Cooligopeptides containing aromatic residues spaced by glycyl residues. IX. Fluorescence properties of tryptophan-containing peptides

The fluorescence properties of several cooligopeptides of glycine, phenylalanine, and tryptophan, containing one or two aromatic residues, are investigated. In particular, a detailed analysis is made of the influence of pH upon the quantum yield and the position of the emission maximum (λ_max) in H-Trp-Trp-OH, H-Trp-Gly-OH, H-Gly-Trp-OH, H-Gly-Trp-Gly-OH, H-Trp-Trp-OH, H-Trp-Trp-Gly-OH, H-Gly-Trp-Trp-OH, H-Phe-Trp-OH, H-Phe-Trp-Gly-OH, H-Gly-Phe-Trp-OH, and H-Gly-X-(Gly)_n-Trp-Gly-OH, with X = Phe or Trp, and n = 0,1,2. It is shown that raising the pH from ca. 2 to 11 results in a red shift of λ_max, and an increase in the quantum yield. These changes, mostly structure dependent, are in most cases attributable to electronic perturbations acting directly upon the λ_max of the fluorophore(s) and upon the quenching efficiency of the free amino and carbonyl groups. For the compounds having two adjacent tryptophyl residues, it is shown that the two fluorophores do not appear to have the same emission properties and the quantum yield is lower than expected. The causes of this behavior are discussed in terms of conformational effects, stacking interactions, and radiationless energy transfer. Finally, an attempt is made to correlate fluorescence data with previous circular dichroism data which had indicated the occurrence of a conformationally rigid structure for some of the compounds having two adjacent aromatic residues.     

Succinic semialdehyde dehydrogenase. Reactivity of lysyl residues.

The enzyme succinic semialdehyde dehydrogenase from pig brain has been 2000-fold purified by a combination of DEAE-cellulose, hydroxyapatite, and AMP-Sepharose chromatography. This preparation has a molecular weight of 160,000 and a specific activity of 5.3 mumol/min.mg at 25 degrees C. The inhibition of succinic semialdehyde dehydrogenase by carbonyl compounds, i.e. P-pyridoxal and o-phthalaldehyde was investigated in detail. The enzyme is reversible, inhibited by preincubation with P-pyridoxal (mixing molar ratio, 300:1) at either 25 degrees or 37 degrees C. Reduction with NaBH1 results in the incorporation of approximately 4 mol of P-pyridoxyl residues/mol of enzyme. NAD+ protects the enzyme against inactivation by P-pyridoxal, whereas the substrate succinic semialdehyde failed to prevent the reaction of P-pyridoxal with lysine residues of the protein. The binding of approximately 10 mol of o-phthalaldehyde/mol of enzyme results in irreversible loss of catalytic activity. The reaction is fast and easily monitored by absorption and fluorescence spectroscopy.     

Peptoid residues and beta-turn formation.

A set of terminally protected tripeptoids containing a residue of either N-methylglycine or N-isobutylglycine in position i + 1/i + 2 were synthesized and tested for intramolecularly H-bonded beta-turn formation. By exploiting FT-IR absorption and 1H NMR techniques, their folding tendencies were compared with those of a variety of reference peptides. The amount of beta-turn induction and the relative extent of the various types of intramolecularly H-bonded beta-turn conformers were determined in chloroform solution.     

Performance of animals fed crop residues.

Ruminants can utilize crop residues as sources of energy, but productivity is low because of the high level of cell walls and lignin. Chemicals, especially sodium hydroxide, have been used to increase the digestibility of crop residues. Hemicellulose is solubilized and the extent and rate of cellulose and hemicellulose digestion are increased. Two systems have been developed for chemical treatment. The first involves pelleting finely ground residue in combination with sodium hydroxide treatment. A dense, easily transported feed-stuff is produced. The second method is an "on-the-farm" method that utilizes a minimum amount of equipment. In vitro and in vivo digestibilities have been increased from 10 to 20 percentage units by sodium hydroxide treatment. While lamb and cattle gains have generally been increased by feeding chemically treated residues, the level of performance often has not been as great as would be predicted from in vitro digestibilities. Sodium residues following chemical treatment have been shown to increase rate of passage from the rumen and reduce rumen fiber digestion. The use of alfalfa with sodium hydroxide-treated residues and the use of ammonium or calcium hydroxides for treatment have good potential.     

Reversible modification of arginine residues. Application to sequence studies by restriction of tryptic hydrolysis to lysine residues.

1, 2-Cyclohexanedione reacts specifically with the guanidino group of arginine or arginine residues at pH 8 to 9 in sodium borate buffer in the temperature range of 25-40 degrees. The single product, N-7, N-8-(1,2-dihydroxycyclohex-1,2-ylene)-L-arginine (DHCH-arginine) is stable in acidic solutions and in borate buffers (pH 8 to 9). DHCH-Arginine is converted to N-7-adipyl-L-arginine by periodate oxidation. The structures of the two compounds were elucidated by chemical and physicochemical means. Arginine or arginyl residues can be regenerated quantitatively from DHCH-arginine by incubation at 37 degrees in hydroxylamine buffer at pH 7.0 FOR 7 TO 8 hours. Analysis of native egg white lysozyme and native as well as oxidized bovine pancreatic RNase, which were treated with cyclohexanedione, showed that only arginine residues were modified. The utility of the method in sequence studies was shown on oxidized bovine pancreatic ribonuclease A. Arginine modification was complete in 2 hours at 35 degrees in borate buffer at pH 9.0 with a 15-fold molar excess of the reagent. The derived peptides showed that tryptic hydrolysis was entirely limited to peptide bonds involving lysine residues, as shown both by two-dimensional peptide patterns and by isolation of the resulting peptides. The stability of DHCH-arginyl residues permits isolation of labeled peptides.     

Tryptophan residues of saccharifying alpha-amylase from Bacillus subtilis. A kinetic discrimination of states of tryptophan residues using N-bromosuccinimide.

Four tryptophan residues of saccharifying alpha-amylase from B. subtilis out of eleven in total are reactive towards N-bromosuccinimide (NBS), suggesting that they are on the surface of the enzyme. This is consistent with the results of solvent perturbation difference spectrophotometry with ethylene glycol. One of four tryptophan residues was clearly distinguished from the other three in reactivity with NBS by the stopped-flow method. This most reactive tryptophan residue was not protected from modification by substrates of analogs, indicating that the tryptophan is not located in the substrate binding site. One of the other three tryptophan residues, probably the second most reactive one, is considered to be related in some way to the glycosyl transfer in the reaction of the enzyme with maltose as a substrate.     

Yeast phenylalanyl-tRNA synthetase. Properties of the histidyl residues.

Reactivity of the histidyl groups of yeast phenylalanyl-tRNA synthetase was studied in the absence or presence of substrates. In the absence of substrates about 10 histidine residues were found to react with similar kinetic constants. Phenylalanine at 10(-3) M was found to protect two histidyl residues; increasing the amino acid concentration to 5 . 10(-3) M resulted in the protection of two more histidyl groups. tRNAPhe did not afford any protection to histidine residues, but acylated phenylalanyl-tRNA (Phe-tRNAPhe) protected two of the four histidyl groups already protected by phenylalanine. These results suggest the existence of two different sets of accepting sites for phenylalanine: one specific for the free amino acid, the other one specific for the amino acid linked to the tRNA, but being accessible to free phenylalanine, with a somewhat lower binding constant, ATP was found to mask around four histidyl residues against diethylpyrocarbonate modification. By photoirradiation of enzyme-phenylalanine complex in the presence of rose bengale, a significant amount of amino acid was bound to the alpha subunit (Mr = 73 000) of phenylalanyl-tRNA synthetase, confirming that the amino acid binding site is located on this subunit, as previously suggested by modification of thiol groups. Upon irradiation of an enzyme-tRNA complex, almost no covalent binding of tRNA occurred during enzyme inactivation, suggesting that the histidyl residues involved in the enzymic activity are not required for tRNA binding.     

Identification of effector-activating residues of Gs alpha.

The heterotrimeric G proteins transduce extracellular signals by interacting with specific intracellular effectors. We have used a scanning mutagenesis approach to identify amino acids of alpha S, the alpha subunit of Gs, that determine the specificity of its interaction with its effector, adenylyl cyclase. In alpha subunit chimeras, residues 236-356 of alpha S comprise the shortest linear stretch that is required for activation of adenylyl cyclase. Within these 121 residues, we identified four clusters of residues in which substitutions prevented effector activation. Mutations in three of these regions did not affect alpha subunit expression or the GTP-induced conformational change. The identified alpha S residues in the NH2-terminal half of the 121-residue region endowed the cognate alpha i2 segment with the ability to activate effector, while those in the COOH-terminal half did not. In a three-dimensional G alpha model, based on the structure of p21ras, the effector-activating residues of alpha S form a surface on the membrane-facing side of the molecule; this surface includes a region that changes conformation upon binding GTP.     

Surface topography of histidine residues in lysozymes.

Several avian and mammalian c-type lysozymes were chromatographed on chelated (to iminodiacetate) and immobilized transition metal ions (Co2+, Ni2+, Cu2+ and Zn2+) under a variety of experimental conditions. The varied affinity of evolutionary variants of the lysozyme family for chelated metal ions, IDA-M(II), can be rationalized primarily in terms of the presence, multiplicity and microenvironments of histidine residues. The chromatographic resolution of some of these closely related proteins attests to the analytical power of immobilized metal-ion affinity chromatography.     

Identification of kinetically hot residues in proteins.

A number of recent studies called attention to the presence of kinetically important residues underlying the formation and stabilization of folding nuclei in proteins, and to the possible existence of a correlation between conserved residues and those participating in the folding nuclei. Here, we use the Gaussian network model (GNM), which recently proved useful in describing the dynamic characteristics of proteins for identifying the kinetically hot residues in folded structures. These are the residues involved in the highest frequency fluctuations near the native state coordinates. Their high frequency is a manifestation of the steepness of the energy landscape near their native state positions. The theory is applied to a series of proteins whose kinetically important residues have been extensively explored: chymotrypsin inhibitor 2, cytochrome c, and related C2 proteins. Most of the residues previously pointed out to underlie the folding process of these proteins, and to be critically important for the stabilization of the tertiary fold, are correctly identified, indicating a correlation between the kinetic hot spots and the early forming structural elements in proteins. Additionally, a strong correlation between kinetically hot residues and loci of conserved residues is observed. Finally, residues that may be important for the stability of the tertiary structure of CheY are proposed.     

Near-heme histidine residues of deoxy- and oxymyoglobins.

Proton NMR titration curves of the histidine Cepsilon-H resonances of the deoxy and oxy forms of human, horse, and sperm whale myoglobins (Mb) were determined and compared with the results for the met and azide forms. One extra titrating resonance (H-8) was observed for each deoxy-Mb compared with the corresponding met-Mb, and a further extra resonance (H-9) was observed for the oxy-Mb form. These resonances correspond to the two additional resonances previously described for azide-Mb [Hayes, M., Hagenmaier, H., & Cohen, J. S. (1975) J. Biol. Chem. 250, 7461--7472]. This new evidence prompts us to reassign these resonances to the near-heme histidine residues.     

Evidence for lysosomal reduction of cystine residues.

Previously reported evidence for the existence of a thiol: protein disulphide oxidoreductase in rat liver lysosomes has been re-examined and ambiguous results obtained. However, incubation of purified rat liver lysosomes with ¹²⁵I-labelled insulin at pH 5.5 shows that cathepsin D and a thiol-dependent enzyme other than cathepsin B or L are important in its digestion. The latter enzyme is most probably a thiol: protein disulphide oxidoreductase.