NMR assignment methods for the aromatic ring resonances of phenylalanine and tyrosine residues in proteins

The unambiguous assignment of the aromatic ring resonances in proteins has been severely hampered by the inherently poor sensitivities of the currently available methodologies developed for uniformly 13C/15N-labeled proteins. Especially, the small chemical shift differences between aromatic ring carbons and protons for phenylalanine residues in proteins have prevented the selective observation and unambiguous assignment of each signal. We have solved all of the difficulties due to the tightly coupled spin systems by preparing regio-/stereoselectively 13C/2H/15N-labeled phenylalanine (Phe) and tyrosine (Tyr) to avoid the presence of directly connected 13C-1H pairs in the aromatic rings. The superiority of the new labeling schemes for the assignment of aromatic ring signals is clearly demonstrated for a 17 kDa calcium binding protein, calmodulin.     

Polarized Raman spectra and intensities of aromatic amino acids phenylalanine,tyrosine and tryptophan

The prominent marker bands in the Raman spectra of the aromatic proteinogenic amino acids phenylalanine, tryptophan and tyrosine have been reinvestigated. Previous studies have been extended by measuring intensities against NaClO₄ as an external standard. Raman spectra were divided into isotropic (trace scattering of symmetric vibrations) and anisotropic (quadrupole scattering of antisymmetric or symmetric vibrations). These intensity and polarization properties of the marker bands were followed through pH changes from about 11–13 to 1–2.     

Synthesis of daunorubicin analogues containing truncated aromatic cores and unnatural monosaccharide residues

The anthracycline antibiotics daunorubicin and doxorubicin have been used widely as anticancer drugs, but their cardiotoxicity limits their clinical use. We describe here the preparation of a small panel of daunorubicin analogues in which the anthraquinone core is replaced with simpler aromatic moieties that lack a quinone functionality. The targets consist of a functionalized 1,2,3,4-tetrahydro-naphthalene or 1,2,3,4-tetrahydro-anthracene core bound to one of three monosaccharides: daunosamine, acosamine, or 4-amino-2,3,6-trideoxy-l-threo-hexopyranose. Key steps in the synthesis included an enantioselective ring opening of benzo-fused norbornene derivatives for the preparation of the core structures and the use of silver hexafluorophosphate-promoted thioglycoside activation in the glycosylation of these cores. Evaluation of these compounds against the MCF-7 cancer cell line demonstrated that the identity of the carbohydrate moiety appeared to have little influence on the cytotoxicity. Moreover, the analogues with the 1,2,3,4-tetrahydro-naphthalene core showed no cytotoxicity, while those possessing the 1,2,3,4-tetrahydro-anthracene moiety were more active. The IC50 values for the latter group of compounds were in the range of 94-134 microM, compared to 17 microM for doxorubicin and 5 microM for daunorubicin.     

Flexibility of active-site gorge aromatic residues and non-gorge aromatic residues in acetylcholinesterase

The presence of an unusually large number of aromatic residues in the active site gorge of acetylcholinesterase is a subject of great interest. Flexibility of these residues has been suspected to be a key player in controlling the ligand traversal in the gorge. This raises the question of whether the over-representation of aromatic residues in the gorge implies higher-than-normal flexibility of these residues. The current study suggests that it does not. Large changes in the hydrophobic cross-sectional area due to dihedral oscillations are probably the reason of their presence in the gorge.     

Determination of binding energies between cyclodextrins and aromatic guest molecules by microcalorimetry

The inclusion of substituted benzoic acids in -CD or selectively methylated -CDs was investigated by titration microcalorimetry. All thermodynamic functions of the inclusion process G°, H° and S° could be obtained very accurately within one experiment. A very strong influence of the substitution pattern at both the host and the guest on the stability of the inclusion compounds was found.     

Van der Waals-London interaction energies in hydrogen bonding between purine and pyrimidine base analogues

The calculation of the Van der Waals-London interaction energies in hydrogen-bonded complexes formed between adenine or its analogue 2,6-diaminopurine and uracil enables to account for the structural differences among these complexes. In particular they indicate, that the most stable A+2U trimer should be of the Watson-Crick-inversed Hoogsteen type, while the most stable 2,6-DAP+2U trimer should be of the reversed Watson-Crick — Hoogsteen type. The observed configurations reflect most probably stable associations formed in solution prior to a possible cocrystallization.

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Zusammenfassung Die Berechnung der Van-der-Waals-London-Energie in wasserstoffbrückengebundenen Komplexen von Adenin bzw. 2,6-Diaminopurin und Uracil ermöglicht die strukturellen Unterschiede zu erklären. Insbesondere ergibt sich, daß das stabilste A+2U-Trimere vom inversen Hoogsteen-Watson-Crick-Typ, das stabilste 2,6-DAP + 2U-Trimere aber vom inversen Watson-Crick-Hoogsteen-Typ sein sollte. Vermutlich geht der Kokristallisation die Bildung stabiler Assoziate in der Lösung voraus.

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Résumé L'évaluation des énergies d'interaction Van der Waals-London se manifestant dans les complexes par liaisons hydrogène formés entre l'adénine ou son analogue 2,6-diaminopurine et l'uracil, permet de rendre compte des différences structurales observées entre ces complexes. Elle indique, en particulier, que la configuration la plus stable du complexe A + 2U devrait être du type Watson-Crick-Hoogsteen inversé, alors que la configuration la plus stable du complexe 2,6-DAP + 2U devrait être du type Watson-Crick inversé-Hoogsteen. Les configurations observées traduisent probablement l'association la plus forte formée en solution avant une cocrystallisation eventuelle.

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This work was supported by grant No. 67-00-532 of the Délégation Générale à la Recherche Scientifique et Technique (Comité de Biologie Moléculaire).     

Redox-active tyrosine residues in pentapeptides

Tyrosyl radicals are important in long-range electron transfer in several enzymes, but the protein environmental factors that control midpoint potential and electron-transfer rate are not well understood. To develop a more detailed understanding of the effect of protein sequence on their photophysical properties, we have studied the spectroscopic properties of tyrosyl radicals at 85 K. Tyrosyl radical was generated by UV-photolysis of pentapeptides in polycrystalline samples. The sequence of the pentapeptides was chosen to mimic peptide sequences found in redox-active tyrosine containing enzymes, ribonucleotide reductase and photosystem II. From EPR studies, we report that the EPR line shape of the tyrosyl radical depends on peptide sequence. We also present the first evidence for a component of the tyrosyl radical EPR signal, which decays on the seconds time scale at 85 K. We suggest that this transient results from a spontaneous, small conformational rearrangement in the radical. From FT-IR studies, we show that amide I vibrational bands (1680-1620 cm(-1)) and peptide bond skeletal vibrations (1230-1090 cm(-1)) are observed in the photolysis spectra of tyrosine-containing pentapeptides. From these data, we conclude that oxidation of the tyrosine aromatic ring perturbs the electronic structure of the peptide bond in tyrosine-containing oligopeptides. We also report sequence-dependent alterations in these bands. These results support the previous suggestion (J. Am. Chem. Soc. 2002, 124, 5496) that spin delocalization can occur from the tyrosine aromatic ring into the peptide bond. We hypothesize that these sequence-dependent effects are mediated either by electrostatics or by changes in conformer preference in the peptides. Our findings suggest that primary structure influences the functional properties of redox-active tyrosines in enzymes.     

Exon deletions of the phenylalanine hydroxylase gene in Italian hyperphenylalaninemics

A consistent finding of many studies describing the spectrum of mutant phenylalanine hydroxylase (PAH) alleles underlying hyperphenylalaninemia is the impossibility of achieving a 100% mutation ascertainment rate using conventional gene-scanning methods. These methods include denaturing gradient gel electrophoresis (DGGE), denaturing high performance liquid chromatography (DHPLC), and direct sequencing. In recent years, it has been shown that a significant proportion of undetermined alleles consist of large deletions overlapping one or more exons. These deletions have been difficult to detect in compound heterozygotes using gene-scanning methods due to a masking effect of the non-deleted allele. To date, no systematic search has been carried out for such exon deletions in Italian patients with phenylketonuria or mild hyperphenylalaninemia. We used multiplex ligation- dependent probe amplification (MLPA), comparative multiplex dosage analysis (CMDA), and real-time PCR to search for both large deletions and duplications of the phenylalanine hydroxylase gene in Italian hyperphenylalaninemia patients. Four deletions removing different phenylalanine hydroxylase (PAH) gene exons were identified in 12 patients. Two of these deletions involving exons 4-5-6-7-8 (systematic name c.353-?_912 + ?del) and exon 6 (systematic name c.510-?_706 + ?del) have not been reported previously. In this study, we show that exon deletion of the PAH gene accounts for 1.7% of all mutant PAH alleles in Italian hyperphenylalaninemics.     

Interaction between peroxyl radicals of polyatomic esters and aromatic nitrons

Reactivity and rate constants in reactions between peroxyl radicals of ethylene glycol diacetate and aromatic nitrons have been investigated.

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Interaction between uracil nucleobase and phenylalanine amino acid: the role of sodium cation in stacking

The stacking interactions in the uracil:phenylalanine (U:PHE) and (U:PHE)···Na⁺ complexes have been studied at different levels of theory, in which the structures were optimized by both standard and gradient counterpoise corrected methods. The Na⁺ cation can interact with different sites of stacked U:PHE unit. The geometrical parameters of the optimized structures and the calculated binding energies reveal the influence of cation interaction on π–π stacking and vice versa. The interplay between π–π stacking and cation interaction has also been investigated by topological analysis of electron charge density using atoms in molecules (AIM) method. A good agreement between the results of AIM analysis and calculated binding energies has been observed in dimer and complexes.     

An investigation of complexes of some model tripeptides containing phenylalanine and tyrosine residues with DNA by Fourier1H NMR spectroscopy

Complexes of native and denatured DNA with model tripeptides containing phenylalanine or tyrosine residues flanked by lysine or arginine residues, respectively have been investigated by pulsed Fourier¹H NMR spectroscopy. The existence of shifts into the strong-field region of the signals of aromatic protons of the model tripeptides in the complexes both with native and with denatured DNA has been shown. Results have been obtained that indicate the possibility of the intercalation of the side chains of aromatic amino acid residues into the DNA double helix.     

Synthesis of enantiomerically pure cis- and trans-cyclopentane analogues of phenylalanine

For the first time, all stereoisomers of 1-amino-2-phenylcyclopentanecarboxylic acid—c₅Phe—have been synthesised. A Strecker reaction on 2-phenylcyclopentanone and further transformations of each amino nitrile into the amino acid provides cis-c₅Phe and trans-c₅Phe with high efficiency. A divergent synthetic route was then developed to obtain the target compounds cis- and trans-c₅Phe in their racemic form. The preparation of the final enantiomerically pure amino acids and their corresponding N-protected derivatives was also achieved by HPLC resolution of one of the intermediates using a cellulose-derived chiral stationary phase. The relative stereochemistry of each amino acid and its precursors have been unambiguously assigned.     

Dissociations of copper(II)-containing complexes of aromatic amino acids: radical cations of tryptophan, tyrosine, and phenylalanine

The dissociations of two types of copper(II)-containing complexes of tryptophan (Trp), tyrosine (Tyr), or phenylalanine (Phe) are described. The first type is the bis-amino acid complex, [Cu(II)(M)(2)].(2+), where M = Trp, Tyr, or Phe; the second [Cu(II)(4Cl-tpy)(M)].(2+), where 4Cl-tpy is the tridendate ligand 4'-chloro-2,2':6',2'-terpyridine. Dissociations of the Cu(ii) bis-amino acid complexes produce abundant radical cation of the amino acid, M.(+), and/or its secondary products. By contrast, dissociations of the 4Cl-tpy-bearing ternary complexes give abundant M.(+) only for Trp. Density functional theory (DFT) calculations show that for Tyr and Phe, amino-acid displacement reactions by H(2)O and CH(3)OH (giving [Cu(II)(4Cl-tpy)(H(2)O)].(2+) and [Cu(II)(4Cl-tpy)(CH(3)OH)].(2+)) are energetically more favorable than dissociative electron transfer (giving M.(+) and [Cu(I)(4Cl-tpy)](+)). The fragmentation pathway common to all these [Cu(II)(4Cl-tpy)(M)].(2+) ions is the loss of NH(3). DFT calculations show that the loss of NH(3) proceeds via a "phenonium-type" intermediate. Dissociative electron transfer in [Cu(II)(4Cl-tpy)(M-NH(3))].(2+) results in [M-NH(3)].(+). The [Phe-NH(3)] (+) ion dissociates facilely by eliminating CO(2) and giving a metastable phenonium-type ion that rearranges readily into the styrene radical cation.     

Conformation-specific spectroscopy and photodissociation of cold, protonated tyrosine and phenylalanine

We present here ultraviolet and infrared spectra of protonated aromatic amino acids in a cold, 22-pole ion trap. Ultraviolet photofragmentation spectra of protonated tyrosine and phenylalanine show vibronically resolved bands corresponding to different stable conformers: two for PheH+ and four in the case of TyrH+. We subsequently use the resolved UV spectra to perform conformer-specific infrared depletion spectroscopy. Comparison of the measured infrared spectra to density functional theory calculations helps assign the geometry of the various conformers, all of which exhibit NH...pi hydrogen bonds and NH...O=C interactions, with the COOH group oriented either anti or gauche to the aromatic ring. In both molecules the majority of the observed fragments result from dissociation on an excited electronic state. In TyrH+, different conformers excited with practically the same energy exhibit different fragmentation patterns, suggesting that the excited-state dynamics depend upon conformation.     

Nonplanar distortions and strain energies of polycyclic aromatic hydrocarbons

On the basis of HF/6-31G(d) optimized structures, the nonplanar distortions of 135 polycyclic aromatic hydrocarbons (PAHs) have been classified as splitting (S-) and arching (A-) distortions. Three bay structures are proposed as the structural origin of S-distortion. Due to the limitation of sample molecules, a set of universal motifs for molecules containing A-distortions is not available; however, a set of motifs and parameters are developed for the semiquantitative estimation of the nonplanar strain energies of PAHs containing the corannulene structure, and the differences between the E(np) values from quantum calculations and those from these estimations vary from -5.60 to 5.51 kcal/mol. The above results are fundamentally important for the understanding of nonplanar distortion of PAHs and fullerenes, and this method can also be employed to semiquantitatively estimate strain energies of such molecules containing hundreds of carbon atoms.     

Determination of phenylalanine and tyrosine by liquid chromatography/mass spectrometry

Phenylketonuria is a common metabolic disorder disease. Those affected appear normal at birth, but without treatment they develop severe psychomotor retardation. Throughout life, they must control their blood levels of phenylalanine (Phe) and consume a diet containing adequate amounts of Phe and tyrosine (Tyr). We have developed a liquid chromatographic/mass spectrometric (LC/MS) method for the quantitative evaluation of Phe and Tyr in food samples. This method takes advantage of the good separation of LC and the selective and reliable quantification provided by MS in the electrospray ionization mode. The LC/MS method is very suitable for the determination of selected amino acids in various matrixes. It is sensitive to levels as low as about 0.30 ppm for Tyr and 0.70 ppm for Phe and robust. Nearly 100 nondietary food samples were analyzed by the developed method.     

Interaction energies of ZnO in acrylic polymer lattices

Water‐based acrylic polymers are frequently used as binders in ceramic materials that contain ZnO as a major component. Thin flexible ceramic films used in semiconductor elements are prepared from ceramic powder, polymer binder, dispergant and plasticizer. In the present work, the chemical reaction of acrylic acid, a part of the polymer, and ceramic powder (ZnO) has been studied by semi‐empirical calculations and Fourier transform infrared spectroscopy (FTIR). Systematic evaluation of model structures using varying contents of acrylic acid showed that ZnO adhesion increases as the carboxylate content in the polymer system increases. Interaction energy surfaces provide a quantitative insight into the spatial distribution of ZnO particles in various model structures. These results are also in good agreement with our infrared spectroscopy measurements.