High-performance liquid chromatography of biopolymers

Origins, Technological Advancement, and Applications of Peptidomics

Peptidomics is the comprehensive characterization of peptides from biological sources instead of heading for a few single peptides in former peptide research. Mass spectrometry allows to detect a multitude of peptides in complex mixtures and thus enables new strategies leading to peptidomics. The term was established in the year 2001, and up to now, this new field has grown to over 3000 publications. Analytical techniques originally developed for fast and comprehensive analysis of peptides in proteomics were specifically adjusted for peptidomics. Although it is thus closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. Fundamental technological advancements of peptidomics since have occurred in mass spectrometry and data processing, including quantification, and more slightly in separation technology. Different strategies and diverse sources of peptidomes are mentioned by numerous applications, such as discovery of neuropeptides and other bioactive peptides, including the use of biochemical assays. Furthermore, food and plant peptidomics are introduced similarly. Additionally, applications with a clinical focus are included, comprising biomarker discovery as well as immunopeptidomics. This overview extensively reviews recent methods, strategies, and applications including links to all other chapters of this book.

Ultra-short columns for the chromatographic analysis of large molecules

Today, reverse phase liquid chromatography (RPLC) analysis of proteins is almost exclusively performed on conventional columns (100-150 mm) in gradient elution mode. However, it was shown many years ago that large molecules present an on/off retention mechanism, and that only a very short inlet segment of the chromatographic column retains effectively the large molecules. Much shorter columns - like only a few centimetres or even a few millimetres - can therefore be used to efficiently analyse such macromolecules. The aim of this review is to summarise the historical and more recent works related to the use of very short columns for the analysis of model and therapeutic proteins. To this end, we have outlined the theoretical concepts behind the use of short columns, as well as the instrumental limitations and potential applications. Finally, we have shown that these very short columns were also possibly interesting for other chromatographic modes, such as ion exchange chromatography (IEX), hydrophilic interaction chromatography (HILIC) or hydrophobic interaction chromatography (HIC), as analyses in these chromatographic modes are performed in gradient elution mode.

Leveraging Parameter Dependencies in High-Field Asymmetric Waveform Ion-Mobility Spectrometry and Size Exclusion Chromatography for Proteome-wide Cross-Linking Mass Spectrometry

Ion-mobility spectrometry shows great promise to tackle analytically challenging research questions by adding another separation dimension to liquid chromatography-mass spectrometry. The understanding of how analyte properties influence ion mobility has increased through recent studies, but no clear rationale for the design of customized experimental settings has emerged. Here, we leverage machine learning to deepen our understanding of field asymmetric waveform ion-mobility spectrometry for the analysis of cross-linked peptides. Knowing that predominantly m/z and then the size and charge state of an analyte influence the separation, we found ideal compensation voltages correlating with the size exclusion chromatography fraction number. The effect of this relationship on the analytical depth can be substantial as exploiting it allowed us to almost double unique residue pair detections in a proteome-wide cross-linking experiment. Other applications involving liquid- and gas-phase separation may also benefit from considering such parameter dependencies.

Improving the Extraction of Active Ingredients from Medicinal Plants by XynA Modification

Active ingredients of medicinal plants have unique pharmacological and clinical effects. However, conventional extraction technology has many disadvantages, such as long-time and low-efficiency. XynA-assisted extraction may overcome such problems, since the plant cell wall is mainly composed of cellulose. Based on the three-dimensional protein structure, we found the C-terminal domain and N-terminal domain twisted together and resulted in more flexibility. We carried out a series of truncations, with XynA_ΔN36 getting more yields of active ingredients. As shown by HPLC analysis, the efficiencies for extraction of salvianic acid A and berberine from Salvia miltiorrhiza and Phellodendron chinense were increased by approximately 38.14% and 35.20%, respectively, compared with the conventional extraction protocol. The yields of the two compounds reached 2.84 ± 0.05 mg g−1 and 3.52 ± 0.14 mg g−1, respectively. Above all, XynA_ΔN36 can be applied to the extraction of salvianic acid A and berberine, and this study provides a novel enzyme for the extraction technology, which aids rational utilization and quality control of medicinal plants.

Review on analytical studies of some pharmaceutical compounds containing heterocyclic rings: brinzolamide, timolol maleate, flumethasone pivalate, and clioquinol

Background

The heterocyclic compounds are extremely important with wide array of synthetic, pharmaceutical, and industrial applications. Heterocyclic-containing compounds have been reported for their broad spectrum of biological activities including antibacterial, antifungal, antiviral, antiprotozoal, and anthelmintic activity.

Main text

Several techniques have been used for the quantitation of heterocyclic compounds in pharmaceutical samples such as high-performance liquid chromatography (HPLC) either equipped with UV-visible or fluorescence, in addition to liquid chromatography-mass spectroscopy, UV-visible spectrophotometry, and electrochemical techniques. This article reviewed several published methods that have been applied to detect and quantify some pharmaceutical drugs containing heterocyclic compounds focusing on four drugs: brinzolamide, timolol maleate, flumethasone pivalate, and clioquinol.

Conclusion

From literature reviews, HPLC is the most widely used analytical technique for the quantitative analysis of the four selected drugs.

Origins, Technological Development, and Applications of Peptidomics

Peptidomics is the comprehensive characterization of peptides from biological sources mainly by HPLC and mass spectrometry. Mass spectrometry allows the detection of a multitude of single peptides in complex mixtures. The term first appeared in full papers in the year 2001, after over 100 years of peptide research with a main focus on one or a few specific peptides. Within the last 15 years, this new field has grown to over 1200 publications. Mass spectrometry techniques, in combination with other analytical methods, were developed for the fast and comprehensive analysis of peptides in proteomics and specifically adjusted to implement peptidomics technologies. Although peptidomics is closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. The development of peptidomics is described, including the most important implementations for its technological basis. Different strategies are covered which are applied to several important applications, such as neuropeptidomics and discovery of bioactive peptides or biomarkers. This overview includes links to all other chapters in the book as well as recent developments of separation, mass spectrometric, and data processing technologies. Additionally, some new applications in food and plant peptidomics as well as immunopeptidomics are introduced.

Methodology and Applications of Disease Biomarker Identification in Human Serum

Biomarkers are biomolecules that serve as indicators of biological and pathological processes, or physiological and pharmacological responses to a drug treatment. Because of the high abundance of albumin and heterogeneity of plasma lipoproteins and glycoproteins, biomarkers are difficult to identify in human serum. Due to the clinical significance the identification of disease biomarkers in serum holds great promise for personalized medicine, especially for disease diagnosis and prognosis. This review summarizes some common and emerging proteomics techniques utilized in the separation of serum samples and identification of disease signatures. The practical application of each protein separation or identification technique is analyzed using specific examples. Biomarkers of cancers of prostate, breast, ovary, and lung in human serum have been reviewed, as well as those of heart disease, arthritis, asthma, and cystic fibrosis. Despite the advancement of technology few biomarkers have been approved by the Food and Drug Administration for disease diagnosis and prognosis due to the complexity of structure and function of protein biomarkers and lack of high sensitivity, specificity, and reproducibility for those putative biomarkers. The combination of different types of technologies and statistical analysis may provide more effective methods to identify and validate new disease biomarkers in blood.

Removal of Pollutants from Water Using Untreated and Treated Sawdust and Water Hyacinth

Sawdust and water hyacinth are waste products which have no economical application in Egypt. They even constitute a solid waste as far as the environment is concerned. As-received sawdust and water hyacinth were treated with phosphoric acid, phosphoric acid + urea or phosphoric acid + urea + dimethylformamide. The as-received and treated samples were used for the removal of Methylene Blue, iodine, phenol and ammonia from their aqueous solutions.

The optimum conditions for the maximum adsorption of each pollutant were determined. The isotherms obtained obeyed the Freundlich and Langmuir equations in a satisfactory manner. The initial stages of adsorption follow first-order kinetics as predicted from the Lagergren equation. Sawdust and water hyacinth show promising potentialities for the removal of pollutants from water and can, at least, be used as precursors for the preparation of efficient adsorbents for the removal of pollutants from water.

Separation techniques: Chromatography

Chromatography is an important biophysical technique that enables the separation, identification, and purification of the components of a mixture for qualitative and quantitative analysis. Proteins can be purified based on characteristics such as size and shape, total charge, hydrophobic groups present on the surface, and binding capacity with the stationary phase. Four separation techniques based on molecular characteristics and interaction type use mechanisms of ion exchange, surface adsorption, partition, and size exclusion. Other chromatography techniques are based on the stationary bed, including column, thin layer, and paper chromatography. Column chromatography is one of the most common methods of protein purification.

Generalized recovery algorithm for 3D super-resolution microscopy using rotating point spread functions

Super-resolution microscopy with phase masks is a promising technique for 3D imaging and tracking. Due to the complexity of the resultant point spread functions, generalized recovery algorithms are still missing. We introduce a 3D super-resolution recovery algorithm that works for a variety of phase masks generating 3D point spread functions. A fast deconvolution process generates initial guesses, which are further refined by least squares fitting. Overfitting is suppressed using a machine learning determined threshold. Preliminary results on experimental data show that our algorithm can be used to super-localize 3D adsorption events within a porous polymer film and is useful for evaluating potential phase masks. Finally, we demonstrate that parallel computation on graphics processing units can reduce the processing time required for 3D recovery. Simulations reveal that, through desktop parallelization, the ultimate limit of real-time processing is possible. Our program is the first open source recovery program for generalized 3D recovery using rotating point spread functions.

Surface Tensions of Proteins in Aqueous Solutions

Changes in conformation of proteins in solution may be detected by determin ing the relative surface tensions of their solutions. Of the proteins examined, all of the enzymes had distinct changes in surface tensions upon going from a 3M NaCl medium to a salt-free aqueous solution. Only two of the seven non- enzymic proteins underwent detectable changes in the same cycle. These relative surface tensions could be of value in determining adsorption/elution profiles for hydrophobic interaction chromatography.

Adsorbents for Industrial Pollution Control

Adsorbent materials used for treating industrial pollutants are reviewed. The article consists of two parts. The first part considers new trends in traditional adsorbents such as activated carbons and zeolites. New low-cost adsorbents such as waste materials and clay minerals are discussed in the second part.

It has been reported that activated carbons can be obtained from agricultural by-products such as shells and stones of various fruit by a simple single-stage method. This method differs from the traditional processes for the production of activated carbons. On the other hand, natural zeolites have been used as low-cost adsorbents in industrial pollution control. The extent of their application is not only related to their low cost, but also to the improved properties and performance characteristics which they possess.

Recently, a variety of agricultural and industrial waste materials and clay minerals have been evaluated as new adsorbents with an excellent potential for the removal of different pollutants from wastewater. The new low-cost adsorbents obtained were found to have large adsorption capacities and good mechanical properties.

Two variables dominating the retention of intact proteins under gradient elution with simultaneous ultrafast high-resolution separation by hydrophobic interaction chromatography

The retention of proteins under gradient elution in HIC is dominated by two variables of steady and migration regions.

Unified superresolution experiments and stochastic theory provide mechanistic insight into protein ion-exchange adsorptive separations

Chromatographic protein separations, immunoassays, and biosensing all typically involve the adsorption of proteins to surfaces decorated with charged, hydrophobic, or affinity ligands. Despite increasingly widespread use throughout the pharmaceutical industry, mechanistic detail about the interactions of proteins with individual chromatographic adsorbent sites is available only via inference from ensemble measurements such as binding isotherms, calorimetry, and chromatography. In this work, we present the direct superresolution mapping and kinetic characterization of functional sites on ion-exchange ligands based on agarose, a support matrix routinely used in protein chromatography. By quantifying the interactions of single proteins with individual charged ligands, we demonstrate that clusters of charges are necessary to create detectable adsorption sites and that even chemically identical ligands create adsorption sites of varying kinetic properties that depend on steric availability at the interface. Additionally, we relate experimental results to the stochastic theory of chromatography. Simulated elution profiles calculated from the molecular-scale data suggest that, if it were possible to engineer uniform optimal interactions into ion-exchange systems, separation efficiencies could be improved by as much as a factor of five by deliberately exploiting clustered interactions that currently dominate the ion-exchange process only accidentally.

Preparative purification of recombinant proteins: current status and future trends

Advances in fermentation technologies have resulted in the production of increased yields of proteins of economic, biopharmaceutical, and medicinal importance. Consequently, there is an absolute requirement for the development of rapid, cost-effective methodologies which facilitate the purification of such products in the absence of contaminants, such as superfluous proteins and endotoxins. Here, we provide a comprehensive overview of a selection of key purification methodologies currently being applied in both academic and industrial settings and discuss how innovative and effective protocols such as aqueous two-phase partitioning, membrane chromatography, and high-performance tangential flow filtration may be applied independently of or in conjunction with more traditional protocols for downstream processing applications.

Insulin structure and function

Throughout much of the last century insulin served a central role in the advancement of peptide chemistry, pharmacology, cell signaling and structural biology. These discoveries have provided a steadily improved quantity and quality of life for those afflicted with diabetes. The collective work serves as a foundation for the development of insulin analogs and mimetics capable of providing more tailored therapy. Advancements in patient care have been paced by breakthroughs in core technologies, such as semisynthesis, high performance chromatography, rDNA-biosynthesis and formulation sciences. How the structural and conformational dynamics of this endocrine hormone elicit its biological response remains a vigorous area of study. Numerous insulin analogs have served to coordinate structural biology and biochemical signaling to provide a first level understanding of insulin action. The introduction of broad chemical diversity to the study of insulin has been limited by the inefficiency in total chemical synthesis, and the inherent limitations in rDNA-biosynthesis and semisynthetic approaches. The goals of continued investigation remain the delivery of insulin therapy where glycemic control is more precise and hypoglycemic liability is minimized. Additional objectives for medicinal chemists are the identification of superagonists and insulins more suitable for non-injectable delivery. The historical advancements in the synthesis of insulin analogs by multiple methods is reviewed with the specific structural elements of critical importance being highlighted. The functional refinement of this hormone as directed to improved patient care with insulin analogs of more precise pharmacology is reported.

Peptide-based Biopolymers in Biomedicine and Biotechnology

Peptides are emerging as a new class of biomaterials due to their unique chemical, physical, and biological properties. The development of peptide-based biomaterials is driven by the convergence of protein engineering and macromolecular self-assembly. This review covers the basic principles, applications, and prospects of peptide-based biomaterials. We focus on both chemically synthesized and genetically encoded peptides, including poly-amino acids, elastin-like polypeptides, silk-like polymers and other biopolymers based on repetitive peptide motifs. Applications of these engineered biomolecules in protein purification, controlled drug delivery, tissue engineering, and biosurface engineering are discussed.

Protein instability during HIC: Hydrogen exchange labeling analysis and a framework for describing mobile and stationary phase effects

Unfolding of marginally stable proteins is a significant factor in commercial application of hydrophobic interaction chromatography (HIC). In this work, hydrogen-deuterium isotope exchange labeling has been used to monitor protein unfolding on HIC media for different stationary phase hydrophobicities and as a function of ammonium sulfate concentration. Circular dichroism and Raman spectroscopy were also used to characterize the structural perturbations experienced by solution phase protein that had been exposed to media and by protein adsorbed on media. As expected, greater instability is seen on chromatographic media with greater apparent hydrophobicity. However, increased salt concentrations also led to more unfolding, despite the well-known stabilizing effect of ammonium sulfate in solution. A thermodynamic framework is proposed to account for the effects of salt on both adsorption and stability during hydrophobic chromatography. Using appropriate estimates of input quantities, analysis with the framework can explain how salt effects on stability in chromatographic systems may contrast with solution stability.

Regio-specific adsorption of cytochrome c on negatively charged surfaces

Studies are reported on the identification of the chromatographic contact domain of equine cytochrome c during its interaction with negatively charged sorbents. A negatively charged resin was designed that would simultaneously adsorb the protein electrostatically and covalently bind it through amide bond formation to succinate groups coupled to the support in an ester linkage. Protein immobilization occurred through lysine residues participating in electrostatic adsorbed cytochrome c to the resin surface. After covalent bond formation in the interface between the protein and the sorbent, ester linkages coupling succinate groups to the support were hydrolyzed, and the protein was released. Lysine residues on the protein that had participated in covalent capture were labeled with succinate residues. The tagged protein was then tryptic-mapped and the peptides were examined by matrix-assisted laser desorption ionization mass spectrometry to determine the position of the amino acids that had been tagged. Comparing the tagged sites with the X-ray crystallographic structure of cytochrome c, it was concluded that a single face of the protein dominated the adsorption process and the 3-D structure of the protein remained largely undisturbed during adsorption.

Predicting the behaviour of polydisperse polymers in liquid chromatography under isocratic and gradient conditions

In this paper we describe how the existing theories to describe retention and peak width in isocratic and gradient-elution liquid chromatography can be expanded to describe the retention behaviour of natural and synthetic repetitive polymers, which feature distributions of molecules with different masses (and often different structures) rather than unambiguous molecular formulas. For polydisperse samples, it is vital that the model accommodates (isocratic) elution of sample components before the onset of a gradient, elution during the gradient, and elution after the completion of the gradient. The expanded models can readily be implemented in standard spreadsheet software, such as Excel. We have created such spreadsheets based on the conventional model for retention in reversed-phase liquid chromatography (RPLC) and on two different models for retention in normal-phase liquid chromatography. The implementation allows an easy visualization of the theoretical concept. Up to three different polymeric series can be entered, with a total of up to 100 peaks being computed and displayed in isocratic or gradient-elution chromatograms. Also visualized are "retention models" (diagrams of isocratic retention vs. composition) and "calibration curves" (retention or elution composition vs. molecular mass or degree of polymerization). The coefficients in the isocratic retention model may be correlated, as has often been observed in RPLC. It is shown that under certain conditions such a correlation corresponds to the existence of so-called critical (isocratic) conditions, at which all the members of a given polymeric series (same composition and end groups, different number of repeat units) show co-elution.

HPLC of peptides and proteins: standard operating conditions

The standard operating conditions for the eight basic modes of HPLC are presented in this unit. They include: size-exclusion chromatography (HP-SEC), ion-exchange chromatography (HP-IEX), normal phase chromatography (HP-NPC), hydrophobic interaction chromatography (HP-HIC), reversed-phase chromatography (RP-HPLC), hydrophilic interaction chromatography (HP-HILIC), immobilized metal ion affinity chromatography (HP-IMAC), and biospecific/biomimetic affinity chromatography (HP-BAC). In addition, some subsets of these chromatographic modes, e.g., mixed mode chromatography (HP-MMC), charge transfer chromatography (HP-CTC), or ligand-exchange chromatography (HP-LEC) are described. Procedures for multimodal column switching are also included, as are guidelines for a systematic approach to method development. Example separations help illustrate the procedures. The standard operating conditions for the eight basic modes of HPLC are presented in this unit.

Determination of albumin and myoglobin in dialysate and ultrafiltrate samples by high-performance size-exclusion chromatography

A high-performance size-exclusion chromatographic method was developed, validated and implemented for simultaneous and quantitative determination of albumin and myoglobin along with inulin, vancomycin and creatinine in dialysate and ultrafiltrate samples from in vitro hemodialysis experiments. The experimental parameters including mobile phase pH, ionic strength, detection wavelength, flow-rate, injection volume were first optimized for the determination of albumin, myoglobin, inulin, vancomycin and creatinine. The peak height ratio and detection limits of the proteins were then comparatively studied at 210, 254 and 280 nm by UV and diode array detection. The method was further validated by evaluating the linearity, precision and accuracy of the proteins. The assay was finally implemented to the simultaneous and quantitative determination of the proteins in dialysate and ultrafiltrate samples.

Synthesis and characterization of new zirconia-based polymeric cation-exchange stationary phases for high-performance liquid chromatography of proteins

Ion-exchange chromatography is a major method used for large-scale protein separations. New zirconia-based polymeric cation-exchange HPLC stationary phases have been developed for protein separations. Two routes were employed for the synthesis. In one method, polyethyleneimine (PEI) was adsorbed onto porous zirconia particles and cross-linked with 1,4-butanediol diglycidyl ether (BUDGE). Succinic anhydride was then reacted with the remaining primary and secondary amine groups on PEI to afford anionic functionalities. The second method utilizes poly(acrylic acid) anhydride as both the crosslinker and the stationary phase. The resulting stationary phases act to separate proteins by a weak cation-exchange mechanism with a slight contribution to retention from hydrophobic interactions. In the presence of 20 mM phosphate buffer, Lewis acid/base interactions between the zirconia support and the proteins, which can significantly broaden the peaks, are sufficiently suppressed. The effects of ionic strength, mobile phase pH, and salt type are discussed. Protein mass recovery and loading capacity for protein separations on these phases have been evaluated. These weak cation-exchange stationary phases exhibit good stability under normal separation conditions for months and are stable in alkaline solution up to pH 10. In contrast to zirconia supports modified with small anionic species, these new phases have no limitation on the type of salt used as the eluent, and they exhibit unique selectivities. Therefore, they offer interesting alternatives for protein separations. To our knowledge, this work represents the first successful example of protein separations using porous zirconia-based polymeric phases under normal chromatographic conditions, which will definitely help make zirconia-based supports more useful for bio-separation.

Importance of heat of adsorption in modeling protein equilibria for overloaded chromatography

The heat of adsorption and its dependence on surface coverage has been measured calorimetrically for protein ion-exchange systems of bovine serum albumin and ovalbumin on an anion-exchanger. Experimental data show that protein adsorption is endothermic for both systems which suggests that the process is entropically driven. Also, heat of adsorption decreased with coverage indicating repulsive lateral interactions between adsorbed proteins. The protein adsorption isotherms were modeled with the nonideal surface solution model. This analysis revealed that it is essential to include the entropic contribution in modeling equilibrium behavior. An empirical method for incorporating this effect has been presented.

Low-molecular-weight displacers for high-resolution protein separations

The resolving power of displacement chromatography using low-molecular-weight displacers was investigated using a model mixture containing bovine and horse heart cytochrome c. The linear and nonlinear adsorption behavior of these two proteins was examined in cation-exchange chromatography and shown to be quite similar. Furthermore, an analysis of the dynamic affinity of these proteins indicated extremely similar affinities under displacement conditions. Despite the extreme similarities in the adsorption behavior, displacement chromatography using a protected amino acid displacer resulted in excellent separation of the proteins with both high yields and purity. These results indicate that displacement chromatography may be efficacious for a wide variety of difficult protein separation problems.