Surfactant-aided size exclusion chromatography

The flexibility and selectivity of size exclusion chromatography (SEC) for protein purification can be modified by adding non-ionic micelle-forming surfactants to the mobile phase. The micelles exclude proteins from a liquid phase similar to the exclusion effect of the polymer fibers of the size exclusion resin. This surfactant-aided size exclusion chromatography technology (SASEC) is demonstrated on the separation of two model proteins; bovine serum albumin (BSA) and myoglobin (Myo). The effect of the added surfactants on the distribution behavior of the proteins is predicted adequately by a size exclusion model presented in this paper.     

Hydraulic characteristics of aerobic granules using size exclusion chromatography

Elution of poly(ethylene glycol) of molecular weight 200-20,000 Da from a size exclusion chromatography column packed with phenol-fed aerobic granules of three different nominal sizes (types I-III) has been investigated. The pore sizes of the three types of granules were evaluated based on the mean hydraulic times of the elution curves that decreased directly proportional to the increased logarithm of the molecular mass of a standard tracer and increased as granule size decreased. The corresponding exclusion limits for types I-III granules were 139,000, 123,000, and 54,500 Da, respectively. A one-dimensional convection-dispersion model described the effective dispersion coefficients of the tracers through the granule column. The intra-granular permeabilities and convective and diffusional transit times through the granule interior were evaluated by a dual porosity model. For small molecules of molecular mass <5,000 Da, intra-granular convection dominated transport mechanisms at fast moving velocity. For comparatively larger molecules, diffusion barrier existed to limit nutrient supply to the granules. The size exclusion test provided intra granular transport characteristics using detailed analysis on the elution data.     

On-line separation of solute mixtures using reciprocating size exclusion chromatography

Solutes of different size in a mixture solution were separated on-line, using a semi-continuous reciprocating size exclusion chromatography. The band of fast-moving large molecules was isolated during the first half cycle, while the band of slow-moving small molecules was isolated during the second half cycle. After 7 cycles of frontal mode operation, 89% of the Blue Dextran in the feed was isolated as a pure solution. Vitamin B₁₂ of constant concentration was also isolated as a pure solution.     

Structure of Rab escort protein-1 in complex with Rab geranylgeranyltransferase

Posttranslational geranylgeranylation of Rab GTPases is catalyzed by Rab geranylgeranyltransferase (RabGGTase), which consists of a catalytic alpha/beta heterodimer and an accessory Rab escort protein (REP). The crystal structure of isoprenoid-bound RabGGTase complexed to REP-1 has been solved to 2.7 A resolution. The complex interface buries a surprisingly small surface area of ca. 680 A and is unexpectedly formed by helices 8, 10, and 12 of the RabGGTase alpha subunit and helices D and E of REP-1. We demonstrate that the affinity of RabGGTase for REP-1 is allosterically regulated by phosphoisoprenoid via a long-range trans-domain signal transduction event. Comparing the structure of REP-1 with the closely related RabGDI, we conclude that the specificity of the REP:RabGGTase interaction is defined by differently positioned phenylalanine residues conserved in the REP and GDI subfamilies.     

Liposome retention in size exclusion chromatography

Background  

Size exclusion chromatography is the method of choice for separating free from liposome-encapsulated molecules. However, if the column is not presaturated with lipids this type of chromatography causes a significant loss of lipid material. To date, the mechanism of lipid retention is poorly understood. It has been speculated that lipid binds to the column material or the entire liposome is entrapped inside the void.     

A method for screening enzyme inhibitors using size exclusion chromatography and ESI-LC-MS/MS

A pilot study was performed for the development of a method to screen compound libraries using an electrospray mass spectrometer interfaced with liquid chromatography (LC). The mixture of compounds was obtained by combining low-molecular weight inhibitors of carboxypeptidase A (CPA), a representative zinc-containing proteolytic enzyme. After the incubation of the mixture with CPA, the enzyme-bound compounds were separated by size exclusion chromatography (SEC) from unbound compounds. The separation of compounds was affected by LC. Three compounds were identified, which represent the tight binding inhibitors of the library. These compounds were quantitated using an automatic switching valve to avoid the interference of buffer salts with the detection of analytes. The quantitated amounts of the compounds were found to be in good accordance with the K(i) values.     

Inclusion body purification and protein refolding using microfiltration and size exclusion chromatography

The presence of inclusion body impurities can affect the refolding yield of recombinant proteins, thus there is a need to purify inclusion bodies prior to refolding. We have compared centrifugation and membrane filtration for the washing and recovery of inclusion bodies of recombinant hen egg white lysozyme (rHEWL). It was found that the most significant purification occurred during the removal of cell debris. Moderate improvements in purity were subsequently obtained by washing using EDTA, moderate urea solutions and Triton X-100. Centrifugation between each wash step gave a purer product with a higher rHEWL yield. With microfiltration, use of a 0.45 micron membrane gave higher solvent fluxes, purer inclusion bodies and greater protein yield as compared with a 0.1 micron membrane. Significant flux decline was observed for both membranes. Second, we studied the refolding of rHEWL. Refolding from an initial concentration of 1.5 mg ml-1, by 100-fold batch dilution gave a 43% recovery of specific activity. Purified inclusion bodies gave rise to higher refolding yields, and negligible activity was observed after refolding partially purified material. Refolding rHEWL with a size exclusion chromatography based process gave rise to a refolding yield of 35% that corresponded to a 20-fold dilution.     

Inhibitors of protein geranylgeranyltransferase I and Rab geranylgeranyltransferase identified from a library of allenoate-derived compounds

Protein geranylgeranylation is critical for the function of a number of proteins such as RhoA, Rac, and Rab. Protein geranylgeranyltransferase I (GGTase-I) and Rab geranylgeranyltransferase (RabGGTase) catalyze these modifications. In this work, we first describe the identification and characterization of small molecule inhibitors of GGTase-I (GGTI) with two novel scaffolds from a library consisting of allenoate-derived compounds. These compounds exhibit specific inhibition of GGTase-I and act by competing with a substrate protein. Derivatization of a carboxylic acid emanating from the core ring of one of the GGTI compounds dramatically improves their cellular activity. The improved GGTI compounds inhibit proliferation of a variety of human cancer cell lines and cause G(1) cell cycle arrest and induction of p21(CIP1/WAF1). We also report the identification of novel small molecule inhibitors of RabGGTase. These compounds were identified first by screening our GGTI compounds for those that also exhibited RabGGTase inhibition. This led to the discovery of a common structural feature for RabGGTase inhibitors: the presence of a characteristic six-atom aliphatic tail attached to the penta-substituted pyrrolidine core. Further screening led to the identification of compounds with preferential inhibition of RabGGTase. These compounds inhibit RabGGTase activity by competing with the substrate protein. These novel compounds may provide valuable reagents to study protein geranylgeranylation.     

On-line recovery of large molecules from mixtures using reciprocating size exclusion chromatography

Blue Dextran, a standard large molecule, was successfully recovered on-line from the aqueous mixture solution with nickel nitrate using a novel reciprocating size exclusion chromatography. After 7 cycles of repeating operations of frontal mode, 70% of Blue Dextran in the feed was isolated as a pure solution. On-line recovery of large molecules from the mixture is an unusual trial, comparing to the routine practice of filtration where small molecule is isolated from the mixture.     

Crystal structure of Rab geranylgeranyltransferase at 2.0 A resolution

BACKGROUND: Rab geranylgeranyltransferase (RabGGT) catalyzes the addition of two geranylgeranyl groups to the C-terminal cysteine residues of Rab proteins, which is crucial for membrane association and function of these proteins in intracellular vesicular trafficking. Unlike protein farnesyltransferase (FT) and type I geranylgeranyltransferase, which both prenylate monomeric small G proteins or short peptides, RabGGT can prenylate Rab only when Rab is in a complex with Rab escort protein (REP). RESULTS: The crystal structure of rat RabGGT at 2.0 A resolution reveals an assembly of four distinct structural modules. The beta subunit forms an alpha-alpha barrel that contains most of the residues in the active site. The alpha subunit consists of a helical domain, an immunoglobulin (Ig)-like domain, and a leucine-rich repeat (LRR) domain. The N-terminal region of the alpha subunit binds to the active site in the beta subunit; residue His2alpha directly coordinates a zinc ion. The prenyl-binding pocket of RabGGT is deeper than that in FT. CONCLUSIONS: LRR and Ig domains are often involved in protein-protein interactions; in RabGGT they might participate in the recognition and binding of REP. The binding of the N-terminal peptide of the alpha subunit to the active site suggests an autoinhibition mechanism that might contribute to the inability of RabGGT to recognize short peptides or Rab alone as its substrate. Replacement of residues Trp102beta and Tyr154beta in FT by Ser48beta and Leu99beta, respectively, in RabGGT largely determine the different lipid-binding specificities of the two enzymes.     

Nonionic polysaccharides as calibration standards for aqueous size exclusion chromatography

Size exclusion chromatography may be used to determine molecular size or mass of solutes. The validity of the method depends on the correct choice of macromolecular standards used to calibrate the chromatographic column. This calibration is an experimental determination of the relationship between the molecular dimensions and the peak migration velocity of the solute, in practice often presented as a semi-logarithmic plot of log(MW) vs elution volume, but more fundamentally expressed as the dependence of for example, the Stokes radius (R_S), or the viscosity radius (R_η) on the chromatographic partition coefficient, K_SEC. The validity of this calibration rests on the absence of enthalpic interactions between the standards and the stationary phase and the ability to determine the standards' molecular dimensions and/or mass in a nonambiguous way. Nonionic polysaccharides are ideal for this purpose, and furthermore provide an excellent paradigm for studying the role of molecular architecture in the relationship between K_SEC and R_η or R_S.     

High productivity refolding of an inclusion body protein using pulsed-fed size exclusion chromatography

Protein refolding using size exclusion chromatography (SEC) is advantageous over conventional refolding methods in terms of ease of automation, simultaneous purification capabilities, and the non-adsorptive protein–matrix interaction which eliminates steric constraints. Despite these advantages, the widespread use of SEC refolding remains restricted by low process productivity and product concentration bottlenecks. This study aims to address those limitations and exploit SEC advantages for large-scale refolding applications. Specifically, this study reports the development of a pulsed-fed size exclusion chromatography (PF-SEC) refolding platform, which successfully refolded E. coli-derived α-fetoprotein (AFP) to achieve 53% refolding yield at 0.9 mg/ml AFP refolding concentration. AFP was introduced into the column by pulsed injection to increase feed load, while suppressing concentration-induced aggregation. Refolding was initiated by a urea gradient in the column, where the gradient length could be readily adjusted to complement pulsed feeding patterns. AFP refolding productivity with PF-SEC improved by 8- and 64-fold compared to ion-exchange chromatography refolding and pulsed dilution refolding, respectively, at a fixed refolding concentration. Through a unique integration of pulsed feeding and urea gradient development, this new PF-SEC refolding methodology overcomes ‘productivity and concentration’-related disadvantages inherent in SEC, and will be scalable for large-scale protein refolding applications.     

Measurements of protein-protein interactions by size exclusion chromatography

A method is presented for determining second virial coefficients (B(2)) of protein solutions from retention time measurements in size exclusion chromatography. We determine B(2) by analyzing the concentration dependence of the chromatographic partition coefficient. We show the ability of this method to track the evolution of B(2) from positive to negative values in lysozyme and bovine serum albumin solutions. Our size exclusion chromatography results agree quantitatively with data obtained by light scattering.     

Characterization of loaded liposomes by size exclusion chromatography

This review focuses on the use of conventional (SEC) and high performance (HPSEC) size exclusion chromatography for the analysis of liposomes. The suitability of both techniques is examined regarding the field of liposome applications. The potentiality of conventional SEC is strongly improved by using a HPLC system associated to gel columns with a size selectivity range allowing liposome characterization in addition to particle fractionation. Practical aspects of size exclusion chromatography are described and a methodology based on HPSEC coupled to multidetection modes for on-line analysis of liposomes via label or substance encapsulation is presented. Examples of conventional SEC and HPSEC applications are described which concern polydispersity, size and encapsulation stability, bilayer permeabilization, liposome formation and reconstitution, incorporation of amphiphilic molecules. Size exclusion chromatography is a simple and powerful technique for investigation of encapsulation, insertion/interaction of substances from small solutes (ions, surfactants, drugs, etc.) up to large molecules (proteins, peptides and nucleic acids) in liposomes.     

Phosphoisoprenoids modulate association of Rab geranylgeranyltransferase with REP-1.

Rab geranylgeranyltransferase (RabGGTase or GGTase-II) catalyzes the post-translational prenylation of Rab proteins. Rab proteins are recognized as substrates only when they are complexed to Rab Escort Protein (REP). The classical model of prenylation complex assembly assumes initial formation of the Rab.REP binary complex, which subsequently binds to RabGGTase loaded with the isoprenoid donor geranylgeranyl pyrophosphate (GGpp). We demonstrate here that REP-1 can also associate with RabGGTase in the absence of Rab protein and that this interaction is dramatically strengthened by the presence of phosphoisoprenoids such as GGpp. The GGpp-dependent interaction between RabGGTase and REP-1 was observed using affinity precipitations and gel filtration and was quantitated on the basis of fluorescence assays. In the presence of GGpp, REP-1 binds to RabGGTase with a K(d) value of approximately 10 nm, while in its absence the affinity between the two proteins is in the micromolar range. We further demonstrate that binding of Rab7 to the RabGGTase.GGpp.REP-1 complex occurs without prior dissociation of REP-1. Analysis of binding and prenylation rate constants indicate that the RabGGTase.GGpp.REP-1 complex can function as a kinetically competent intermediate of the prenylation reaction. We conclude that, depending on the prevailing concentrations, binding of REP-1 to RabGGTase in the presence of GGpp may serve as an alternative pathway for the assembly of the prenylation machinery in vivo. Implications of these findings for the role of REP-1 in the prenylation reaction are discussed.     

Refolding of denatured ribonuclease observed by size exclusion chromatography

The unfolding and refolding of pancreatic ribonuclease have been observed by absorbance, fluorescence, and size exclusion chromatographic measurements in solutions of guanidinium chloride continuously maintained at pH 6.0 and 4 degrees C. The spectral measurements were fitted with a minimal number of kinetic phases while the chromatographic measurements were simulated from an explicit mechanism. All of the measurements are consistent with a minimal mechanism involving seven components. The folded components include the native protein and two transiently stable intermediates each having the same hydrodynamic volume. The intermediate having all native peptide isomers has an unfolding midpoint in 3.8 M denaturant while the intermediate having one nonnative peptide isomer has an unfolding midpoint in 1.3 M denaturant. The unfolded protein is distributed among four components having the same hydrodynamic volume but differing peptide isomers. At equilibrium, 10% of the denatured protein has all native isomers, 60% has one nonnative isomer, 5% has a different nonnative isomer, and 25% has both nonnative isomers. In low denaturant concentrations, the dominant component with one nonnative isomer can refold to transiently populate the compact intermediate with the same nonnative isomer.     

Monitoring xanthan quality during fermentation by size exclusion chromatography

Summary Xanthan concentration and molecular weight distribution are determined by size exclusion chromatography in the fermentation medium after dilution and cell removal by centrifugation. The analysis is rapid enough for process control. During a batch fermentation, the average molecular weight is found to be in the range of 7.2–9.3·10⁶ g/mole and to run through a maximum.     

Ultrahigh pressure fast size exclusion chromatography for top‐down proteomics

Top‐down MS‐based proteomics has gained a solid growth over the past few years but still faces significant challenges in the LC separation of intact proteins. In top‐down proteomics, it is essential to separate the high mass proteins from the low mass species due to the exponential decay in S/N as a function of increasing molecular mass. SEC is a favored LC method for size‐based separation of proteins but suffers from notoriously low resolution and detrimental dilution. Herein, we reported the use of ultrahigh pressure (UHP) SEC for rapid and high‐resolution separation of intact proteins for top‐down proteomics. Fast separation of intact proteins (6–669 kDa) was achieved in < 7 min with high resolution and high efficiency. More importantly, we have shown that this UHP‐SEC provides high‐resolution separation of intact proteins using a MS‐friendly volatile solvent system, allowing the direct top‐down MS analysis of SEC‐eluted proteins without an additional desalting step. Taken together, we have demonstrated that UHP‐SEC is an attractive LC strategy for the size separation of proteins with great potential for top‐down proteomics.     

Quantification of amyloid fibrils using size exclusion chromatography coupled with online fluorescence and ultraviolet detection

An amyloid fibrils investigation within biofilm samples requires distinguishing the amyloid β-sheet structure of these proteins and quantifying them. In this study, the property of amyloids to incorporate the fluorescent dye Thioflavin T has been exploited to propose a method of quantification. The experimental protocol includes the preparation of amyloids from commercial κ-casein (κCN) and their fractionation through size exclusion chromatography (SEC) to provide calibration curves from fluorescence and absorbance signals. Finally, a bacterial biofilm extract was injected into SEC, and the amyloid fibrils could be expressed as equivalent κCN, representing approximately 21% of the total proteins.