Peptide purification by gel filtration in aqueous pyridine--ammonia.

A method is described for the purification of peptides by gel filtration on Sephadex. The success of the method is due mainly to the use of 70% ($\text{v}\text{v}$) pyridine-30% ($\text{v}\text{v}$) 1 m aqueous ammonia, an excellent volatile solvent for peptides which does not degrade Sephadex. The method has been used to purify all of the major peptides of cowpea chlorotic mottle virus coat protein, after an initial fractionation by ion-exchange chromatography, and selected separations are used to illustrate the degree of fractionation which can be achieved.     

A comparison of gel filtration chromatographic supports for plasmid purification

Two gel filtration chromatographic supports, Superose 6 and Sephacryl S1000 SF, were used to purify supercoiled plasmids using a 4.8 kb plasmid as a model. Both supports purified the plasmid from RNA and other small molecular weight contaminants, as shown by agarose electrophoresis and ion exchange HPLC, with an overall yield of 70%. Sephacryl S1000 SF was the better support as it resolved supercoiled, relaxed, linear and concatamer plasmid forms, and chromosomal DNA.     

Agarose gel filtration of fluorescent labeled protein-sodium dodecyl sulfate complexes

A procedure has been developed for estimation of the molecular weight of fluorescent labeled protein-SDS complexes by gel filtration of 4% agarose. The fluorescent label allows high sensitivity while the nature of the technique readily lends itself also to preparative separations. Evidence is presented for the linear dependence of log molecular weight of the fluorescent complexes on the relative elution volume. A representative preparative run is also shown illustrating a separation of the chains of gamma globulin.     

A procedure for the purification of beta-lactoglobulin from bovine milk using gel filtration chromatography at low pH

A simple and rapid procedure for the purification of beta-lactoglobulin (β-LG) from bovine milk is described. The procedure exploits the major difference in molecular mass of β-LG and other whey components and the existence of the former in monomeric form at acidic pH. Gel filtration of whey was carried out using a Bio-Gel P10 column at pH 3.0. Residual caseins and other milk proteins were excluded from the gel and β-LG and alpha-lactalbumin (α-LA) emerged as two fully resolved peaks. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) suggested that β-LG was purified to apparent homogeneity, while absorption, fluorescence, and circular dichroism spectroscopy indicated the native-like conformation of the protein. Western blot analysis revealed that the antibodies raised against the purified β-LG in rabbits also readily react with the commercial bovine protein. This procedure requires only 4-5 hr for the purification of about 10 mg of β-LG from a single run while using a small column (2.3 cm x 83 cm) of Bio-Gel P10 and has the potential for scaling up.     

Partial purification and determination of molecular weights of glyoxalases by filtration on dextran gel

Glyoxalase I and glyoxalase II (EC. 4.4.1.5 and EC 3.1.2.6) were separated by gel filtration on Sephadex G-75 and G-100. This simple procedure permitted also the partial purification of glyoxalase II. The purification coefficient in a single run from supernatant from beef liver was about 1 : 30 compared with 1 : 15 after the fifth step of purification with classical methods.     

A high performance gel filtration chromatography method for gamma-glutamyltransferase fraction analysis

The clinical relevance of serum gamma-glutamyltransferase (GGT) activity, in areas other than hepatic function, has recently been increased by several epidemiological associations. Still, GGT remains a nonspecific test because of the influence of various pathophysiological factors. We devised a procedure based on gel filtration chromatography, followed by postcolumn injection of fluorescent GGT substrate (gamma-glutamyl-7-amido-4-methylcoumarin), permitting the quantification of GGT fractions in serum or plasma. Plasma GGT molecular weight distribution was analyzed in healthy volunteers (20 males; mean+/-SD age 38+/-10 years; 20 females; age 44+/-13; total GGT 21+/-11 for males vs 13+/-7 for females; P<0.01). The method is highly sensitive (determination limit: 0.5 U GGT/L), with a linear dynamic range between 0.5 and 150 U/L for each fraction. Four GGT fractions of different molecular weight were detected in all subjects of both genders: b-GGT, m-GGT, s-GGT (likely lipoprotein-bound, molecular masses >2000, 940, and 140kDa, respectively), and a free fraction (f-GGT, 70kDa). f-GGT and s-GGT were the main fractions in subjects with lower and higher total GGT activity, respectively. Higher total GGT activity in males is related mainly to f-GGT (P<0.01). GGT fraction analysis may increase the sensitivity and specificity of the GGT activity test.     

Validation of the use of intermolecular NOE constraints for obtaining docked structures of protein-ligand complexes

Summary The use of intermolecular NOEs for docking a small ligand molecule into its target protein has been investigated with the aim of determining the effectiveness and methodology of this type of NOE docking calculation. A high-resolution X-ray structure of a protein-ligand complex has been used to simulate loose distance constraints of varying degrees of quality, typical of those estimated from experimental NOE intensities. These simulated data were used to examine the effect of the number, distribution and representation of the experimental constraints on the precision and accuracy of the calculated structures. A standard simulated annealing protocol was used, as well as a more novel method based on rigid-body dynamics. The results showed some analogies with those from similar studies on complete protein NMR structure determinations, but it was found that more constraints per torsion angle are required to define docked structures of similar quality. The effectiveness of different NOE-constraint averaging methods was explored and the benefits of using R^–6 averaging rather than centre averaging with small sets of NOE constraints were shown. The starting protein structure used in docking calculations was obtained from previous X-ray or NMR structure studies on a related complex. The effects on the calculated conformations of introducing structural differences into the binding site of the initial protein structure were also considered.To whom correspondence should be addressed.     

The construction and analysis of sucrose gradients for use with zonal rotors.

The rate of sedimentation of a particle in a sucrose solution depends on the viscosity and density of the medium. These two variables are related to the sucrose concentration and the temperature of the medium by new simple equations. These equations were used in a rapid iterative procedure that relates the distance moved by a zone in a continuous sucrose gradient to its sedimentation coefficient. It is shown by comparison with experiment that this iterative method allows the distance moved by a zone to be calculated rapidly. The method may therefore be used to optimize the separation of particles in a sucrose-gradient-centrifugation experiment. The method also allows the unknown sedimentation coefficients of several zones to be measured from a single sucrose-gradient-centrifugation experiment.     

A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E.coli

As enzymes evolve and diverge from common ancestor sequences, they often keep their overall reaction chemistry but specialize in the binding of different cognate ligands. This study borrows methods for the computational assessment of 2D similarity of small molecules from the field of chemoinformatics, to examine the extent of structure conservation of cognate ligands binding to similar proteins. Proteins from 87 structural superfamilies from Escherichia coli form the core dataset, which is extended using homologues with functional assignments from any organism. We find that correlation of the substrate similarity with protein similarity (measured by either sequence-based or structure-based scores) can only be clearly established for very similar proteins. At low sequence identities, the superfamily to which a protein belongs can give helpful clues to its function, and more importantly, the confidence attached to such clues is superfamily-dependent. Our data indicate that only a few superfamilies show great substrate diversity, and that most exhibit conservation of at least part of the structural scaffold of the substrate.     

Isolation and purification of myelin proteolipid protein using high speed gel filtration in sodium dodecyl sulfate

Small and preparative gel filtration columns were studied for high pressure liquid chromatography of myelin proteins in sodium dodecyl sulfate. The preparative column proved useful for isolating and purifying proteolipid protein almost free (0.3–0.5%) of myelin basic protein as demonstrated by SDS-PAGE, MBP RIA, and immunoblotting. The small columns were not as useful as SDS-PAGE for analytical purposes.     

Proteoglycan complexes from bovine heart valve. Fractionation by density-gradient centrifugation and gel filtration under dissociative conditions.

Proteoglycan complexes from collagenase [EC 3.4.24.3]-indigestible materials of bovine heart valves were extracted with 4 M guanidinium chloride, purified by ion-exchange column chromatography in a urea-containing solution, then fractionated by density-gradient centrifugation under dissociative conditions. Electrophoretic characteristics and enzymic susceptibility of the density-gradient fractions revealed that the glycosaminoglycans constituting the proteoglycan complexes in this indigestible materials were mainly dermatan sulfate in the top three fractions, and dermatan sulfate and chondroitin sulfates in the bottom fraction; a minor constituent which was common to all the fractions was hyaluronic acid. A gel-like substance (Fr. Ig) at the top of the gradient, amounting to about 25% of the loaded dry sample, contained only a trace of hydroxyproline (less than 1%) and was composed of proteodermatan sulfate, glycoprotein, and a small amount of hyaluronic acid. Sodium dodecyl sulfate-polyacrylamide gel electrophoretic analyses of Fr. Ig with 2-mercaptoethanol showed that the major part of the proteins in this gel-like substance was cross-linked by disulfide bridges. Chromatography of Fr. Ig on Sepharose 4B in buffered 4 M guanidinium chloride containing 2-mercaptoethanol, together with the electrophoretic patterns of the resulting fractions, suggested that proteodermatan sulfate was not associated with hyaluronic acid through covalent bonds. The amino acid composition of Fr. Ig was very similar to that reported in the literature for "dermatan sulfate-protein complex", and "structural glycoprotein" or "acidic structural protein".