Synthesis of peptide bonds by proteinases. Addition of organic cosolvents shifts peptide bond equilibria toward synthesis.
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Chymotrypsin↗
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Characterization and site of action of a soluble protein that stimulates peptide-bond synthesis.
A recently identified soluble protein, named EF-P, stimulates peptide bond synthesis from ribosomal-bound N-formylmethionyl-tRNA and the aminoacyl-tRNA analog, puromycin. Using this model of peptide bond formation we have purified this activity approximately 100-fold from ribosome-free extracts of Escherichia coli. In order to study the mechanism by which the EF-P factor stimulates peptide bond formation, we examined and compared the requirements and site of action of the spontaneous and the EF-P-mediated synthesis of peptide bonds. We find that "enzymic" peptide bond synthesis (+EF-P) is characterized by relatively broad temperature and NH4Cl optima, a sharp Mg2+ optimum at 12 mM, and an apparent pKa of approximately 8.5. The characteristics of enzymic peptide bond synthesis closely resemble those reported for native peptidyl-puromycin formation rather than other models of peptide synthesis. Factor EF-P requires both 30-S and 50-S subunits for activity. The 30-S particle is inactive by itself and may function in the reaction merely to bind the fMet-tRNA substrate. Both the peptidyl transferase and the EF-P binding site may be part of the 50-S subunit. Unlike all other propagation factors, EF-P does not require the 50-S ribosomal proteins L7 and L12 and may therefore occupy a different ribosomal site.
Bacterial Proteins↗
Selective chemical cleavage of tryptophanyl peptide bonds by oxidative chlorination with N-chlorosuccinimide.
Tryptophanyl peptide bonds are selectively cleaved by N-chlorosuccinimide (NCS) under acidic conditions. All other peptide bonds are resistant to cleabage by this reagent. Optimal conditions for cleavage are: 2 equiv of NCS, pH 4-5, or 50-80% acetic acid for 30 min at room temperature. Under these conditions methionine residues are oxidized to methionine sulfoxides and cysteine. Other amino acids are not modified. The cleavage reaction was studied with several peptides containing tryptophan residueas successfully applied to several proteins. In alpha-lactalbumin, Kunitz trypsin inhibitor ,and apomyoglobin, selective cleavage of the expected tryptophanyl peptide bonds was obtained in 19-58% yield. The glucagon molecule was fragmented into two peptides in 32% yield.
Amino Acid Sequence↗
Energetics of peptide bond formation at elevated temperatures.
The free energies of formation of the peptide bond between carbobenzoxy-glycine and L-phenylalanine amide in aqueous solution at temperatures up to 60 degree C were calculated from experimentally determined equilibrium constants. The reaction was catalyzed by a thermophylic enzyme. The thermodynamic energy barrier to peptide bond formation was found to decrease with increasing temperature: the standard free energy of peptide bond formation did appear to become negative in the region of 60 degrees C. The possible significance of these results for peptide bond formation under prebiotic conditions is discussed.
Biological Evolution↗
Selective cleavage of peptide bonds by a serine protease from rat skeletal muscle.
The selective cleavage of peptide bonds by a serine protease from skeletal muscle (SK-protease) was examined using glucagon and neurotensin as substrates. Among the peptide bonds cleaved in these substrates, the most susceptible were Phe-Thr-Ser, Tyr-Leu, Trp-Leu, and Tyr-Ile. These results indicate that the SK-protease hydrolyzed the carboxyl side of aromatic amino acid residues under the experimental conditions. When the amino acid on the carboxyl side of aromatic amino acid residues was serine, threonine or glutamic acid, these peptide bonds, such as Phe-Thr, Tyr-Ser, and Tyr-Glu, were not susceptible to another serine protease from small intestine (SI-protease) under the same experimental conditions. The peptide bond between the arginines of Pro-Arg-Arg-Pro in neurotensin was hydrolyzed by the SI-protease, but not by the SK-protease. Thus the specificity of the SK-protease differs from that of the SI-protease. These results suggest that the specificity of the hydrolytic action of the SK-protease is more like that of bovine chymotrypsin A than like that of porcine chymotrypsin C and of the SI-protease.
Amino Acids↗
Reduced peptide bond cyclic somatostatin based opioid octapeptides. Synthesis, conformational properties and pharmacological characterization.
The conformational and pharmacological properties that result from peptide bond reduction as well as the use of secondary amino acids in a series of cyclic peptides related to the mu opioid receptor selective antagonist D-Phe1-Cys2-Tyr3-D-Trp4-Orn5-Thr6-Pen7+ ++-Thr8-NH2 (IV), have been investigated. Peptide analogues that contain [CH2NH] and [CH2N] pseudo-peptide bonds (in primary and secondary amino acids, respectively) were synthesized on a solid support. Substitution of Tyr3 in IV by the cyclic, secondary amino acid 1,2,3,4-tetrahydroisoquinoline carboxylate (Tic) and of D-Trp4 with D-1,2,3,4-tetrahydro-beta-carboline(D-Tca4), gave peptides 4 and 1, respectively. Both analogues displayed reduced affinities for mu opioid receptors. Conformational analysis based on extensive NMR investigations demonstrated that the backbone conformations of 1 and 4 are similar to those of the potent and selective analogue D-Phe-Cys-Tyr-D-Trp-Lys-Thr-Pen-Thr-NH2 (I), while the conformational properties of the side chains of Tic3 (4) and D-Tca4 (1) resulted in topographical properties that were not well recognized by the mu opioid receptor. Peptide bond modifications were made including (Tyr3-psi[CH2NH]-D-Trp4), 3; (Tyr3-psi[CH2N]-D-Tca4), 2; and (Cys2-psi[CH2N]-Tic3), 6. These analogues showed decreases in their mu opioid receptor affinities relative to the parent compounds IV, 1, and 4, respectively. 1H NMR based conformational analysis in conjunction with receptor binding data led to the conclusion that the reduced peptide bonds in 2, 3, 5, and 6 do not contribute to the process of discrimination between mu and delta opioid receptors, and in spite of their different dynamic behaviors (relative to 1 and 4), they are still capable of attaining similar receptor bound conformations, possibly due to their increased flexibility.
Amino Acid Sequence↗
Ribosome dynamics at the conserved PGP motif governs 2A peptide-bond-skipping efficiency.
Viral 2A oligopeptides drive an unusual ribosome recoding event in which peptide-bond formation fails at a conserved PG↓P motif, producing two discrete proteins without canonical termination. Despite decades of study, the molecular basis of 2A-mediated peptide-bond skipping remains poorly understood. Here, we combine quantitative 2A reporters with high-resolution ribosome profiling to interrogate ribosome dynamics at the core 2A sequences. We identify a pausing event at the terminal proline codon of the PGP motif that functions as a kinetic decision point: ribosome dwell time at this site inversely correlates with skipping efficiency. Increasing nascent chain flexibility by inserting linkers immediately upstream of the 2A sequence reduces ribosome occupancy at the terminal proline codon and enhances peptide-bond skipping. Strikingly, amino acid repeats positioned distally upstream also modulate 2A activity, indicating long-range coupling between nascent chain properties outside of the ribosome and the peptidyl transferase center inside the ribosome. In particular, hydrophobic residues potently suppress skipping, an effect that can be rescued by extending flexible segments within the peptide exit tunnel. Together, our findings support a model in which nascent chain features-beyond the core 2A motif-dynamically tune ribosomal recoding efficiency through co-translational feedback into the catalytic center.
Ribosomes↗
Structural characterization by nuclear magnetic resonance of a reactive-site 13carbon-labelled basic pancreatic trypsin inhibitor with the peptide bond Arg-39--Ala-40 cleaved and Arg-39 removed.
With the use of an enzymatic replacement method, 90%-enriched [1-13C]lysine was introduced into the reactive site of the basic pancreatic trypsin inhibitor. Characterization of the labelled inhibitor with 13C nuclear magnetic resonance (NMR), 1H NMR and chemical methods showed that while the reactive-site peptide bond Lys-15--Ala-16 was properly resynthesized, the polypeptide chain was cleaved at the peptide bond Arg-39--Ala-40 and Arg-39 was removed. Detailed 1H NMR studies showed further that, with the exception of the immediate environment of the modification site, the average spatial structure of the native inhibitor was preserved in the modified protein. Compared to the native inhibitor, the thermal stability of the globular conformation was found to be reduced, interior amide protons exchanged at a faster rate and the internal mobility of aromatic rings located outside the immediate environment of the cleaved peptide bond was essentially unchanged. These observations coincide closely with previous reports on different modifications of the inhibitor and can be explained by a recently proposed dynamic multi-state model for globular proteins. Since the fundamental structural properties of the native inhibitor and full inhibitory activity are preserved after resynthesis, the [1-13C]lys-15-labelled inhibitor with the peptide bond Arg-39--Ala-40 cleaved and Arg-39 removed should be suitable for 13C NMR studies of mechanistic aspects of proteinase-inhibitor interactions.
Alanine↗
Interaction of the peptide bond with solvent water: a vapor phase analysis.
A dynamic technique, using radioactivity as a means of detection, makes it possible to measure the partial pressures of highly polar compounds in dilute aqueous solution. The results can be expressed in terms of the dimensionless distribution coefficient for transfer of a compound from dilute aqueous solution to the vapor phase. For acetic acid this coefficient is 1.1 X 10(-5), for acetamide 7.6 X 10(-8), for N-methylacetamide 4.1 X 10(-8), and for N,N-dimethylacetamide 5.4 X 10(-7). Thus acetamide is much more strongly solvated than the uncharged acetic acid molecule. The results suggest: (1) that the peptide bond represents an extreme among uncharged functional groups in the degree to which it is stabilized by solvent water; (2) that the very great hydrophilic character of the peptide bond may be associated mainly with hydrogen bonding of the solvent to the carbonyl oxygen atom (rather than the N-H group); and (3) that the observed equilibria of biosynthesis and hydrolysis of peptide bonds in aqueous solution are largely determined by differences between reactants and products in their free energies of solvation. It is anticipated that where "bound" water is found in proteins, it will often be found to be associated with peptide bonds, and will tend to be associated with the C-O group rather than with the N-H group.
Acetamides↗
Identification of a soluble protein that stimulates peptide bond synthesis.
A soluble protein factor was isolated, free of elongation factor (EF)-T and EF-G, based on its ability to stimulate the synthesis of peptide bonds using ribosomal bound 70S-AUG-N-formyl-[35S]methionyl-tRNA complex and added puromycin as substrates. Over 90% of this activity was found in the ribosome-free cytoplasm of Escherichia coli extracts. Otherfeatures such as molecular weight, purification properties, and catalytic activities distinguish this factor from ribosomal proteins and known activators of translation. The factor requires all components needed for peptide bond synthesis and is inhibited by antibiotics known to specifically block the peptidyl transferase activity of ribosomes. The factor increases the binding affinity of the ribosome for the aminoacyl-tRNA analog puromycin about 10-fold. We suggest that this extraribosomal factor modulates the intrinsic activity of ribosomes to catalyze peptide-bond synthesis, and regard it as a new factor required for peptide chain elongation, which we call EF-P.
Bacterial Proteins↗
Peptide bond formation stimulated by protein synthesis factor EF-P depends on the aminoacyl moiety of the acceptor.
Elongation factor EF-P is a soluble protein that stimulates peptide bond synthesis catalyzed by the 50-S ribosomal subunit. This factor was previously identified and characterized based on its ability to promote the synthesis of formylmethionine-puromycin. In the present work, we tested the ability of EF-P to promote peptide bond synthesis between ribosome-bound fMet-tRNA and several analogues of the 3' terminus of aminoacyl-tRNA, i.e. the cytidylyl(3'-5')-[2'(3')-O-L-aminoacyladenosines]. EF-P promoted synthesis to the greatest extent with certain acceptors which were otherwise inefficient in the peptidyl transferase reaction. This activity of EF-P could not be replaced by the other soluble proteins known to be involved in polypeptide synthesis, such as EF-Tu, EF-Ts and EF-G. One role of EF-P in protein synthesis may be to allow peptide bond synthesis to occur more efficiently with some aminoacyl-tRNAs that are poor acceptors for the ribosomal peptidyl transferase.
Escherichia coli↗
Hydrolysis-resynthesis equilibrium of the lysine-15--alanine-16 peptide bond in bovine trypsin inhibitor (Kunitz).
Catalytic amounts of bovine beta-trypsin, bovine alpha-chymotrypsin and porcine plasmin establish a true thermodynamic equilibrium between virgin (I) (reactive site Lys15-Ala16 peptide bond intact) and modified (I) (this bond hydrolyzed) bovine trypsin/kallikrein inhibitor (Kunitz). The very slow reaction rates for attaining equilibrium are pH-dependent and differ for different enzymes. Optimal rates are for beta-trypsin at pH 3.75, for alpha-chymotrypsin at pH 5.5, and for plasmin at pH 5.0. Under conditions of optimum pH the equilibrium is reached with the highest rate by plasmin. In 10(-5)M inhibitor solutions the equilibrium concentrations of virgin and modified inhibitor are established by plasmin after almost 300 days starting from either pure virgin or pure modified inhibitor. Thus, the hydrolysis constant KHyd = [I]/[I] is determined to be 0.33 at pH 5.0. In spite of many unsuccessful attempts, this demonstrates that the reactive site peptide bond Lys15-Ala16 in the bovine trypsin inhibitor (Kunitz) can be hydrolyzed by catalytic amounts of endopeptidase. It further confirms that the hydrolyzed Lys15-Ala16 peptide bond in modified inhibitor is subject to thermodynamic control resynthesis.
Alanine↗
Purification of an acid proteinase from Aspergillus saitoi and determination of peptide bond specificity.
The specificity and mode of action of an acid proteinase (EC 3.4.23.6) from Aspergillus saitoi were investigated with oxidized B-chain of insulin, angiotensin II and bradykinin. Further purification of acid proteinase was performed with N,O-dibenzyloxycarbonyl-tyrosine hexamethylene-diamino-Sepharose 4B affinity chromatography and isoelectric focusing. The purified enzyme was free of any other proteolytic activity demonstrated in Asp. saitoi. Acid proteinase from Asp. saitoi hydrolyzed primarily two peptide bonds in the oxidized B-chain of insulin, the Leu(15)-Tyr(16) bond and the Phe(24)-Phe(25) bond. Additional cleavages of the bonds His(10)-Leu(11), Ala(14)-Leu(15) and Tyr(16)-Leu(17) were also noted. Primary splitting sites at Leu(15)-Tyr(16) and Phe(24-)-Phe(25) with acid proteinase from Asp. saitoi were identical with those reported in the work of cathepsin D (EC 3.4.23.5) from human erythrocyte. Hydrolysis of angiotensin II was observed at the Tyr(4)-Ile(5) bond. In conclusion, peptide bonds which have a hydrophobic amino acid such as phenylalanine, tyrosine, leucine and isoleucine in the P'1 position (as defined by Berger and Schechter, [29]) are preferentially cleaved by the trypsinogenactivating acid proteinase from Asp. saitoi.
Amino Acids↗
Bonded peptide stationary phases for the separation of amino acids and peptides using liquid chromatography.
Bonded optically active tripeptides have been applied as stationary phases for liquid chromatography. Significant retention variations are shown for some UV absorbing amino acids when compared to a silica gel column using the same mobile phase. The separation of certain isomeric dipeptides has been accomplished using the bonded optically active tripeptide stationary phases. It is shown that these separations are superior to those possible on silica gel, although the efficiencies of the column are low. Phenylthiohydatoin (PTH)-amino acids have also been analyzed using the bonded tripeptide L-Val-L-Ala-L-Ser on silica gel CT and 1% citric acid-water as the mobile phase. No two PTH-amino acids showed the same capacity ratio out of 25 tested and the separation of 15 in one isocratic run is presented. The implications and future for the use of bonded opitcally active peptides as stationary phases for liquid chromatography are discussed.
Amino Acids↗
Use of N-chlorosuccinimide/urea for the selective cleavage of tryptophanyl peptide bonds in proteins. Cytochrome c.
The conditions and utility of the N-chlorosuccinimide/urea (NCS/urea) reagent for the selective cleavage of tryptophanyl peptide bonds in proteins is demonstrated with cytochrome c. At low concentrations of NCS/urea the oxidation of thioether side chains in cytochrome c is the predominant reaction. Methionyl residues are oxidized to sulfoxide and the heme-thioether bridge is partially cleaved. At 10-fold excess of NCS/urea reagent, cleavage of the tryptophanyl peptide bond is optimal at approximately 50% yield in several species of cytochrome c studied. Analytical data on isolated horse cytochrome c peptide fragments demonstrate lack of modification and cleavage at tyrosyl and histidyl residues. However, at high concentrations of NCS/urea reagent (30-fold) unexpected conversions of methionine to sulfone and cysteine to cysteic acid in intact proteins are observed. This is in contradistinction to the absence of sulfone in NCS/urea-reacted amino acid mixtures. The mechanisms of halogenation and cleavage by N-bromosuccinimide, N-iodosuccinimide, and N-chlorosuccinimide are discussed. It is porposed that the selectivity with respect to halogenation by N-chlorosuccinimide is due to the insignificant participation of molecular chlorine in the NCS/urea reaction. A mechanism of halogenation and cleavage by NCS at tryptophan is also offered.
Amino Acids↗
Trypsin hydrolysis of the Tyr(42)-Ser(43) bond, the chymotrypsin reactive-site peptide bond, of faba bean Bowman-Birk type inhibitor.
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Amino Acid Sequence↗
Cleavage of tryptophanyl peptide bonds in cytochrome b5 by cyanogen bromide.
Quantitative cleavage of peptide bonds adjacent to tryptophanyl and methionyl residues in the polar moiety of cytochrome b5 was effected using cyanogen bromide in the presence of heptafluorobutyric and formic acids. Application of this method to native cytochrome b5 resulted in cleavage at tryptophanyl and methionyl residues in the polar and membranous segments in high yield. Amino acid analysis of peptides isolated from such digests indicated that tyrosine was modified and the derivative eluted in a position preceding lysine; however, the color constant with ninhydrin remained unchanged. Hydriodic acid hydrolysis of the phenylthiohydantoin derivative of the modified tyrosine regenerated the parent amino acid. Peptides containing the altered tyrosine remained susceptible to chymotryptic cleavage at this residue. Cleavage of methionyl bonds could be prevented by methylene blue-sensitized photooxidation prior to cyanogen bromide/anhydrous heptafluorobutyric acid treatment. The conditions employed for photooxidation were selective for methionyl residues, and the yield and specificity of tryptophanyl cleavage by the cyanogen bromide/anhydrous heptafluorobutyric acid method was unaffected.
Amino Acid Sequence↗
Cross-peptide bond 13C--15N coupling constants by 13C and J cross-polarization 15N NMR.
Comparative 13C--15N coupling constants are reported for the linear dipeptide tBoc-L-[U-13C]Ala-[15N]GlyOMe and the corresponding cyclic diketopiperazine, both in dimethylsulfoxide (DMSO) and, upon removal of the tBoc group, in water solutions. Spectra were obtained by 13C NMR and by the first application of J cross-polarization (JCP) 15N NMR, which greatly reduces the time required to accumulate 15N NMR spectra. In DMSO there was evidence for the formation of complexed species which were not present in water. The values obtained for the cross-peptide bond coupling constant 2J13C alpha--15N were consistently less (by 2.2 Hz in DMSO, 4.3 Hz in water) for the cyclic than for the linear peptide, which may be related to the cross-peptide bond conformation. The 15N resonance for the cyclic peptide was shifted only 2 ppm downfield from the linear peptide chemical shift value in both solvents.
Alanine↗