Simultaneous determination of protein aggregation, degradation, and absolute molecular weight by size exclusion chromatography-multiangle laser light scattering

The feasibility of size exclusion chromotography (SEC)-multiangle laser-light scattering as a technique to investigate aggregation and degradation of glycosylated and nonglycosylated proteins, and antibodies under various conditions such as addition of detergent, changes in pH, and variation of protein concentration and heat stress temperature was examined. Separation of proteins and their aggregates was performed using SEC-high-performance liquid chromatography. Detection of analytes was carried out with on-line UV, refractive index, and multiangle laser light-scattering detectors. Quantification and molecular weight determination were performed using commercial software. Aggregation and degradation were examined under various conditions and quantitative results are presented for bovine serum albumin, choriogonadotropin, glyceraldehyde-3-phosphate dehydrogenase, Herceptin, and ReoPro. This method can simultaneously determine both the quantities and the molecular weights of macromolecules from a single injection. The determination of molecular weight is absolute which avoids misleading results caused by molecular shape or interactions with the column matrix. This technique is valuable not only for assessing the extent of aggregation but also for effectively monitoring molecule degradation as evidenced by molecular weight reduction and change in monomer amount.     

The yeast mitochondrial adenosine triphosphatase complex. Subunit stoichiometry and physical characterization

Immunoprecipitation of uniformly labeled yeast submitochondrial preparations using a subunit-specific or a holoenzyme antiserum has been employed to determine the subunit stoichiometry of the oligomycin-sensitive ATPase complex. The Triton-solubilized enzyme consists of 10 types of subunits. The number of copies of each subunit, in order of decreasing molecular weight, is 3:3:1:2:1:2:2:1:2:3. on the basis of the stoichiometry data, the ATPase complex has a molecular weight of 5.8 x 10(5) and contains a minimum of 20 polypeptide chains. Analysis of water-soluble ATPase (F1-ATPase) indicates that the stoichiometry of the three largest subunits of the enzyme is preserved in the absence of the other subunits. The molecular weights of both forms of the ATPase, derived from stoichiometry data, agree well with measurements obtained from gel filtration and sedimentation studies. The implications of these data for the structure, function, and assembly of the complex are discussed.     

Characterization and analysis of thermal denaturation of antibodies by size exclusion high-performance liquid chromatography with quadruple detection

Size exclusion chromatography (SEC) coupled with online light scattering, viscometry, refractometry, and UV-visible spectroscopy provides a very powerful tool for studying protein size, shape, and aggregation. This technique can be used to determine the molecular weight of the component peaks independent of the retention times in the SEC column and simultaneously measure the hydrodynamic radius and polydispersity of the protein. We applied this technology by coupling an Agilent Chemstation high-performance liquid chromatography system with a diode array UV-visible detector and a Viscotek 300 EZ Pro triple detector (combination of a light scattering detector, refractometer, and differential pressure viscometer) to characterize and compare the molecular properties of a number of monoclonal antibodies. Our studies reveal that different monoclonal immunoglobulin Gs (IgGs) and chimeric IgGs show slightly different retention times and therefore different molecular weights in gel filtration analysis. However, when they are analyzed by light scattering, refractometry, and viscometry, different IgGs have comparable molecular weight, molecular homogeneity (polydispersity), and size. Gel filtration coupled with UV or refractive index detection suggests that antibodies purified and formulated for preclinical and clinical development are more than 95% monomer with little or no detectable soluble aggregates. Light scattering measurements showed the presence of trace amounts of soluble aggregate in all the IgG preparations. The different IgG molecules showed different susceptibility to heat and pH. One of the murine antibodies was considerably less stable than the others at 55 degrees C. The application of this powerful technology for the characterization of monoclonal antibodies of therapeutic potential is discussed.     

Refractive index-based determination of detergent concentration and its application to the study of membrane proteins

The concentration of detergent in membrane protein preparations can have a critical role on protein stability, function, and the potential for crystallization. Unfortunately, dialysis or protein concentration can lead to an unknown amount of detergent in the final membrane protein preparations. Here we present a method for the determination of detergent concentration based on refractive index of the detergent solution. This method was applied to quantitate the amount of detergent remaining in solution after concentration in various concentrators. We found that the ability of the tested detergents to pass through the molecular weight cutoff membrane correlates well with detergent micelle size. Therefore, the micelle size can be used as a rough guide to estimate the retention of a given detergent in various molecular weight cutoff concentrators. The refractive index method is exceptionally informative when coupled with size exclusion chromatography and light scattering, and can be used to determine the oligomeric state of the membrane protein, the size of a protein-associated micelle, as well as the amount and size of the unbound detergent micelle.     

Measurement of the molecular weight distribution of debranched starch

Combining molecular weight distribution (MWD) data for linear chains of debranched starch from capillary electrophoresis and from size exclusion chromatography (SEC) with detection by differential refractive index and by multi-angle laser light scattering has enabled Mark-Houwink parameters to be determined for linear starch chains. For accurate results, it was found to be important to take SEC band broadening into account, and a methodology for implementing this is presented. This deconvolution technique can be used to reveal features such as maxima or shoulders in the MWD which have qualitative as well as quantitative significance. Remarkably, these data show that the empirical Mark-Houwink relation between molecular weight and hydrodynamic volume is, for linear debranched starch, valid for much lower molecular weights than synthetic polymers. This implies that these Mark-Houwink parameters can be used with "universal calibration" to enable SEC to be used with relative ease to provide MWDs for debranched starch for essentially any degree of polymerization.     

Characterization of noncovalent complexes of recombinant human monoclonal antibody and antigen using cation exchange, size exclusion chromatography, and BIAcore.

The binding of fully human monoclonal antibodies (MAbs) D2E7 and 2SD4 to their antigen, human tumor necrosis factor-alpha (TNFalpha), was investigated by BIAcore, cation exchange (CIEX), and size exclusion liquid chromatography (SEC) using ultraviolet and laser light scattering detectors. D2E7 has a higher affinity for TNFalpha than 2SD4 and the two antibodies (Abs) differ by 12 amino acids in the antigen (Ag) binding regions. A BIAcore biosensor instrument was used to determine the association, k(on) and dissociation, k(off), rate constants for the binding of TNFalpha to D2E7 and 2SD4. The HPLC methods were used to resolve and to study D2E7, 2SD4, and TNFalpha molecules and the noncovalent complexes of D2E7 and 2SD4 with TNFalpha. The CIEX method demonstrated that all D2E7 charged-variants bound TNFalpha equally well. There was no preferential binding for any one of D2E7 charged-variants to TNFalpha. D2E7 and 2SD4 Abs were resolved by the CIEX method. When a mixture of D2E7 and 2SD4 was mixed with excess TNFalpha, D2E7. TNFalpha complexes were formed before any 2SD4. TNFalpha complexes. Thus, the CIEX method was able to rank the affinities of the MAbs. D2E7 and TNFalpha formed complexes of 600-5000 kDa. The molecular weights of various D2E7. TNFalpha complexes were determined by a SEC method with light scattering (LS) and refractive index (RI) detectors. Upon overnight incubation, a 598-kDa complex emerged as the most stable and the only D2E7. TNFalpha complex. The molar ratio of D2E7 to TNFalpha in this complex was approximately 1:1. Based on molecular weights and the molar ratio, an immune complex, consisting of alternating three D2E7 and three TNFalpha molecules, is proposed as the most stable complex.     

Studies on cytochrome c oxidase, X. Isolation and amino-acid sequence of polypeptide VIIIb

The isolation and sequence determination of the cytoplasmically synthesized polypeptide VIIIb from beef heart cytochrome c oxidase is described. Several methods for isolating polypeptide VIIIb with gelchromatographic technics are presented. The complete amino-acid sequence is deduced from a N-terminal sequencer run, overlapping tryptic peptides and peptides obtained after tryptophan specific cleavage with cyanogen bromide in heptafluorobutyric acid/formic acid. The small protein consists of 46 amino acids and has a molecular mass of 4 962 Da. The existence of a hydrophobic segment with a length of 20 residues characterizes it as a membrane penetrating protein. The stoichiometry of this polypeptide in the functional monomer of cytochrome c oxidase (complex IV) is 2 and is thus different from all the other polypeptides constituting the respiratory complex IV. The function of this component of the terminal oxidase is as yet unknown.     

Structural properties of poly C-scleroglucan complexes

Successive changes of solvent conditions can be used to dissociate and reassociate the triple-helical structure of (1,3)-beta-D-glucans. Ultramicroscopic techniques have revealed a blend of circular and other structures following renaturation. When this solvent exchange process is carried out in the presence of certain polynucleotides, the process creates a novel macromolecular complex. Here, we use size exclusion chromatography (SEC) to study such (1,3)-beta-D-glucan-polynucleotide complexes. Online multi-angle laser-light scattering (MALLS) and refractive index (RI) detectors allowed determination of molecular weight and radius of gyration of the molecules. An ultraviolet (UV) detector allowed specific detection of the polynucleotide. The poly-cytidylic acid (poly C) shifted to coelution with the linear fraction of the scleroglucan following the renaturation of poly C-scleroglucan blends, indicating that poly C is incorporated in linear, but not in circular, structures of scleroglucan. This conclusion was consistent with AFM topographs that revealed a decreased fraction of circular structures upon addition of poly C during the renaturation process. The combined information about radius of gyration (R(g)) and molecular weight (M(w)) allowed us to conclude that the poly C-scleroglucan complexes are more dense and have a higher persistence length than linear scleroglucan triple helixes. The experimentally determined mass per unit length was used as a basis for elucidating possible molecular arrangements within the poly C-scleroglucan complex.     

Purification and characterization of two leaf polypeptide inhibitors of leaf protease from alfalfa (Medicago sativa)

Two polypeptides with antiproteolytic activities have been isolated from alfalfa leaves. Polypeptide I resembles the previously described plant protease inhibitors in both structural and functional features; it has a molecular weight of 15,000, a random coil secondary structure, and inhibits exogenous protease as well as alfalfa leaf protease. Polypeptide II is a novel type of plant inhibitor with a molecular weight of 6300 and a highly organized structure with a high (40-50%) alpha-helix content. It only inhibits endogenous protease with a molar stoichiometry polypeptide/enzyme protein of 1.     

Tyrosine sulfation of yolk proteins 1, 2, and 3 in Drosophila melanogaster

Protein sulfation was studied in Drosophila melanogaster after in vivo labeling of flies with inorganic [35S]sulfate. After separation of total fly protein by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, proteins with sulfated carbohydrates and proteins containing tyrosine sulfate were found in all the molecular weight ranges analyzed. When female and male fly proteins were compared with each other, the electrophoretic patterns of protein-bound carbohydrate sulfate were found to be similar, whereas those of protein-bound tyrosine sulfate were distinct. The most prominent difference was the exclusive presence in female flies of three major tyrosine-sulfated proteins with apparent molecular masses between 48 and 45 kDa. Radioimmunolabeling after two-dimensional polyacrylamide gel electrophoresis was used to identify these proteins as yolk proteins 1, 2, and 3. Each of the three yolk proteins existed in several isoelectric forms, all of which were sulfated. Since the number of tyrosine residues in the yolk proteins is known, the stoichiometry of tyrosine sulfation could be determined by a novel method and was found to be 2.2, 0.9, and 1.2 mol of tyrosine sulfate per mol of yolk protein 1, 2, and 3, respectively. The present results, together with the recently reported molecular cloning of the yolk protein genes, make the yolk proteins suitable objects for genetic approaches to investigate the biological role(s) of tyrosine sulfation of secretory proteins.     

The Saccharomyces cerevisiae SEC14 gene encodes a cytosolic factor that is required for transport of secretory proteins from the yeast Golgi complex

We have obtained and characterized a genomic clone of SEC14, a Saccharomyces cerevisiae gene whose product is required for export of yeast secretory proteins from the Golgi complex. Gene disruption experiments indicated that SEC14 is an essential gene for yeast vegetative growth. Nucleotide sequence analysis revealed the presence of an intron within the SEC14 structural gene, and predicted the synthesis of a hydrophilic polypeptide of 35 kD in molecular mass. In confirmation, immunoprecipitation experiments demonstrated SEC14p to be an unglycosylated polypeptide, with an apparent molecular mass of some 37 kD, that behaved predominantly as a cytosolic protein in subcellular fractionation experiments. These data were consistent with the notion that SEC14p is a cytosolic factor that promotes protein export from yeast Golgi. Additional radiolabeling experiments also revealed the presence of SEC14p-related polypeptides in extracts prepared from the yeasts Kluyveromyces lactis and Schizosaccharomyces pombe. Furthermore, the K. lactis SEC14p was able to functionally complement S. cerevisiae sec14ts defects. These data suggested a degree of conservation of SEC14p structure and function in these yeasts species.     

A carotenoid-protein from cyanobacteria

Easily solubilized carotenoid-containing proteins have been found in aqueous extracts from three genera of cyanobacteria. The three proteins have been purified, and the absorption spectra have been determined to be virtually identical with absorption maxima at 495 and 465 nm. During the purification the orange protein spontaneously changed to a red protein with a single, broad absorption maximum at 505 nm. The orange protein showed a molecular weight of 47 000 on gel filtration while that of the red protein was 26 700. Sodium dodecyl sulfate polacrylamide gel electrophoresis indicated a single polypeptide of M_r 16 000 in both the red and orange forms, but this method removed the chromophore from the proteins. The main carotenoid component of the complex was determined to be 3′-hydroxy-4-keto-ββ-carotenoid or 3′-hydroxyechinenone. The number of carotenoid molecules per molecule of orange protein of molecular weight 47 000 was between 20 and 40. The stoichiometry of carotenoid to protein seemed reasonably constant.     

Graphical analysis of nonideal monomer N-mer, isodesmic, and type II indefinite self-associating systems by equilibrium ultracentrifugation.

A graphical procedure is described by which one can obtain in principle the monomer molecular weight, stoichiometry, equilibrium constant, and second virial coefficient of nonideal monomer N-mer, isodesmic, and type II indefinite self-associating systems. In addition, a method is presented for obtaining both the equilibrium constant and the second virial coefficient from the maximum in a plot of apparent molecular weight vs. concentration if the monomer molecular weight and stoichiometry are known. The usefulness and limitations of the methods are discussed, as well as the quality and range of data required for determination of the relevant parameters. The techniques described are applicable to analysis of self-associating systems by osmotic pressure and light scattering, as well as equilibrium ultracentrifugation measurements.     

NMR spectroscopic and molecular modeling studies of protein-carbohydrate and protein-peptide interactions

Investigations of the conformations of carbohydrates, their analogues and their molecular mimics are described, with emphasis on structural and functional information that can be gained by NMR spectroscopic techniques in combination with molecular modeling. The transferred nuclear Overhauser effect (trNOE) has been employed to determine the bound conformations of carbohydrates and other bioactive molecules in complex with protein receptors. The corresponding experiments in the rotating frame (trROE) and selective editing experiments (e.g., QUIET-NOESY) are used to eliminate indirect cross-relaxation pathways (spin diffusion), thereby minimizing errors in the data used for calculation of conformations. Saturation transfer difference NMR experiments reveal detailed information about intermolecular contacts between ligand and protein. Computational techniques are integrated with NMR-derived information to construct structural models of these bioactive molecules and of their complexes with proteins. Recent investigations into the nature of molecular mimicry with regard to protein-ligand interactions are described, along with applications in determining the mode of action of enzyme inhibitors. The results are relevant for the design of the next generation of drug and vaccine candidates.     

Prediction of the viscosity radius and the size exclusion chromatography behavior of PEGylated proteins

Size exclusion chromatography (SEC) was used to determine the viscosity radii of equivalent spheres for proteins covalently grafted with poly(ethylene glycol) (PEG). The viscosity radius of such PEGylated proteins was found to depend on the molecular weight of the native protein and the total weight of grafted PEG but not on PEG molecular weight, or PEG-to-protein molar grafting ratio. Results suggest grafted PEG's form a dynamic layer over the surface of proteins. The geometry of this layer results in a surface area-to-volume ratio approximately equal to that of a randomly coiled PEG molecule of equivalent total molecular weight. Two simple methods are given to predict the viscosity radius of PEGylated proteins. Both methods accurately predicted (3% absolute error) the viscosity radii of various PEG-proteins produced using three native proteins, alpha-lactalbumin (14.2 kDa MW), beta-lactoglobulin dimer (37.4 kDa MW), and bovine serum albumin (66.7 kDa MW), three PEG reagents (2400, 5600, and 22500 MW), and molar grafting ratios of 0 to 8. Accurate viscosity radius prediction allows calculation of the distribution coefficient, K(av), for PEG-proteins in SEC. The suitability of a given SEC step for the analytical or preparative fractionation of different PEGylated protein mixtures may therefore be assessed mathematically. The methods and results offer insight to several factors related to the production, purification, and uses of PEGylated proteins.     

Cell attachment on replicas of SDS polyacrylamide gels reveals two adhesive plasma proteins

A novel procedure that detects adhesive proteins in complex mixtures was used to characterize such proteins in plasma. The proteins are separated by SDS PAGE and transferred to nitrocellulose filters. Cells incubated on these filters attach to those proteins that have adhesive properties. When applied to human plasma proteins this procedure reveals, in addition to fibronectin, a cell-attachment protein with a polypeptide molecular weight of 70,000. Using a monoclonal antibody that inhibits attachment of cells to fibronectin, we show that this polypeptide is not a fragment of fibronectin and we present evidence that it is a component of the serum spreading factor. Therefore, as defined by our assay, this protein and fibronectin are the major attachment proteins for fibroblastic cells in plasma or serum.     

Redox-linked proton translocation in the b-c1 complex from beef-heart mitochondria reconstituted into phospholipid vesicles. Studies with chemical modifiers of amino acid residues

Possible involvement of polypeptides of b-c1 complex of beef-heart mitochondria in its redox and protonmotive activity has been investigated, by means of chemical modification of amino acid residues in the soluble as well as in the phospholipid-reconstituted b-c1 complex. Treatment of the enzyme with tetranitromethane (C(NO2)4) or with ethoxyformic anhydride (EFA), that modify reversibly tyrosyl and hystidyl residues respectively, resulted in a marked inhibition of electron transport from reduced quinols to cytochrome c. This was accompanied, in b-c1 reconstituted into phospholipid vesicles, by a parallel inhibition of respiratory-linked proton translocation; the H+/e- stoichiometry remained unchanged. Treatment of b-c1 complex with DCCD, that specifically modifies carboxylic groups of glutammic or aspartic residues caused a marked depression of proton translocation in b-c1 vesicles, under conditions where the rate of electron flow in the coupled state, was enhanced. As a consequence the H+/e- stoichiometry was lowered. SDS gel electrophoresis and [14C]DCCD-labelling of the polypeptides of the b-c1 complex showed a major binding of 14C-DCCD to the 8-kDa subunit of the complex and possible cross-linking, induced by DCCD treatment, of polypeptide(s) in the 8-kDa band and the 12-kDa band, with the Fe-s protein of the complex, with the appearance of a new polypeptide band with an apparent molecular mass of about 40 kDa. Involvement of polypeptides of low molecular mass, for which no functional role was so far described, and possibly of the Fe-S protein in the redox-linked proton translocation in b-c1 complex is suggested.     

Structural properties of the microsomal triglyceride-transfer protein complex

The microsomal triglyceride-transfer protein (MTP), which catalyzes the transport of triglyceride and cholesteryl ester between membranes, is a complex composed of two proteins having apparent molecular weights of 58,000 and 88,000. The 58,000 molecular weight component of MTP has been identified as the multifunctional protein, protein disulfide isomerase (PDI). The multisubunit nature of MTP as well as the presence of PDI as one of the subunits distinguishes this protein from previously characterized lipid-transfer proteins. In this study, we have more clearly defined structural elements of MTP that may play important functional roles. The molecular weight of the transfer protein complex was determined to be 150,000 by sedimentation equilibrium experiments performed at three different speeds, suggesting that MTP is a complex of one PDI and one 88,000 molecular weight polypeptide (88K). Following SDS-polyacrylamide gel electrophoresis, the Coomassie Blue staining intensity of PDI in a known amount of MTP was compared to that of known amounts of a PDI standard. A 1 to 0.98-1.30 ratio of PDI to 88K was determined, confirming the 1:1 stoichiometry of MTP. The sedimentation coefficient (5.85) determined by analytical ultracentrifugation and the Stokes radius (47 A) determined by polyacrylamide gradient gel electrophoresis indicate that the 150,000 molecular weight MTP complex is asymmetric and/or has an unusually high water of hydration. PDI and 88K form a stable protein complex; there was no evidence of a dissociation-reassociation reaction occurring between the two components. Analysis of far-ultraviolet circular dichroism spectra revealed MTP has about 28% alpha-helical and 28% beta-structural content.(ABSTRACT TRUNCATED AT 250 WORDS)     

Improved methods for the structural analysis of the amylose-rich fraction from rice flour

Cooking and sensory properties of rice are largely determined by the amylose content and structure. For relationships between functional and structural properties, a more accurate method to determine the structure of amylose is required. Here we calibrate size exclusion chromatography (SEC) columns, using Mark-Houwink parameters for linear starch and pullulan standards, to obtain the true molecular weight distribution of linear starch. When the molecular weight distribution is reported relative to pullulan, rather than the actual molecular weight which is readily obtained from universal calibration, it is seen that the molecular weights of longer amylose chains are greatly underestimated. We validate the SEC method to enable the measurement of the hydrodynamic volume distribution of the starch by examining reproducibility and recovery. Analysis of the starch in the sample pre- and post-SEC shows that 20% of the carbohydrate is not recovered. Comparison of the weight-average degree of polymerization, X(w), of (undebranched) starch of pre- and post-SEC is made using iodine binding as well as Berry plots of data from multi-angle laser light scattering (MALLS). These both show that current SEC techniques for starch analysis lead to significant loss of high molecular weight material. Indeed, for the systems studied here, the values for X(w) after SEC are about three times lower than those before SEC. Iodine-starch complexes of pre- and post-SEC samples reveals that the SEC techniques give reliable data for the amylose fraction but not for amylopectin. We address reports in the literature suggesting that the conventional isoamylase method for debranching starch would lead to incomplete debranching and thus incorrect molecular weight distributions. However, it is shown using (1)H NMR that isoamylase can completely debranch the amylose (to within the detection limit of 0.5%), and by SEC that successive incubation with isoamylase, alpha-amylase, and beta-amylase can degrade the amylose-rich fraction completely to maltose. We develop a method to obtain a hot water soluble fraction (HWSF), rich in undamaged amylose molecules, directly from rice flour, avoiding the structural degradation of previous techniques. With appropriate sample handling, the formation of associations between starch chains is minimized. With the combination of calibrated and validated SEC methods, and an improved extraction of amylose from rice, the X(w) for both HWSF and debranched HWSF are found to be much larger than has previously been reported.