Ion-exchange displacement chromatography of proteins, using narrow-range carboxymethyldextrans and a new index of affinity

A new method of characterizing carboxymethyldextrans with respect to their relative affinities for an anion exchanger can be applied not only to pure preparations but also to fractions of a displacement chromatogram in which these polyanions have been used as spacers. This, along with the development of a means of preparing carboxymethyldextrans with narrow ranges of affinity, as contrasted with the very heterogeneous preparations previously used, has greatly facilitated the focusing of resolving power on critical regions of the chromatogram. The effectiveness of this approach is illustrated by the separation of proteins that differ only slightly in affinity, using the genetic variants of beta-lactoglobulin as one model and the numerous components of purified ovalbumin as another.     

Amino acid spacing in isotachophoresi; on polyacrylamide gel: a critical evaluation.

Isotachophoresis of colored model proteins was carried out on polyacrylamide gel, using the stack of a multiphasic buffer system computed on the basis of the Jovin theory and operative at pH 10.4. The stack was elongated by milligram loads of various amino acids per analytical gel. The extent of the stack was determined by chemical localization of the leading and trailing constituents. The isotachophoretic nature of the stack was ascertained by determining the positions of all protein specles under study as intermediate between the leading and trailing constituents. The shallow pH gradient across the extended stack was measured. Spacing of proteins in isotachophoresis is restricted, with regard to constituent multiplicity and constituent load, by the practical limitations of electrophoresis time and gel length. Therefore, spacing by a small number of constituents at relatively low loads was attempted. Amino acids were chosen as spacers because they can be selected conveniently, in radioactively labeled form, for the specific separation between pairs of proteins with particular mobilities. In the particular buffer system used, lysine, histidine, serine, and threonine were found to be effective spacers between bovine serum albumin (BSA) and hemoglobins, while no amino acids effectively spaced between hemoglobins A and S. It is concluded that specific spacing in isotachophoresis on polyacrylamide gel (ITPPA) can be useful in improving resolution. However, in practice, few spacers exist in the mobility range of proteins, the positions of which relative to specific proteins could be convenlently located on the basis of isotope analysis or other assays. Mixtures of multiple spacers with undefined mobilities appear applicable as “blind spacers” only at concentrations so low that their effectiveness is annulled.     

The use of poly(2-acrylamido-2-methyl-1-propanesulfonic acid) polymers as spacers for isotachophoresis in sieving gel matrices

The electric field strength gradients generated in isotachophoresis (ITP) may be used for the separation of biomolecules. Poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (polyAMPS) polymers of a uniform distribution of molecular mass were synthesized and used as novel spacers in ITP. Since these polymeric spacers are strongly acidic species, their ionic charges remain constant over a wide pH range, so that their ionic mobilities are governed solely by their molecular masses and not by the pH of the milieu. A modification of ITP known as telescope electrophoresis was used to separate a number of acidic dyes of varying ionic mobility, using polyAMPS polymers as spacers. The resolution obtained was superior to that obtained by polyacrylamide gel electrophoresis (PAGE), due to the focusing effect of the electric field strength gradient. Since these novel polymeric spacers are designed to operate within sieving medium, it was decided to test their suitability for the separation of DNA molecules. DNA molecules up to 1000 bp long were successfully resolved, with a similar resolution to that obtained with conventional PAGE.     

Preparative displacement electrophoresis (isotachophoresis) of proteins on cellulose columns

This paper describes the separation of proteins by displacement electrophoresis on columns packed with cellulose powder as a stabilizing medium. Cellulose has virtually no molecular sieving properties and thus differs from dextran, polyacrylamide, and agarose in this respect. Therefore, without the risk of unstacking, columns packed with cellulose permit conventional elution of the protein zones and the use of a counter flow (to increase the effective length of the bed). For the same reason, electroosmotic flow is less disturbing. A continuous elution-migration technique adapted to suit the special requirements of displacement electrophoresis gave better separation than was obtainable by conventional elution. Normal human serum and a fresh hemolysate from human erythrocytes were used as samples. An expression for the volume velocity of the boundaries is derived. This parameter can be used to determine the maximum duration of a run and a suitable pump speed when continuous elution or a counter flow is employed. The special advantages of displacement electrophoresis in cellulose beds are discussed as well as general disadvantages of the displacement technique, including the risk that proteins precipitate during a run.     

Bifunctional adsorbents for hydrophobic displacement chromatography of proteins

The separation of pancreatic trypsinogen and alpha-chymochypsinogen A by displacement chromatography was tested on a bifunctional adsorbent containing both butyl and carboxymethyl groups. Methacrylic triblock copolymer was synthesized and used as the displacer. Compared to the displacement results on commercial Butyl-Sepharose, it was found that both the separation and recovery of trypsinogen and alpha-chymochypsinogen A were improved. Adsorption isotherms of proteins were measured on both the commercial Butyl-Sepharose and the synthesized bifunctional adsorbents. It was found that the improvement of protein separation on bifunctional adsorbents was attributed to the alteration of the adsorption of trypsinogen. Charge repulsion between trypsinogen and the negatively charged carboxymethyl groups may account for the alteration. In addition, taking advantage of the effect of charge repulsion, the column regeneration became much easier on the column packed with bifunctional adsorbents.     

Comparison of particulate and continuous-bed columns for protein displacement chromatography

A conventional anion exchange column packed with porous particles (BioScale Q2), and a novel continuous-bed column (UNO Q1) were compared for displacement separation of dairy whey proteins with polyacrylic acid as displacer. The steric mass action model was investigated as a means to aid and accelerate this development. Characteristic charges and steric factors were measured for the proteins and the displacer according to the model, and used together with the affinity constant derived from the adsorption isotherms for simulations, as well as for the construction of the affinity and operating regime plots. If possible, the latter two were used to select conditions for the actual experiments. In the case of the particle-based column, experimental results and simulations did not agree. In addition, the operating regime plot could not be constructed. The affinity plot did predict the order in the displacement train correctly, but gave misleading information concerning the possible effect of a change in displacer concentration. This is taken to be a result of the porous nature of the particles, which handicaps, to some extent, the interaction of the proteins and the displacer molecules with the adsorptive surface. Results were considerably better in case of the continuous-bed column, where there is no intraparticulate surface.     

Phase separation in amino acid mixtures is governed by composition

Macromolecular phase separation has recently come to immense prominence as it is central to the formation of membraneless organelles, leading to a new paradigm of cellular organization. This type of phase transition, often termed liquid-liquid phase separation (LLPS), is mediated by molecular interactions between biomolecules, including nucleic acids and both ordered and disordered proteins. In the latter case, the separation between protein-dense and -dilute phases is often interpreted using models adapted from polymer theory. Specifically, the “stickers and spacers” model proposes that the formation of condensate-spanning networks in protein solutions originates from the interplay between two classes of residues and that the main determinants for phase separation are multivalency and sequence patterning. The duality of roles of stickers (aromatics like Phe and Tyr) and spacers (Gly and polar residues) may apply more broadly in protein-like mixtures, and the presence of these two types of components alone may suffice for LLPS to take place. In order to explore this hypothesis, we use atomistic molecular dynamics simulations of capped amino acid residues as a minimal model system. We study the behavior of pure amino acids in water for three types of residues corresponding to the spacer and sticker categories and of their multicomponent mixtures. In agreement with previous observations, we find that the spacer-type amino acids fail to phase separate on their own, while the sticker is prone to aggregation. However, ternary amino acid mixtures involving both types of amino acids phase separate into two phases that retain intermediate degrees of compaction and greater fluidity than sticker-only condensates. Our results suggest that LLPS is an emergent property of amino acid mixtures determined by composition.     

Force measurement for antigen-antibody interaction by atomic force microscopy using a photograft-polymer spacer

To determine the intermolecular force on protein-protein interaction (PPI) by atomic force microscopy (AFM), a photograft-polymer spacer for protein molecules on both surfaces of the substrate and AFM probe tip was developed, and its effectiveness was assessed in a PPI model of a pair of human serum albumin (HSA) and its monoclonal antibody (anti-HSA). A carboxylated photoiniferter, N-(dithiocarboxy)sarcosine, was derivatized on both surfaces of the glass substrate and AFM probe tip, and subsequently water-soluble nonionic vinyl monomers, N,N-dimethylacrylamide (DMAAm), were graft-polymerized on them upon ultraviolet light irradiation. DMAAm-photograft-polymerized spacers with carboxyl groups at the growing chain end but with different chain lengths on both surfaces were prepared. The proteins were covalently bound to the carboxyl terminus of the photograft-polymer chain using a water-soluble condensation agent. The effects of the graft-spacer length on the profile of the force-distance curves and on the unbinding characteristics (unbinding force and unbinding distance) were examined in comparison with those in the case of the commercially available poly(ethylene glycol) (PEG) spacer. The frequency of the nonspecific adhesion force profile was markedly decreased with the use of the photograft spacers. Among the force curves detected, a high frequency of single-peak curves indicating the unbinding process of a single pair of proteins and a very low frequency of multiple-peak profiles were observed for the photograft spacers, regardless of the graft chain length, whereas a high frequency of no-force peaks was noted. These observations were in marked contrast with those for the PEG spacer. The force peak values determined ranged from 88 to 94 pN, irrespective of the type of spacer, while the standard deviation of force distribution observed for the photograft spacer was lower than that for the PEG spacer, indicating that the photograft spacers provide a higher accuracy of force determination.     

Functional reconstitution of beta-glucan elicitor-binding activity upon incorporation into lipid vesicles.

In temperature-induced Triton X-114 phase separation experiments the beta-glucan elicitor-binding site from soybean (Glycine max L.) root membranes was identified as (a) hydrophobic membrane protein(s). The Zwittergent 3-12-solubilized beta-glucan-binding proteins were incorporated into lipid vesicles by the detergent-dilution procedure. Reconstituted binding proteins were functional in that binding of the hepta-beta-glucoside ligand was saturable, reversible and of high affinity (K(d)=6-7 nM). Competition studies using beta-glucans with different degrees of polymerization (DP 7-15; DP 15-25) showed effective displacement of the radioligand from the binding site whereas beta-glucan fragments with DP <7 were ineffective. The total amount of reconstituted binding activity was dependent on the acyl chain length of the phospholipids used for the reconstitution with a preference for decanoic (C10) and dodecanoic (C12) chains. Restored ligand binding was maximally 37% as compared to the former detergent-solubilized binding activity. The presence of a lipid environment stabilized the purified beta-glucan-binding proteins.     

Highly selective membranes in protein ultrafiltration

A new ultrafiltration technique based on a multimembrane stack has been developed to fractionate solutes closer in size than conventionally possible. The technique is illustrated here by obtaining a pure protein product from a binary protein mixture. By employing membranes in series without any gaskets or spacers in-between, ultrafiltration is carried out to separate two proteins relatively close in molecular weight or size. Flat YM30 regenerated cellulose membranes, all of the same molecular weight cut-off (MWCO) 30,000, are stacked together in the desired number, and ultrafiltration takes place. The membrane rejection of a protein is amplified with each additional membrane, ultimately resulting in a completely rejected species. Complete purification of the more permeable protein may be achieved regardless of the physicochemical condition that may be optimal or suboptimal for selective separation by a single membrane. Two systems, myoglobin and beta-lactoglobulin, as well as myoglobin and alpha-lactalbumin were studied, under various operating conditions. The solvent flux reduction encountered when each membrane is added may also be avoided, by operating at increased pressure, while still achieving the desired purification. Cleaning in situ is achievable with reproducible experimental results before and after on-line cleaning. The results clearly demonstrate that multimembrane stacks can be used for fractionation of proteins that are quite close in molecular weight/size.     

Reversed-phase HPLC separation of proteins on chemically bonded silica gel columns

Reversed-phase high-performance liquid chromatographic (RP-HPLC) separation of proteins on chemically bonded silica gel columns is described. Efficiency of nonporous alkylsilyl bonded silica gel is compared with that of a macroporous gel that has been widely used for the purpose. A comparative study of the separation under conventional and fast separation conditions is also given. The fast separation technique on the nonporous reversed-phase column has the advantage of improving the recovery of late-eluting hydrophobic and large proteins, such as ovalbumin and apoferritin.     

Application of displacement chromatography for the analysis of a lipid raft proteome

Defining membrane proteomes is fundamental to understand the role of membrane proteins in biological processes and to find new targets for drug development. Usually multidimensional chromatography using step or gradient elution is applied for the separation of tryptic peptides of membrane proteins prior to their mass spectrometric analysis. Displacement chromatography (DC) offers several advantages that are helpful for proteome analysis. However, DC has so far been applied for proteomic investigations only in few cases. In this study we therefore applied DC in a multidimensional LC–MS approach for the separation and identification of membrane proteins located in cholesterol-enriched membrane microdomains (lipid rafts) obtained from rat kidney by density gradient centrifugation. The tryptic peptides were separated on a cation-exchange column in the displacement mode with spermine used as displacer. Fractions obtained from DC were analyzed using an HPLC-chip system coupled to an electrospray-ionization ion-trap mass spectrometer. This procedure yielded more than 400 highly significant peptide spectrum matches and led to the identification of more than 140 reliable protein hits within an established rat kidney lipid raft proteome. The majority of identified proteins were membrane proteins. In sum, our results demonstrate that DC is a suitable alternative to gradient elution separations for the identification of proteins via a multidimensional LC–MS approach.     

Erwinia amylovora CRISPR Elements Provide New Tools for Evaluating Strain Diversity and for Microbial Source Tracking

Clustered regularly interspaced short palindromic repeats (CRISPRs) comprise a family of short DNA repeat sequences that are separated by non repetitive spacer sequences and, in combination with a suite of Cas proteins, are thought to function as an adaptive immune system against invading DNA. The number of CRISPR arrays in a bacterial chromosome is variable, and the content of each array can differ in both repeat number and in the presence or absence of specific spacers. We utilized a comparative sequence analysis of CRISPR arrays of the plant pathogen Erwinia amylovora to uncover previously unknown genetic diversity in this species. A total of 85 E. amylovora strains varying in geographic isolation (North America, Europe, New Zealand, and the Middle East), host range, plasmid content, and streptomycin sensitivity/resistance were evaluated for CRISPR array number and spacer variability. From these strains, 588 unique spacers were identified in the three CRISPR arrays present in E. amylovora, and these arrays could be categorized into 20, 17, and 2 patterns types, respectively. Analysis of the relatedness of spacer content differentiated most apple and pear strains isolated in the eastern U.S. from western U.S. strains. In addition, we identified North American strains that shared CRISPR genotypes with strains isolated on other continents. E. amylovora strains from Rubus and Indian hawthorn contained mostly unique spacers compared to apple and pear strains, while strains from loquat shared 79% of spacers with apple and pear strains. Approximately 23% of the spacers matched known sequences, with 16% targeting plasmids and 5% targeting bacteriophage. The plasmid pEU30, isolated in E. amylovora strains from the western U.S., was targeted by 55 spacers. Lastly, we used spacer patterns and content to determine that streptomycin-resistant strains of E. amylovora from Michigan were low in diversity and matched corresponding streptomycin-sensitive strains from the background population.     

Spacer length in clonal plants and the efficiency of resource capture in heterogeneous environments: A Monte Carlo simulation

A stochastic, spatially explicit simulation model for clonal growth is presented which relates growth patterns to the pattern of resource availability in the environment in both space and time. The effects of two simple growth rules were examined which affect the length of spacers depending on the local environmental conditions. According to one of the rules, shorter spacers were developed in resource-rich microsites than in resource-poor microsites (growth rule G-). If the other rule acted, the spacers were lengthened in resource-rich sites (growth rule G+). The neutral reference, G0, represented a plant of rigid growth form. A wide range of habitat types was used in the tests and characterized by an information theory model. It was found that the effectiveness of resource capture in most habitat types can be explained by spatio-temporal predictability of the environment, measured on the scale of spacer length. Shortening the spacers in resource-rich microsites, as hypothesized by “foraging theory”, reduced the proportion of misplaced ramets. Lengthening the spacers never reduced this proportion. However, the degree of intraclonal competition was significantly reduced by both shortening and lengthening the spacers in response to site quality. There were certain types of environment where plastic modification of spacers had no effect on the efficiency of resource capture when compared to the reference random (non-environment-dependent) search pattern. Such habitats can be identified exactly on the basis of the information content of habitat pattern, measured here by spatio-temporal predictability. This study emphasizes that a wide range of environmental types should be taken into consideration when examining the adaptive nature of a certain growth pattern. Generalizing from experimental results gained in temporally constant environments may strongly bias our view on morphological adaptation.     

Sequence Variation and Comparison of the 5S rRNA Sequences in <Emphasis Type="Italic">Allium</Emphasis> Species and their Chromosomal Distribution in Four <Emphasis Type="Italic">Allium</Emphasis> Species

The gene structure and sequence diversity of 5S rRNA genes were analyzed in 13 Allium species. While the lengths and sequences of the coding gene segments were conserved, the spacers were highly variable and could be characterized as either short (213–404 bp) or long (384–486 bp) spacers. The short spacers were further classified into five subtypes (SS-I to SS-V) and the long spacers into four subtypes (LS-I to LS-IV). The short spacers were more conserved than were the long spacers. There was a sequence duplication of 85 bp in SS-III that distinguished it from SS-II. The coding sequences of the 5S rRNA genes started with CGG and ended with either CCC or TCC. Both long and short spacers started with TTTT at their 5′-ends. However, the long spacers ended with a 3′-TGA sequence, whereas the short spacers terminated with various sequences, such as TTA, ATA, or TGA. GC content ranged from 27 to 41% in whole repeats, and the GC content in the long spacers was lower than in the short spacers. The nucleotide diversity in the coding regions was lower than in the spacers, and the nucleotide diversity in the coding regions did not correlate with that of the spacers. FISH analysis confirmed that each Allium species has either short spacers or long spacers. Although chromosomal locations of the 5S rRNA genes in Allium wakegi confirmed the allodiploid nature of A. cepa and A. fistulosum, spacer sequences revealed the absence of SS-II in A. cepa and in A. wakegi. The current study demonstrated that the 5S rRNA genes diverged in early stages in Allium species differentiation except of the allodiploid A. wakegi.     

PEGylated protein separation using different hydrophobic interaction supports: Conventional and monolithic supports

Protein hydrophobicity can be modified after a PEGylation process. However, hydrophobic interaction chromatography (HIC) has been used to separate PEGylation reaction products less frequently than other techniques. In this context, chromatographic monoliths represent a good alternative to continue exploring the separation of PEGylated proteins with HIC. In this work, the separation of PEGylated proteins using C4 A monolith as well as Toyopearl Butyl 650C and Butyl Sepharose was analyzed. Three proteins were used as models: RNase A, β‐lactoglobulin, and lysozyme. All proteins were PEGylated in the N‐terminal amino groups with 20 kDa methoxy poly(ethylene glycol) propionaldehyde. The concentration of ammonium sulfate (1 M) used was the same for all stationary phases. The results obtained demonstrated that the C4 A monolith could better resolve all protein PEGylation reaction mixtures, since the peaks of mono‐ and di‐PEGylated proteins can be clearly distinguished in the chromatographic profiles. On the contrary, while using Butyl Sepharose media only the PEGylation reaction mixtures of RNase A could be partially separated at 35 and 45 CVs. PEGylated proteins of β‐lactoglobulin and lysozyme could not be resolved when Toyopearl Butyl 650C and Butyl Sepharose were used. It is then clear that monoliths are an excellent choice to explore the purification process of PEGylated proteins exploiting the advantages of HIC. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:702–707, 2016     

Molecular spacers for physicochemical investigations based on novel helical and extended peptide structures

A proper understanding of the detailed nature and mechanism of physicochemical interactions depends heavily upon our ability to design and synthesize conformationally constrained 3D structures whose intercomponent geometry (either rigorously rigid or able to undergo destructuration, if required, but in all cases precisely tunable) would be well defined. To this end we have recently reported a few initial studies and we are currently working on the exploitation of stable, short, helical peptide spacers based on achiral and/or chiral Calpha-tetrasubstituted alpha-amino acids. These building blocks are known to force the peptides either to predominantly fold into a 3(10)-helical structure or to adopt a fully extended, planar 2.0(5)-helix. The systems under investigation involve a donor and an acceptor moiety linked to the N- and C-termini of the oligopeptide spacer main chain. By increasing the number of intervening residues the donor.acceptor separation can be easily modulated. This review highlights details of these two novel peptide secondary structures and their use as molecular spacers in physicochemical investigations.     

Biochemical basis of polyvalency as a strategy for enhancing the efficacy of P-glycoprotein (ABCB1) modulators: stipiamide homodimers separated with defined-length spacers reverse drug efflux with greater efficacy

Human P-glycoprotein (Pgp) is as an ATP-dependent efflux pump for a variety of chemotherapeutic drugs. The aim of this study is to evaluate whether Pgp modulators can be engineered to exhibit high-affinity binding using polyvalency. Five bivalent homodimeric polyenes based on stipiamide linked with polyethylene glycol ethers in the range of 3-50 A were synthesized and quantitatively characterized for their effect on Pgp function. The stipiamide homodimers displaced [(125)I]iodoarylazidoprazoin (IAAP), an analogue of the Pgp substrate prazosin. A minimal spacer of 11 A is necessary for inhibition of IAAP labeling, beyond which there is an inverse correlation between the length of the spacer and the IC(50) for the displacement of IAAP. ATP hydrolysis by Pgp on the other hand is stimulated by the dimers with spacers of up to 22 A, whereas dimers with longer spacers inhibit ATP hydrolysis. Finally, the homodimers reverse Pgp-mediated drug efflux in intact cells overexpressing Pgp, and 11 A is a threshold beyond which the effectiveness of the homodimers increases exponentially and levels off at 33 A. We demonstrate that dimerization and identification of an optimal spacer length increase by 11-fold the affinity of stipiamide, and this is reflected in the efficacy with which Pgp-mediated drug efflux is reversed. These results suggest that polyvalency could be a useful strategy for the development of more potent Pgp modulators.     

Separation of hemagglutinin and neuraminidase from influenza virus membrane by column displacement electrophoresis (isotachophoresis) with preservation of their activities

Triton X-100-solubilized membrane glycoproteins (neuraminidase and hemagglutinin) from purified equine influenza virus particles were separated by column displacement electrophoresis (isotachophoresis) in the presence of Pharmalyte spacers. Electrophoresis was performed in a 1.80 cm glass electrophoresis column with Sephadex G-25 Fine serving as supporting medium. Triton X-100 was present in the system to suppress protein aggregation. Neuraminidase and hemagglutinin activities were preserved and appeared in the electropherogram as separate peaks with some overlapping.     

Purification of high value proteins from particle containing potato fruit juice via direct capture membrane adsorption chromatography

Potato fruit juice (PFJ) is a by-product from industrial starch production. It still contains several valuable components such as amino acids, minerals and proteins. An economic technology for the isolation and purification of different native potato proteins is the ion exchange chromatography, which can be performed either by classical bed chromatography or by membrane adsorption chromatography (MA-IEX). An already published MA-IEX process for the downstreaming of PFJ is based on the following steps: prefiltration/microfiltration, fractionation with MA-IEX, ultra-/diafiltration and finally drying. In order to further minimize process complexity and costs, new MA-IEX-modules were designed and tested in this research project to facilitate the processing of crude, particle-containing solutions using a tangential flow through the membranes. Modules with fleece polymer spacers and extruded polymer spacers, as well as different spacer channel sizes were tested for their binding capacities and their long-term stability. An optimized setup was found for the technical scale. Modules with extruded polymer spacers channel size 250 μm show the highest binding capacities (anion exchanger approx. 0.34 mg/cm², cation exchanger approx. 0.16 mg/cm²), while the modules with extruded polymer spacers channel size 480 μm show the best long-term stability with 23 passes without intermediary cleaning.