A modified amino acid analyzer with greater versatility

An older amino acid analyzer was easily modified with commercially available components to update it by providing more convenient sample application, more accurate timing, greater sensitivity, and automatic regeneration. New features were introduced to permit the optional use of different buffer systems and methodologies as well as the convenient analysis of unusual basic amino acids.     

Sequential elution of proteins in small volumes by preparative polyacrylamide gel electrophoresis

A simple flexible method for separation of proteins by polyacrylamide gel electrophoresis and sequential elution into dialysis bags has been devised. The system was applied to isolation of three glycoproteins from the peritoneal fluid of mice bearing Ehrlich ascites tumor.     

A modified radioisotopic assay for measuring glutamine synthetase activity in tissue extracts.

A radioisotope assay for the measurement of glutamine synthetase activity has been developed in which tandemly arranged ion-exchange columns of Dowex 1-acetate and Amberlite CG-50 (H⁺) are used to separate the product, [¹⁴C]glutamine, from unreacted [U-¹⁴C]glutamate and other labeled compounds, particularly γ-aminobutyrate, that are formed by competing reactions. The technique is sensitive, reproducible, and suitable for multiple determinations. The assay has been used successfully to measure glutamine synthetase activity in neural and nonneural tissues which contain appreciable amounts of glutamate decarboxylase activity.     

A combined theoretical and experimental study of the interaction of metrizamide with proteins

A theory of isopycnic sedimentation of interacting systems provides a theoretical explanation for the isopycnic behavior of catalase and other proteins in metrizamide gradients of pH 7.0–7.5, particularly the bimodal banding patterns reported by some investigators. As for whether or not the model is realistic, a spectroscopic investigation provides an unambiguous demonstration of a reversible interaction between metrizamide and the catalase dimers formed by dissociation of catalase tetramer at pH 3. The metrizamide-catalase dimer complex(es) is of high bouyant density. In addition, metrizamide at pH 7.4 interacts with heat-denatured ovalbumin. These observations suggest that the denser band in the experimental bimodal isopycnic patterns might be a complex(es) of metrizamide with a comformationally altered state of the protein.     

A study of the preferred environment of amino acid residues in globular proteins

In the native folded conformation of a globular protein, amino acid residues distant along the polypeptide chain come together to form the compact structure. This spatial structure is such that most of the polar residues are on the surface and have contact with the solvent medium and the nonpolar residues buried in the interior which have contact with similar nonpolar side chains. This cooperativity and mutual interaction among the randomly aligned amino acid residues suggest that each type of residue may prefer to have a specific environment. To gain more insight into this aspect of residue-residue cooperativity, a detailed analysis of the preferred environment associated with each of the 20 different amino acid residues in a number of protein crystals has been carried out. The variation of nonpolar nature computed for different sizes of spheres shows that the spatial region between radii of 6 and 8 Å is more favored for hydrophobic interactions and indicates that the influence of each residue over the surrounding medium extends predominantly up to a distance of 8 Å. The analysis of the surrounding amino acid residues associated with each type of residue shows that there is a definite tendency for each type of residue to have association with specific residues. The variation in environment is found even within the polar group as well as in the nonpolar group of residues. The surrounding residues associated with isoleucine, leucine, and valine are purely nonpolar. Proline, a nonpolar residue, is often surrounded by polar residues. The surrounding nonpolar nature of the tryptophan and tyrosine residues implies that even a single polar atom in a nonpolar side chain is sufficient to reduce their hydrophobic environment. There exists a high degree of mutual residue-residue cooperativity between the pairs glutamic acid-lysine, methionine-arginine, asparagine-tryptophan, and glutamine-proline, and the mutual residue-residue noncooperativity is high for the pairs methionine-aspartic acid, cysteine-glutamic acid, histidine-glutamine, and leucine-asparagine. The formation of secondary and tertiary structures is discussed in terms of the preferred environment and mutual cooperativity among various types of amino acid residues.     

A method for determining amino acid concentrations and specific activities of amino acids and some other compounds in biological fluids

A method is described for obtaining plasma ultrafiltrates from which the concentrations of all amino acids, including tryptophan and ammonia, are obtained. A split-stream methodology is described for obtaining, in addition to the concentrations, the radioactivities of amino acids, glucose, and plasma water.     

Synthesis and quantitation of glucitollysine, a glycosylated amino acid elevated in proteins from diabetics

A conceptually simple method of vertical gel electrophoresis is presented. It involves the use of pliable plastic envelopes to house individual gels and their constituent buffer reservoirs and electrical systems completely submersed in coolant separate from other gels. In conjunction with a common cooling tank this envelope technique provides unusual versatility for running a variety of different type gels simultaneously.     

Separation of poly(ADP-ribosylated) nuclear proteins by polyacrylamide gel electrophoresis at acidic pH and low temperature

A method for the extraction and electrophoresis of poly(ADP-ribosylated) nuclear proteins is described. An extraction method using lithium dodecyl sulfate as detergent at pH 2.4 and room temperature is shown to fully extract nuclear proteins under conditions where full stability of protein-linked polymer is ensured. The polyacrylamide gel electrophoresis is performed again under conditions where full stability is ensured. This work provides a technique whereby misinterpretation of relative ADP ribosylation of nuclear proteins can be avoided.     

A radiochemical assay for N5-formyltetrahydrofolic acid (citrovorum factor) in serum and urine.

N⁵-Methyltetrahydrofolate, but not N⁵-formyltetrahydrofolate, can be measured in biological fluids by ligand-binding radioassay. Therefore, in order to measure N⁵-formyltetrahydrofolate by radioassay, it is chemically converted to N⁵-methyltetrahydrofolate by acidification followed by reduction with borohydride. By this method, 70–113% of N⁵-formyltetrahydrofolate added to serum and urine was recovered. The plasma clearance of the mixture of diastereoisomer of N⁵-formyltetrahydrofolate (Leucovorin) following intravenous administration to two normal subjects was rapid for the first 30 min, but then plateaued and cleared very slowly over the next 90 min, most probably because of the accumulation of the inactive isomer which was slowly excreted in the urine during this time period.     

On the crystallization of proteins

We report on theoretical and experimental work aimed at a systematic approach to the crystallization of proteins. Successful crystallization depends on the competition between the growth rates for compact three-dimensional structures and long-chain structures leading to an amorphous precipitate. Quasi-elastic light scattering was used to monitor the size and shape distribution of small aggregates in a model system (lysozyme) during the pre-nucleation stage. With the aid of a simple model, the line-width of the scattered light was used to predict whether crystals or an amorphous precipitate would result. Once visible crystals appeared, the lysozyme concentration near the crystal surface was monitored and the kinetic parameters for growth obtained. A peculiar self-limiting phenomenon causes crystals to stop growing after a certain size has been reached. When these terminal size crystals were cleaved, growth occurred at the surface until the original size was approximately restored.     

A manganese catalyzed covalent binding of estradiol - 17 beta to cytosol proteins of rabbit uterus.

Studies of the temperature sensitivity of estradiol receptor binding in rabbit uterine cytosol have revealed the existence of an enzyme which catalyzes the covalent binding of estradiol to cytosol proteins. A fraction, prepared by chromatography on Biogel P-200 and incubated at 37 degrees C in the presence of Mn++, exhibited a time-dependent, temperature-sensitive, oxidative binding of estradiol not seen in the crude cytosol preparation. Although the activity of this enzyme was shown to be independent of estradiol binding by the high affinity estrogen receptor, its presence may complicate studies of estrogen receptor action which involve the use of elevated temperatures.     

A method using 3-O-methyl-D-glucose and phloretin for the determination of intracellular water space of cells in monolayer culture.

A method is presented for determining the extent of methylation of tRNAs synthesized in mammalian and bacterial cell systems and is based upon determining the distribution of radioactivity associated with the guanine constituents of total cellular tRNA preparations previously labeled with [2-¹⁴C]guanosine and with [methyl]-³H or -¹⁴C]methionine. Whereas labeling with guanosine provides a means of assessing the extent of methylation of the [2-¹⁴C]guanine residues incorporated into tRNA, methionine labeling provides a measure of the percentage of [methyl-³H or -¹⁴C]methylated constituents that are methylated guanines. Analyses such as the above reveal that the tRNA of KB cells acquires approximately three times as many methyl groups as that of E. coli B tRNA. Coupled with the knowledge that both mammalian and bacterial tRNA preparations contain an average of 24 guanine residues per molecule, the above analyses further reveal that 7.2 and 2.4 methyl groups are incorporated into each tRNA molecule synthesized in exponentially growing KB- and E. coli B-cells, respectively. Additional information regarding the extent of formation of individual methylated constituents per tRNA molecule synthesized is presented.     

High resolution gel chromatography of proteins

An assay for the determination of l-glutaminase in extracts and intact cells is described. The method is based on the stereospecific release of ³H₂O from l-[2-³H]glutamine when l-glutaminase is coupled to l-aspartate:2-oxoglutarate amino transferase. The substrate, glutamine, and intermediate product, glutamate, are separated from the final reaction product, tritiated water, on a mixed-bed ion-exchange column which retains amino acids and organic acids but not water. The method has been adapted to determine the activity of l-glutaminase in cultured human diploid fibroblasts.     

Avian fatty acid synthetase: Evidence for short-term regulation of activity

Liver biopsies were performed on starved chicks at 0 and 4 h after refeeding a fat-free diet. Fatty acid synthetase activity increased after refeeding, and administration of cycloheximide did not prevent the rise of enzyme activity. Incorporation of [carboxyl-¹⁴C]leucine into fatty acid synthetase was measured in enzyme purified from the livers of starved chicks, starved-refed (4 h) chicks, and starved-refed chicks injected with cycloheximide. The data suggest that the synthesis of enzyme protein was inhibited in starved and cycloheximide-treated refed chicks in comparison with refed chicks. Liver cytosol from fed or starved chicks was filtered through centrifuge ultrafiltration membranes and the residues were suspended in the same or opposite filtrates. Fatty acid synthetase activity in residues from starved chicks was stimulated when suspended in filtrates from fed chicks. The evidence is consistent with the hypothesis that a portion of the fatty acid synthetase in the liver of starved chicks is present as an inactive form which can be activated upon refeeding.     

Pairing of inosine with adenosine in codon position two in the translation of polyinosinic acid

Poly (I) codes for valine even more than for glycine. Since the ratio is constant over a wide range of Mg²⁺ concentrations the ambiguity appears to be inherent in the translation of I-I-I, rather than induced by the relatively high Mg²⁺ concentration (or the streptomycin) required with this messenger. These findings indicate that I in codon position 2 can pair readily not only with C (complementing glycine codon GG_⁵) but also with A (complementing valine codon GU_).I in anticodon position 3 is also known to pair with A (as well as with U and C). Crick's model for this pair would require a large increase in interstrand distance, rather than simply “wobble”. This stretch would be avoided in an alternative model, suggested by Sakore &; Sobell (1969), in which A would rotate from the usual anti to the syn conformation. Since a large stretch would seem difficult to accommodate in the less flexible middle codon position the present findings suggest that the rotation model for I·A pairing merits further exploration.     

Analysis of collagen cyanogen bromide peptides using electrophoresis in continuous concave gradient polyacrylamide gels.

A rapid and simple spectrophotometric method is described for the estimation of microgram quantities of glycosaminoglycans following the formation of soluble complexes with alcian blue dye. The method is based on the different absorption spectra of the dye and dye-glycosaminoglycan complexes. No heating, centrifugation, lengthy equilibration, or sophisticated instrumentation which hamper other methods are required. Samples are mixed with freshly prepared dye solution and absorbance readings at 480 nm are compared to an appropriate standard curve. Albumin and individual monosaccharides do not interfere with the assay but high concentrations of chloride ion do. The method is suitable for the estimation of total glycosaminoglycan levels in biological fluids such as urine and blood.     

Structural and functional role of leucine residues in proteins

Circular dichroism and potentiometric titration studies of leucine random copolymers in aqueous solutions, as well as a comparison of the conformational stability in poly-α-amino acids, indicate that leucine may possibly be the amino acid with the highest propensity for forming α-helical structures. This suggests that leucine might be found most frequently in the helical regions of proteins. A survey was made on 15 different proteins containing 2473 residues with known sequence and conformation determined by X-ray crystallography: carboxy-peptidase A, α-chymotrypsin, cytochrome b₅, elastase, ferricytochrome c, α- and β-hemoglobin, insulin, lysozyme, myogen, myoglobin, papain, ribonuclease A, staphylococcal nuclease, and subtilisin BPN′. It was found that 888 residues in these proteins are in helices, and 422 of them reside in the internal turns of helical regions. While Glu, Ala, Leu and His were found to be present with the highest percentages in helical regions, Leu was clearly the most abundant residue in the inner helical cores of proteins. Polar residues are found preferentially at the helix-coil boundary regions; Asp and Glu at the N-terminal and His, Lys and Arg at the C-terminal helical ends. These findings agree with Ptitsyn's (1969) analysis on seven proteins containing 1132 residues. A more comprehensive analysis in the present survey showed that Ile, Met and Val occur with the greatest frequency in the β-regions of proteins. Leu was also found as the strongest structure-forming residue in proteins (total helical and β-regions). The functional-structural role of leucine was established by showing that it occurs most frequently among residues surrounding the heme in five of the heme proteins. In addition, the greater abundance of leucine as neighbors to active-site residues in enzymes provides strong evidence that hydrophobic residues create a non-aqueous environment, aiding the polar residues in substrate binding and enzymic catalysis. Examples of conservative and non-conservative mutations of leucine in heme proteins are given to illustrate the structure—function relation of proteins, and explain why most leucine residues in the insulin, hemoglobin, and cytochrome c homologs are invariant. Finally, the strong helical-forming power of leucine, as demonstrated experimentally in synthetic copolypeptides and its high occurrence in the inner helical cores of proteins, suggests that it could have a major role as nucleation centers in the folding and evolution of large protein molecules.