New Synthetic Amino Acids for the Design and Synthesis of Peptide-Based Metal Ion Sensors

The syntheses of two new nonstandard amino acids, Flu (6) and XBp (20), and a new synthesis of Dmd (12) are reported. These residues exhibit fluorescence, metal-coordination, and fluorescence-quenching properties, respectively. These building blocks have been incorporated into peptides via solid phase peptide synthesis to afford the prototype for a photoinduced electron transfer-based metal ion chemosensor. The fluorescence of the peptides is modulated upon metal binding. This results from a metal ion-induced conformational change that brings the side chains of the Flu and Dmd amino acids into proximity, thereby favoring photoinduced electron transfer (PET) fluorescence quenching.     

PHOTOCHEMICAL ADDITION OF AMINO ACIDS AND PEPTIDES TO DNA

Abstract— The quantum yields for photochemical addition of twenty of the amino acids commonly occurring in proteins to denatured calf thymus DNA have been determined in deoxygenated phosphate buffer at λ 254 nM and pH 7 using a fluorescamine assay technique. Fifteen were found to be reactive, with cysteine, lysine, phenylalanine, tryptophan and tyrosine being the most reactive. Alanine, aspartic acid, glutamic acid, serine and threonine were unreactive. Analogous quantum yields for a series of eighteen peptides of the form glycyl X (X being one of the commonly occurring amino acids) were also determined, along with the corresponding quantum yields for L-alanyl-L-alanine, L-alanyl-L-tryptophan, L-seryl-L-seryl-L-serine, L-threonyl-L-threonyl-L-threonine, and L-cystine- bis -glycine. All of the peptides were found to be reactive. The modified amino acids N^ε-methyllysine, N^ε, N^ε, N^ε-trimethyllysine and N^ε-acetyllysine, all occurring in minor amounts in the histone group of chromosomal proteins, were also found to be reactive as was N^α-acetyllysine. The quantum yields for photoaddition of a selected group of amino acids and peptides to denatured DNA and native DNA are compared. In some cases higher quantum yields for photoaddition to denatured DNA are observed while in other cases the reverse is true. The effect of oxygen on the quantum yields for photoaddition of selected peptides to DNA was examined. While for most systems studied the amount of reaction in aerated systems was less than in deoxygenated systems, in the case of glycyl-L-phenylalanine the reverse was true.     

THE FLUORESCENCE OF TRYPTOPHYL PEPTIDES

Abstract— Tryptophan lifetimes and relative quantum yields have been determined for a group of small (1–4 residues) peptides and peptide hormones [luteinizing releasing factor. mellitin, glucagon. glucagon 22–29, glucagon 1–26. glucagon 1–27 (homoserine)]. All of the larger peptides and most of the smaller peptide anions exhibit nonexponential decay. Peptide quenching in the small peptides is more effective when the bonding is at the amino rather than at the carboxyl end of tryptophan. With the exception of tryptophylglycine. quenching by NH⁺₃ is thought not to involve proton transfer. The results suggest that a decay component of 3–4 ns is expected whenever large peptides and proteins contain a solvent exposed tryptophan.     

QUENCHING OF TYROSINE FLUORESCENCE BY PHOSPHATE IONS: A MODEL STUDY FOR PROTEIN-NUCLEIC ACID COMPLEXES

Abstract— In order to test the ability of phosphate groups to quench the tyrosine fluorescence in nucleic acid-protein complexes, we have studied the effect of several phosphate ions on the fluorescence of tyrosine derivatives. Mono and bianions (H₂PO₄ and HPO₄^2–) which are good proton acceptors quenched the fluorescence of all the phenolic compounds studied except that of O -methyl tyrosine. With the other derivatives (tyrosine, N -acetyl tyrosinamide and lysyl-tyrosyl-α lysine) fluorescence inhibition was accompanied by the appearance of a long wavelength emission (345 nm) attributed to tyrosinate anions. The quenching of tyrosine emission was due to the deprotonation of the phenolic group promoted in the excited state by phosphate ions and leading to the weakly fluorescent tyrosinate ion. Mono and dianions of phosphate mono ester inhibited tyrosine fluorescence as did unesterified phosphates. However, phosphate diester did not have any effect on the fluorescence of tyrosine derivatives. We conclude from this study that in nucleic acid-protein complexes phosphate groups are not able to quench tyrosine fluorescence except at the end of polynucleotide chains. Since monoester and diester monoanions have a different behavior, we propose that quenching of tyrosine fluorescence by monoanions requires the formation of two hydrogen bonds. This complex cannot form with diesters which consequently do not quench tyrosine fluorescence.     

FLUORESCENCE QUENCHING OF INDOLIC COMPOUNDS BY ALIPHATIC AMINO ACIDS. EVIDENCE FOR EXCITED STATE COMPLEXES

Abstract The fluorescence quenching of indole, tryptophan, tryptamine and indole-3-acetic by aliphatic amino acids was studied. The bimolecular rate constant ( k _q) for the deactivation of the excited state was determined. The k _q values were in the range 0.6 × 10⁸–1.6 × 10⁹ M ^–1 S^–1 and they increased in the order tryptophan < tryptamine < indole ≈ indole-3-acetic acid. When the rate constant was corrected for diffusion al effects a good linear correlation was found between the log ( k '_q) and the ionization equilibrium constant of the carboxylic group of the amino acid (p ^k _a1). This was interpreted as arising from a charge transfer mechanism in which the indole moiety acts as an electron donor and the carbonyl group of the amino acid as the acceptor.
The activation parameter for the quenching processes were also determined. The ΔH^≠ values were in the range —4.0 to +4.0 kcal/mol and the ΔH^≠ in the range –7 to –37 e.u. For the systems with lower values of k _q negative values for ΔH^≠ were observed. A good enthalpy-entropy compensation was found with an isokinetic temperature of 229 K. These results suggest that a common mechanism is operating for all the systems and that it involves the formation of an excited state complex between the indolic compound and the amino acid.     

GEOMETRIC REQUIREMENTS FOR THE INTRAMOLECULAR QUENCHING OF INDOLE FLUORESCENCE BY AMIDE AND CARBOXYLIC ACID GROUPS IN RIGID MOLECULES WITH THE [2,2,1]BICYCLOHEPTENYL SKELETON

Abstract— The geometric requirements for intramolecular fluorescence quenching of indole by carboxylic acid and amide functions have been determined in rigid norbornyl ([2.2,1]bicycloheptenyl) skeleton: trans and cis 3-(3'-indolyl) norbornene 2-dimethylcarboxamides or carboxylic acids. The reference compound was the 3-(3'-indolyl) N-dimethylpropionamide or -propanoic acid. The quenching occurs mainly in protic solvents. In the cis compounds, the quantum yields are strongly decreased when compared to the trans and open chain compounds. As determined by the pH dependence of fluorescence of the acids, it is in the acid form—COOH that the fluorescence is quenched; in the ionized species -CO⁻₂, only small quenching is observed. The K_s of Stern-Volmer equations are very small for the cis bicyclic acid and amide, the indole nucleus being shielded on one side only. The results support the hypothesis that small rearrangement of the peptide bond in protein conformation changes may be detected by fluorescence.     

FLUORESCENCE AND THE STRUCTURE OF PROTEIN—XX. FLUORESCENCE OF 3-AMINOTYROSINE AND OTHER AMINOPHENOLS

Abstract— –The fluorescence of 3-NH₂ tyrosine and of simpler isomeric aminophenols was observed in aqueous solution at room temperature. Marked changes in both emission spectrum and fluorescence efficiency were observed upon change of pH and solvent composition. An explanation for the observed behavior is offered on the basis of two effects. First, peculiarities in the emission spectra were accountable in terms of proton dissociation from the cationic amino group in the excited singlet state so that emission characteristic of the free base was observed even in acidic solutions. Second, the unexpectedly low fluorescence efficiency from the free base was shown to result from quenching by the aqueous solvent. The relevance of these studies for the fluorescence of 3-NH₂ tyrosyl groups in proteins is discussed briefly.     

REACTIVITY OF SINGLET OXYGEN TOWARD LARGE PEPTIDES

Abstract— The reactions of singlet oxygen, ¹O₂, with amino acids and their derivatives have been studied previously. It was found that only five amino acid residues interact readily with ¹O₂. Here we describe its reactions with the large peptides melittin, neuropeptide Y (NPY) and insulin in their native and in their denatured forms. The singlet oxygen quenching by a polypeptide was compared with that of a solution at the same concentration as those of its constituent amino acids, which are known to react efficiently with ¹O₂. It was found that the quenching rate by such a mixture exceeded that of the polypeptides in their native form. The ratio of the rate constants for NPY to that of the corresponding amino acid mixture in solution was 0.75. For melittin in its monomeric form it was 0.83 and for a tetramer of melittin (at high ionic strength) it was 0.70. For native insulin the ratio of the rate constants was 0.55. For oxidized insulin with its -S-S- bridges opened the figure became 0.80. However, the quenching by all the polypeptides in their fully denatured form (in the presence of 6 M urea) equalled that of the corresponding amino acid mixtures. Although polypeptides are generally supposed not to possess a stable secondary structure in solution the effects are explained by shielding of some of the reactive amino acid residues in the chain by temporary folding or incipient secondary structures of the native polypeptide.
It is shown that the kinetics for a homogeneous solution of quenchers applies also to measurements in a polypeptide solution where the quenchers are localized along the polypeptide backbone and thus form clusters in solution.     

Tyrosinase-induced cross-linking of tyrosine-containing peptides investigated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Tyrosinase-induced oxidation of tyrosine is known to lead to melanin by cross-linking of 5,6-dihydroxyindole (DHI) and indole-5,6-quinone intermediates. However, tyrosinase-induced cross-linking of tyrosine-containing peptides has not been reported. We observed tyrosinase-induced adducts of tyrosine-containing peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). MALDI-TOFMS was also used to observe tyrosine adducts at various levels of oxidation derived from acid hydrolysis of the peptide adducts. The rate of tyrosinase-induced browning of lys-tyr-lys was about half of that of tyrosine. These results indicate that tyrosinase-induced browning of tyrosine-containing peptides via direct oxidation and cross-linking of the benzene ring of the tyrosine residue occurs at a significant rate and needs to be considered in melanogenesis.     

CHEMICAL REACTION RATES OF AMINO ACIDS WITH SINGLET OXYGEN

Abstract— The chemical reactions of amino acids with singlet oxygen have been measured in D₂O solution where the singlet oxygen was generated directly by irradiation of the oxygen ³∑_g^-→¹δ_g+ lv electronic transaction with the 1.06 μm output of an Nd-Yag laser. Chemical reaction was measured as amino acid loss by an amino acid analyzer or by fluorescence in the cases of tryptophan and tyrosine.
The chemical rate constants, in units of 10⁷ M ^-1s^-1, are histidine 10, tryptophan 3, methionine 1.7, tyrosine 0.8 and alanine 0.2, In the cases of histidine, methionine and alanine the interaction appears to be entirely chemical, i.e. there is no evidence for physical quenching in addition to the chemical reaction. The histidine chemical reaction rate constant shows an increase with pD with a p K of 6.9.     

THE QUENCHING OF SINGLET OXYGEN BY AMINO ACIDS AND PROTEINS

Abstract— The physical quenching of singlet molecular oxygen (¹Δ_g) by amino acids and proteins in D₂O solution has been measured by their inhibition of the rate of singlet oxygen oxidation of the bilirubin anion. Steady-state singlet oxygen concentrations are produced by irradiating the oxygenated solution with the 1–06 μm output of a Nd-YAG laser, which absorbs directly in the electronic transition ¹Δ_g+ 1 v →³Σ_g^-. The rate of quenching by most of the proteins studied is approximated by the sum of the quenching rates of their amino acids histidine, tryptophan and methionine, which implies that these amino acids in the protein structure are all about equally accessible to the singlet oxygen. The quenching constants differ from those obtained by the ruby-laser methylene-blue-photosensitized method of generating singlet oxygen, or from the results of steady-state methylene-blue-photosensitized oxidation, where singlet oxygen is assumed to be the main reactive species. The singlet oxygen quenching rates in D₂O, pD 8, are (10⁷ℒ mol^-1 s^-1): alanine 0–2, methionine 3, tryptophan 9, histidine 17, carbonic anhydrase 85, lysozyme 150, superoxide dismutase 260, aposuperoxide dismutase 250.     

Thioamide quenching of intrinsic protein fluorescence

Thioamides quench tryptophan and tyrosine fluorescence in a distance-dependent manner and thus can be used to monitor the binding of thioamide-containing peptides to proteins. Since thioamide analogs of the natural amino acids can be synthetically incorporated into peptides, they can function as minimally-perturbing probes of protein/peptide interactions.     

INTERACTION BETWEEN TYROSINE AND DIVALENT SULFUR IN FLUORESCENCE QUENCHING AND IN THE PHOTOCHEMISTRY OF RIBONUCLEASE

Abstract— –Ribonuclease is inactivated in aqueous solution by u.v. light through different mechanisms according to whether divalent sulfur or aromatic amino acids are the primary light absorbers. At 284 nm, absorbed mainly by tyrosine, the presence of O₂ inhibits photoinactivation and H₂S formation, but does less so at 254 or 313 nm. Based on data with model substances containing disulfide groups a mechanism is indicated in which excited tyrosine is quenched through electron transfer to adjacent divalent sulfur within the protein. Disulfide compounds are shown to be very efficient quenchers of tyrosine fluorescence.     

Oligomerization of uniquely folded mini-protein motifs: development of a homotrimeric betabetaalpha peptide.

The discovery of a discretely folded homotrimeric betabetaalpha motif (BBAT1) was recently reported (J. Am. Chem. Soc. 2001, 123, 1002-1003). Herein the design, synthesis, and analysis of a small library of peptides which led to the isolation of BBAT1 is described. betabetaalpha peptides based on the monomeric sequence of BBA5 (Folding Des. 1998, 120, 95-103) were synthesized to include the anthranilic acid/nitrotyrosine fluorescence quenching pair to rapidly detect interpeptide association. In the first generation of peptides synthesized, truncations in the loop region connecting the beta-hairpin to the alpha-helix revealed that a two-residue deletion in the loop promoted an interpeptide association as detected by fluorescence quenching. An additional library of 22 loop-truncated betabetaalpha peptides was subsequently synthesized to include a variety of sequence mutations in an effort to enhance the observed peptide-peptide binding. From the fluorescence quenching screen, peptide B2 was found to possess the strongest fluorescence-quenching response, indicative of a strong peptide-peptide association. Due the poor solubility of peptide B2, the S-methylated cysteine at position 9 in the loop was substituted with a glycine to generate peptide BBAT1 which possessed greatly improved water solubility and formed discrete trimers. The successful design of this oligomeric betabetaalpha structure will likely aid the design of more complex alpha-beta superstructures and further our understanding of the factors controlling protein-protein interactions at alpha-beta protein interfaces.     

PHOTOCHEMICAL COUPLING OF 5-BROMOURACIL TO TRYPTOPHAN, TYROSINE AND HISTIDINE, PEPTIDE-LIKE DERIVATIVES IN AQUEOUS FLUID SOLUTION

Direct irradiation of 5-bromouracil (BU) in aqueous fluid solution in the presence of tryptophan (trp), tyrosine (tyr) or histidine (his) derivatives using a XeCl excimer laser at 308 nm yielded photocoupling of BU to the aromatic ring of each amino acid. Irradiation of BU at 308 nm most likely results in excitation of the n-φ* transition, intersystem crossing to the triplet manifold, and coupling via electron transfer from the aromatic amino acid. The coupling observed was regiospecific between the 5-position of uracil (U) and the 2-position of the indole and phenol rings and the 5-position of the imidazole ring of the respective amino acids. Quantum yields of photocoupling to BU ranged from 1 × 10^-3 to 7 × 10^-3 and paralleled known rates of electron transfer and ionization potentials of the aromatic rings. The photocoupling between BU and some of the aromatic amino acid peptide-like derivatives possibly mimics photocrosslinking of BU-DNA to associated proteins, a potentially useful photoreaction for studying nucleic acid-protein interactions. Formation of crosslinks of the type proposed here might be detected by the characteristic fluorescence emission of the uracil amino acid adducts.     

DEUTERIUM-ISOTOPE EFFECT ON THE FLUORESCENCE YIELDS AND LIFETIMES OF INDOLE DERIVATIVES–INCLUDING TRYPTOPHAN AND TRYPTAMINE

Abstract— The fluorescence yields and lifetimes of indole, five of its alkyl detivatives, tryptophan, and tryptamine have been determined in degassed, heavy and light water at room temperature. All of the compounds have radiative lifetimes nearly identical to the parent compound indole, and a comparison of these results with recently reported data on tryptophyl derivatives disclosed a striking uniformity in radiative lifetimes between indole and many amino acids and peptides which contain the indole group as the fluorescence unit. The fluorescence rate k _f in H₂O, was found to be 4.5 × 10⁷ sec^-1. The nonradiative decay rates were found to vary between 5.1 and 46 × 10⁷ sec^-1 and from a study of the deuterium-solvent isotope effect and the deuterium-substituent effect a mechanism for nonradiative deactivation is proposed which includes an isotopically dependent proton transfer and a pathway involving energy loss via the ring carbon hydrogen vibrations. Tryptophan at pH 7 was found to have a unique nonradiative decay scheme not evidenced at a pH 1 or pH 10.     

Photochemical addition of amino acids and peptides to homopolyribonucleotides of the major DNA bases

Abstract— The photochemical quantum yields for addition of glycine and the L-amino acids commonly occurring in proteins (excluding proline) to polyadenylic acid, polycytidylic acid, polyguanylic acid and polyribothymidylic acid have been determined in deoxygenated phosphate buffer at Λ 254 nm and pH 7, using a fluorescamine assay technique. Polyadenylic acid was reactive with eleven of the twenty amino acids tested, with phenylalanine, tyrosine, glutamine, lysine and asparagine having the highest quantum yields. Polyguanylic acid reacted with sixteen amino acids; phenylalanine, arginine, cysteine, tyrosine, and lysine displayed the largest quantum yields. Polycytidylic acid showed reactivity with fifteen amino acids with lysine, phenylalanine, cysteine, tyrosine and arginine having the greatest quantum yields. Polyribothymidylic acid, reactive with fifteen of nineteen amino acids surveyed, showed the highest quantum yields for cysteine, phenylalanine, tyrosine, lysine and asparagine. None of the polynucleotides were reactive with aspartic acid or glutamic acid.
The quantum yields for photoaddition of eighteen dipeptides of the form glycyl X (X being one of the amino acids commonly occurring in proteins, including proline), and of L-alanyl-L-tryptophan, L-seryl-L-seryl-L-serine, L-threonyl-L-threonyl-L-threonine, L-cystine- bis -glycine, and N_α-acetyllysine to polyadenylic acid, polycytidylic acid and polyguanylic acid were measured. All of these were found to add photochemically to each of these polymers. Polyribothymidylic acid, tested with eleven of these peptides and with N_α-acetyllysine, was found to be reactive with all.     

Probing biocatalytic transformations with CdSe-ZnS QDs

CdSe/ZnS QDs enable the optical probing of the biocatalytic oxidation of tyrosine derivatives and of the scission of peptides by thrombin. CdSe/ZnS QDs were modified with tyrosine methyl ester or with a tyrosine-containing peptide. The tyrosine units were reacted with tyrosinase/O2 to yield the respective l-DOPA and quinone derivatives. The luminescence of QDs modified by the enzyme-generated quinone units is quenched. The quinone-functionalized peptide associated with the QDs was cleaved by thrombin, a process that restored the luminescence of the QDs.     

LASER FLASH PHOTOLYSIS OF INDOLE IN THE PRESENCE OF AMINO ACIDS

The laser flash photolysis of indole at 265 nm in the presence of glycine, proline and hydroxy proline was studied. The relative yields of c _aq, triplet state, and indole cation radical were determined in the absence and in the presence of the amino acids. The yields were determined as a function of laser intensity and the values at very low intensity were compared with the fluorescence quenching results. It was concluded that in these conditions the photoionization of indole occurs via the fluorescent state. From the curves of triplet yield vs laser intensity, the triplet quantum yield extrapolated at low laser intensity was obtained, φr = 0.55 φ 0.05, relative to the literature value of 0.15 for φ_eag. This gives φ_F+φ_eaq= 1.0 ± 0.1 at room temperature. When proline and hydroxy proline were used as singlet quenchers, the yield of In was greater than the yield of c_aq. This was considered as evidence that a fraction of the quenching processes leads to complete electron transfer from indole to the amino acids.     

Interference with ammonium determination by the indophenol-type reaction of salicylate and dichloroisocyanurate

Two widely accepted indophenol-type reactions with ammonium, which use phenol/hypochlorite and salicylate/dichloroisocyanurate as reagents, were compared for possible interferences with other naturally occurring nitrogen-containing compounds. Unlike the first method, the second showed strong interference from all amino acids and peptides tested. As much as 57 mole % of threonine and 49 mole % of serine were degraded to ammonium. Pyrimidines, purines, nucleosides and urea were negative in both reactions. The wide distribution and importance of free and combined amino acids in naturally occurring waters favours the application of the classical phenol/ hypochlorite reaction with ammonium rather than the modified salicylate/dichloroisocyanurate reaction.