome present significant analytical challenges and demand highly efficient separations and detection technologies. A number of recent technological advancements have been in direct response to these challenges. Currently, strategically mated combinations of sophisticated separations techniques and advanced mass spectrometric detection represent the best approach to addressing the intricacies of the proteome. Liquid-phase separations, often within capillaries, are increasingly recognized as the best separations technique for this approach. In combination on-line with mass spectrometry, liquid-phase separations provide the improved analytical sensitivity, sample throughput, and quantitation capabilities necessitated by the multifaceted problems within proteomics analyses. This review focuses primarily on current high-efficiency capillary separations techniques, including both capillary liquid chromatography and capillary electrophoresis, applied to the analysis of complex proteomic samples. We emphasize developments at our laboratory and illustrate technical advances that attempt to review the role of separations within the broader context of a state-of-the-art integrated proteomics effort.

Boundary between Protein and Peptide Shown by Their Chromatographic Behavior

It has previously been pointed out that two different mechanisms exist in the reversed-phase (RP) HPLC of polypeptides, including proteins. We systematically investigated the separation of various peptides and proteins over a wide range of molecular weight using a nonporous octadecylsilyl (ODS) silica-gel column to provide a precise explanation for the separation mechanism of polypeptides, including proteins in RP-HPLC. As a result, we clarified that a critical point between a typical reversed-phase partition mode applicable to small peptides (molecular weight < 3000) and a characteristic elution mode applicable to proteins is in the vicinity of the molecular weight of 3500-4500. We also proposed a new concept, the "Transitional Desorption Mode", as a separation mechanism that can precisely explain the RP-LC separation of a wide range of polypeptides including proteins.

Possibilities of replacing and reducing animal tests in the pharmacopoeias: an evaluation of unused methods and proposals for change

The animal tests currently carried out according to the German and European pharmacopoeias are evaluated. The routine testing of biological medicines, excluding vaccines and pyrogen tests, is examined. The opportunities for replacing obligatory bioassays and safety tests are assessed, taking into account both pharmaceutical quality and animal welfare aspects. The aim is to encourage institutions, public authorities, and the pharmaceutical industry to investigate the importance and the necessity of the remaining tests. In addition, all parties should be encouraged to initiate integrated projects to develop, validate and establish alternative methods.

Calculation of peptide retention coefficients in normal-phase liquid chromatography

The retention of 121 peptides was studied on a TSK Amide-80 column using solutions containing 0.1% trifluoroacetic acid and an increasing linear gradient of water in acetonitrile. The contribution of each residue to retention was calculated by linear multiple regression analysis. This paper described the contribution values 'hydrophilicity retention coefficients'. The result is an index of hydrophilicity retention coefficients for normal-phase liquid chromatography, analogous to the hydrophobicity indices calculated for the reversed-phase liquid chromatography. The order of residues in the index of one mode was substantially the inverse of the others'. Using the new hydrophilicity retention coefficients, retention times could be predicted for peptides of known amino acid content and sequence.

Reversed-phase liquid chromatography on a microspherical carbon column at high temperature

The chromatographic conditions for the use of a spherical carbon column at high temperatures up to 160 degrees C are described. The column heating system and the eluate cooling system are also described. Under the conditions studied, it was found that the carbon column at elevated temperature was stable and could be applicable to any compounds that are durable under these conditions. The peptide bonds at this high temperature and at this acidity were still stable enough for analysis, but the indole residues showed poor stability.

Peptide chemistry: development of high performance liquid chromatography and capillary zone electrophoresis

The development of relatively non-compressible supporting media of small particle size as well as pumps that deliver constant flow rates at high pressures has enabled investigators to perform rapid, high resolution liquid chromatography for more than two decades. Studies initiated in this laboratory in 1975, evaluating the compatibility of unprotected peptides with commercially available chromatographic supports and development of solvent systems ultimately led to separations not previously observed with both synthetic peptides and native peptides from tissue extracts. It was rapidly realized however, that recovery of certain molecules could be problematic. To meet the challenges presented by the isolation of natural hormones (such as corticotropin releasing factor and growth hormone releasing hormone) and proteins (such as inhibin and activin) and the need for large quantities of highly purified peptides for clinical investigations, our group invested heavily in identifying new supports (high carbon loading and 300 A pore sizes) and solvent systems (triethylammonium phosphate and trifluoroacetic acid) compatible with reverse phase, size exclusion and ion exchange chromatographies from a practical and economical perspective. More recently, we have contributed to the identification of unusual buffer systems (inclusive of organic modifiers) compatible with capillary zone electrophoresis that will both modulate the capillaries' selectivity, increase resolution and serve as an orthogonal approach to determining peptide purity. From a pragmatic point of view, in this paper we highlight the original and timely contributions (technical and strategical) of this laboratory in the field of analytical and preparative high performance liquid chromatography and capillary zone electrophoresis of synthetic and native biologically active peptides and proteins over the past twenty years.

Aqueous stability of human epidermal growth factor 1-48

Human epidermal growth factor 1-48 (hEGF 1-48, Des(49-53)hEGF) is a single chain polypeptide (48 amino acids; 3 disulfide bonds; 5445 Da) possessing a broad spectrum of biologic activity including the stimulation of cell proliferation and tissue growth. In this study, three primary aqueous degradation products of hEGF 1-48 were isolated using isocratic, reverse phase/ion-pair HPLC. The degradation products were characterized using amino acid sequencing, electrospray ionization mass spectrometry, isoelectric focusing, and degradation kinetics. Results indicate that hEGF 1-48 degrades via oxidation (Met21), deamidation (Asn1), and succinimide formation (Asp11). The relative contribution of each degradation pathway to the overall stability of hEGF 1-48 changes as a function of solution pH and storage condition. Succinimide formation at Asp11 is favored at pH < 6 in which aspartic acid is present mostly in its protonated form. Deamidation of Asn1 is favored at pH > 6. The relative contribution of Met21 oxidation is increased with decreasing temperature, storage as a frozen solution (-20 degrees C), and exposure to fluorescent light.

Preparative isolation of recombinant human insulin-like growth factor 1 by reversed-phase high-performance liquid chromatography

The isolation of recombinant human insulin-like growth factor 1 (rhIGF-1) is complicated by the presence of several rhIGF-1 variants which co-purify using conventional chromatographic media. These species consist primarily of a methionine-sulfoxide variant of the properly folded molecule and a misfolded form and its respective methionine-sulfoxide variant. An analytical reversed-phase high-performance liquid chromatography procedure using a 5-micron C18 column, an acetonitrile-trifluoroacetic acid (TFA) isocratic elution, and elevated temperature gives baseline resolution of the four species. Using this analytical method as a development tool, a process-scale chromatography step was established. The 5-micron analytical packing material was replaced with a larger-size particle to reduce back-pressure and cost. Since the TFA counter-ion binds tightly to proteins and is difficult to subsequently dissociate, a combination of acetic acid and NaCl was substituted. Isocratic separations are not good process options due to problems with reproducibility and control. A shallow gradient elution using premixed mobile phase buffers at the same linear velocity was found to give an equivalent separation at low load levels and minimized solvent degassing. However, at higher loading there was a loss of resolution. A matrix of various buffers was evaluated for their effects on separation. Elevated pH resulted in a significant shift in both the elution order and relative retention times of the principal rh-IGF-1 variants, resulting in a substantial increase in effective capacity. An increase in the ionic strength further improved resolution. Several different media were evaluated with regard to particle size, shape and pore diameter using the improved mobile phase. The new conditions were scaled up 1305-fold and resulted in superimposable chromatograms, 96% recovery and > 99% purity. Thus, by optimizing the pH, ionic strength and temperature, a high-capacity preparative separation of rhIGF-1 from its related fermentation variants was obtained.

Structural characterisation of native and recombinant forms of the neurotrophic cytokine MK

The retinoic acid (RA)-inducible midkine (MK) gene encodes a heparin-binding protein which can induce neurite outgrowth in cultured mammalian embryonic brain cells. This cytokine shares 65% amino acid sequence identity with another RA-inducible cytokine, pleiotropin (PTN). Both proteins contain 10 conserved cysteine residues, all of which appear to be disulphide linked. MK and PTN are also rich in lysine and arginine residues rendering them susceptible to proteolysis during purification, and making large-scale preparation of these molecules inherently difficult. Recombinant MK has been expressed as a fusion protein using a pGEX vector transfected into E. coli. To enable refolding of MK, the fusion protein was stored in solution at 4 degrees C for 14 days in the presence of dithiothreitol (DTT). Thrombin cleavage of the fusion protein, post storage, typically generated 5 mg of MK per litre of bacterial pellet. To establish the structural integrity of the recombinant product, we have analysed the refolding kinetics and compared the disulphide bond assignment of recombinant MK with that of native MK and native PTN. The synergistic use of micropreparative HPLC, to separate and recover in small eluant volumes enzymatically derived peptide fragments, with matrix assisted laser desorption mass spectrometry (MALD-MS) and N-terminal sequence analysis has allowed the unambiguous identification of the disulphide bonded fragments of native and recombinant MK. The disulphide bond assignment of MK is C12-C36, C20-C45, C27-C49, C59-C91 and C69-C101, and is equivalent to that of PTN.

Implementation and use of gradient predictions for optimization of reversed-phase liquid chromatography of peptides. Practical considerations

The options in the implementation of gradient theory for optimization work are critically reviewed and evaluated for the case of the reversed-phase liquid chromatography of peptides. Various models are covered together with methods for the determination of model parameters. Approaches for calculating retention times and band widths from experimental data are discussed. Different kinds of extrapolation are compared with interpolation. This study was aimed at finding the best compromise between number of experiments, accuracy of predictions and simplicity of calculations. Implementation and the use of gradient predictions can be simple, and practical recommendations are given.

Reversed-phase chromatographic behaviour of beta-endorphin: evidence of conformational change

The effect of alteration in isocratic mobile phase constituents, composition of sample solution, flow-rate and column temperature on the reversed-phase chromatographic behaviour of beta-endorphin was investigated. Beta-Endorphin was shown to be particularly sensitive to the concentration of organic modifier within the mobile phase. The relative contact area of beta-endorphin was demonstrated to be less than that of the much smaller molecule, gamma-endorphin, indicating that beta-endorphin is in a folded form under the mobile phase conditions utilised. Buffer molarity and pH were implicated in the conformational transition of beta-endorphin. In addition, the micro-environment of beta-endorphin prior to its injection onto the high-performance liquid chromatographic (HPLC) column is crucial to its chromatographic behaviour. Manipulation of the sample solvent environment produced reversible conformational modifications ultimately resulting in asymmetric and even split peaks. This phenomenon was more clearly seen when altering HPLC flow-rate. Elevation of HPLC column temperature provided additional evidence of structural change in beta-endorphin, with further conformational forms of this molecule being observed at higher temperatures. This work suggests that the chromatography of beta-endorphin involves a complex mechanism of separation which cannot be adequately explained by the two-state model of kinetic processes.

Purification and characterization of three molecular forms of insulin-like growth factor II from human Cohn paste IV

The somatomedins or insulin-like growth factors (IGFs) are a family of peptides present in human serum. They are bound to specific carrier proteins and are thought to mediate growth-promoting actions of human growth hormone. Starting from Cohn fraction IV of human plasma, we describe here a rapid and highly efficient procedure for the purification to homogeneity, in addition to IGF I. of three forms of insulin-like growth factor II: IGF IIA (10-12 kDa), IGF IIB (the "classical" 7.5 kDa IGF II) and IGF IIC, identified as the IGF II variant of Jansen by fast-atom bombardment mass spectrometry. The procedure is based on ion-exchange chromatography and gel permeation chromatography on Biogel P10. As judged by specific radioimmunoassay methods for IGF I and IGF II, one of the most striking advantages of this process at this stage is the yield of IGF I not contaminated by 7.5 kDa IGF II. Isoelectric focusing or chromatofocusing, which require affinity chromatography to separate proteins from the polybuffers, are not necessary in this procedure. Final purification was directly achieved by preparative, followed by analytical high-performance liquid chromatography. The N-terminal sequence of peptide IGF IIB (39 amino acids) and peptide IGF I (29 amino acids) showed total homology with those previously described by Rinderknecht and Humbel [FEBS Lett., 89 (1978) 283]. The final yields of purified human IGF I and IGF IIB were 15 and 25 micrograms, respectively, from 11 of serum. All peptides interact with specific receptors on human lymphocytes and red blood cells, and are biologically active (stimulation of 35S uptake, increasing [3H]thymidine incorporation in human and chick embryo fibroblasts).