Fourth derivative UV-spectroscopy of proteins under high pressure I. Factors affecting the fourth derivative spectrum of the aromatic amino acids

A tunable fourth derivative UV absorbance method based on a variable spectral shift has been developed and compared to the Savitzky-Golay method and the analytical derivative. The parameters of the method were optimised for the analysis of the UV absorbance spectra of the aromatic amino acids to quantify the effect of decreasing solvent polarity on their fourth derivative spectra. The wavelength of the highest maximum (_max) (for tyrosine and phenylalanine) or the amplitude of the highest maximum (A_max) (for tryptophan), were shown to depend linearly on the dielectric constant of the solvent, ranging from water to cyclohexane. The only effect of pressure in the 1 to 500 MPa range is a small decrease in the fourth derivative amplitude. This method appears therefore as a suitable tool to evaluate changes of the dielectric constant in the vicinity of the aromatic amino acids in proteins which undergo pressure induced structural changes.     

Partial intercalation with DNA of peptides containing two aromatic amino acids

The interactions with DNA of tetrapeptide amides containing lysine at the N-terminal position and aromatic amino acids at the second and fourth positions (Ala at position three), 1-6, have been investigated by nmr, CD, and viscometric methods. Tetrapeptides with N-terminal lysine and a single aromatic amino acid, 7-10, were investigated as controls. Significant decreases in DNA viscosity occurred on addition of 7, with the aromatic group at the second position, but not with any of the other single aromatic amino acid peptides. All of the tetrapeptides with two aromatic groups caused DNA viscosity decreases which were two to three times larger than with 7. Peptides with p-nitrophenylalanine (p-NO2Phe) as the aromatic group were synthesized for nmr studies because of its simpler aromatic nmr spectrum relative to Phe. Large upfield shifts of the aromatic proton signals were obtained when the amino acid in the second position was L-p-NO2Phe, and the fourth position contained either p-NO2Phe or Phe. Such peptides also caused the largest DNA viscosity decreases on complex formation. Smaller upfield shifts of the aromatic signals were obtained when the amino acid in the second position was L-Phe or a D isomer of Phe or p-NO2Phe. With all peptides, larger upfield nmr shifts were obtained with heat-denatured, recooled DNA than with native DNA under the same conditions. As with nmr, CD results are quite different for the peptides with L and D amino acids at the second position. All of the results can be interpreted in terms of a model in which lysine interacts stereospecifically with the backbone in a DNA double helix and the aromatic group at the second position stacks strongly with the base pairs when the amino acid is an L isomer. The aromatic group at the fourth position can also interact with the base pairs, but primarily through a sideways stacking of the aromatic group with base pairs for either L or D isomers. Because of covalent constraints on the separation distance for the two aromatic groups in the tetrapeptides, they must stack on opposite sides of the same base pair in violation of the neighbor exclusion principle observed with classical intercalators. This stacking at the same base pair no doubt accounts for the larger viscosity decreases in DNA with the peptides containing two aromatic groups relative to those with a single aromatic group.(ABSTRACT TRUNCATED AT 400 WORDS)     

Determination of absorption coefficients of purified proteins by conventional ultraviolet spectrophotometry and chromatography combined with multiwavelength detection

The direct, ultraviolet spectrophotometric determination of protein absorption coefficients was found to be more reproducible and accurate when diluting was replaced by chromatography and multiwavelength detection. Four different ultraviolet spectrophotometric methods, described in the literature, were compared by calculating A0.1%280 values from the spectra of 25 proteins, obtained by chromatography. Only two methods, i.e., one based on the absorbance at 210 nm and the other on the absorbance at 205 nm, corrected for the absorbance of aromatic amino acids at that wavelength, were sufficiently accurate to be of potential use for the determination of unknown proteins. It was found, however that with uncorrected A203 values even better results could be achieved. Using 7 well-defined proteins the equation A0.1%280 = 38.69 X A280/A203 - 0.01 was established by linear regression. A0.1%280 values for 14 pure proteins calculated with this equation showed a mean deviation of only 4% from literature values. Since similar deviations were seen with 5 chromophoric and 7 glycoproteins, 3 and 7% respectively, the method may have universal applicability. In the configuration used, only 40 micrograms of a protein is required for the chromatographic determination of its absorption coefficient.     

Quantitative determination of tryptophanyl and tyrosyl residues of proteins by second-derivative fluorescence spectroscopy

Second-derivative spectroscopy has been applied to the study of the fluorescence of aromatic amino acids. The spectral features of the second derivative emission spectra of free aromatic amino acids and proteins are described, the emission of each aromatic fluorophore being characterized by a particular minimum-maximum pair. An easy, accurate, and rapid method is proposed for the quantitative determination of tyrosine and tryptophan, based on the addition of small amounts of a standard solution to the samples followed by the measurement of the increase in the distance between a selected minimum and an adjacent maximum, in the second-derivative spectrum. For tyrosine determination, excitation wavelength was 275 nm, and the selected minimum-maximum (m,M) pair was (300; 330 nm), while an excitation of 300 nm and a minimum-maximum pair (357; 377 nm) were employed for the tryptophan determination. This method enables the tryptophan content of proteins to be determined directly, without the need for correction for the presence of tyrosine. The tyrosine content of proteins can also be determined at neutral pH, in the presence of both tryptophan and phenylalanine. The proposed method has also been applied to trypsin activation of frog epidermis tyrosinase.     

Photoacoustic spectroscopy of aromatic amino acids in proteins

This paper concerns the use of photoacoustic spectroscopy (PAS) to study the presence of aromatic amino acid in proteins. We examined the aromatic amino acids in six proteins with well-known structures using absorption spectra of near ultraviolet PAS over the wavelength range 240–320 nm. The fundamental understanding of the physical and chemical properties that govern the absorption of light and a subsequent release of heat to generate a transient pressure wave was used to test the concept of monitoring aromatic amino acids with this method. Second derivative spectroscopy in the ultraviolet region of proteins was also used to study the regions surrounding the aromatics and the percentage area in each band was related in order to determine the contribution in function of the respective molar extinction coefficients for each residue. Further investigation was conducted into the interaction between sodium dodecyl sulphate (SDS) and bothropstoxin-I (BthTx-I), with the purpose of identifying the aromatics that participate in the interaction. The clear changes in the second derivative and curve-fitting procedures suggest that initial SDS binding to the tryptophan located in the dimer interface and above 10 SDS an increased intensity between 260 and 320 nm, demonstrating that the more widespread tyrosine and phenylalanine residues contribute to the SDS/BthTx-I interactions. These results demonstrate the potential of near UV-PAS for the investigation of membrane proteins/detergent complexes in which light scattering is significant.     

Expression cloning of a Na+-independent aromatic amino acid transporter with structural similarity to H+/monocarboxylate transporters

A cDNA was isolated from rat small intestine by expression cloning which encodes a novel Na+-independent transporter for aromatic amino acids. When expressed in Xenopus oocytes, the encoded protein designated as TAT1 (T-type amino acid transporter 1) exhibited Na+-independent and low-affinity transport of aromatic amino acids such as tryptophan, tyrosine, and phenylalanine (Km values: approximately 5 mm), consistent with the properties of classical amino acid transport system T. TAT1 accepted some variations of aromatic side chains because it interacted with amino acid-related compounds such as l-DOPA and 3-O-methyl-DOPA. Because TAT1 accepted N-methyl- and N-acetyl-derivatives of aromatic amino acids but did not accept their methylesters, it is proposed that TAT1 recognizes amino acid substrates as anions. Consistent with this, TAT1 exhibited sequence similarity (approximately 30% identity at the amino acid level) to H+/monocarboxylate transporters. Distinct from H+/monocarboxylate transporters, however, TAT1 was not coupled with the H+ transport but it mediated an electroneutral facilitated diffusion. TAT1 mRNA was strongly expressed in intestine, placenta, and liver. In rat small intestine TAT1 immunoreactivity was detected in the basolateral membrane of the epithelial cells suggesting its role in the transepithelial transport of aromatic amino acids. The identification of the amino acid transporter with distinct structural and functional characteristics will not only facilitate the expansion of amino acid transporter families but also provide new insights into the mechanisms of substrate recognition of organic solute transporters.     

Isolation and quantitation of isotopically labeled amino acids from biological samples

To face the problem of simultaneous isolation and quantitation of isotopically labeled amino acids in biological samples, two semi-preparative chromatographic methods were developed. One method was especially designed to isolate radioactively labeled amino acids for which we used derivatization with the fluorophore o-phtaaldialdehyde (OPA), which is known to be easy and reliable. Isolation of amino acids labeled with stable isotopes required another approach as we wanted to use isotope ratio mass spectroscopy (IRMS), which can only be performed on pure, non-derivatized amino acids. Becuase the OPA probe cannot be removed after isolation of the derivative, we used 9-fluorenylmethylchloroformate (FMOC) instead. This probe is linked to an amino acid via a peptide bond which can easily be broken byb gas-phase acid hydrolysis (103% recovery after 5 h at 150°C: S.D = 3.5%, n = 14). Run time (injection to injection) was 60 min for the OPA method and 75 min for the FMOC method. Both fluorescence and UV absorbance detection can be employed. The coefficient of variation (C.V.) for peak area measurement was below 2% for most OPA amino acids and below 3% for most FMOC amino acids. At maximum, a total of 1000 μl could be injcted, representing approximately 200 μl of deproteinized plasma. The methods were linear up to injection of 0.5 μmol of all amino acids (OPA: r²=0.995−0.999; FMOC: r²=0.992−0.999). The C.V. of the IRMS measurement within the range which can be isolated maximally in one chromatographic run (50–500 nmol), was less than 3% above 100 mmol, indicating that chromatographic isolation fulfils the needs of the IRMS determination. The resulting methods are suitable for the isolation and quantitation of micromolar amounts of labeled amino acids from biological samples.     

A protein and peptide monitor with a hollow-cathode light source.

This communication describes an inexpensive system that will monitor protein and peptide concentration in chromatogram eluates by light absorbance at an adjustable wavelength.Proteins in chromatogram eluate streams are commonly metered for concentration by absorbance measurement at 280 nm. Besides a range of commercially manufactured monitors, there is the apparatus described by Bennett et al. (1) which uses a selectively modulated magnesium lamp. Measurements in the region of 280 nm are of no value, however, when the material does not contain aromatic amino acids. Monitoring then becomes necessary at 230 nm in the region of absorption due to the peptide bond. The common resort in such a case is the standard ultraviolet-visible spectrophotometer, which has the disadvantage of being both unnecessarily elaborate and expensive for the purpose required. The deuterium lamps in these instruments require frequent replacement because of the extended periods of operation, adding to the cost factor.We have investigated the use of a hollow-cathode lamp of the type manufactured for use in an atomic absorption spectrophotometer. These lamps have high stability and a long working life, due to the considerably lower level of power dissipation compared with deuterium lamps. Their emission spectra are discontinuous, but the lamp for the element iron provides adequately strong lines at both 229.5 and 279.2 nm, suitable for a protein monitor.     

Probing protein structure and dynamics by second-derivative ultraviolet absorption analysis of cation-{pi} interactions

We describe an alternate approach for studying protein structure using the detection of ultraviolet (UV) absorbance peak shifts of aromatic amino acid side chains induced by the presence of salts. The method is based on the hypothesis that salt cations (Li+, Na+, and Cs+) of varying sizes can differentially diffuse through protein matrices and interact with benzyl, phenyl, and indole groups through cation-pi interactions. We have investigated the potential of this method to probe protein dynamics by measuring high resolution second-derivative UV spectra as a function of salt concentration for eight proteins of varying physical and chemical properties and the N-acetylated C-ethyl esterified amino acids to represent totally exposed side chains. We show that small shifts in the wavelength maxima for Phe, Tyr, and Trp in the presence of high salt concentrations can be reliably measured and that the magnitude and direction of the peak shifts are influenced by several factors, including protein size, charge, and the local environment and solvent accessibility of the aromatic groups. Evaluating the empirical UV spectral data in light of known protein structural information shows that probing cation-pi interactions in proteins reveals unique information about the influence of structure on aromatic side chain spectroscopic behavior.     

氨基酸分析检测方法的研究进展

对氨基酸分析常用的检测方法:分光光度法、气相色谱法、液相色谱法、毛细管电泳法及其它方法(近红外光谱法、化学发光法、荧光光谱法)进行综述,并介绍了这些方法在氨基酸检测中的应用,为建立快速、高效的氨基酸分析方法提供参考.     

Production of aromatic α-hydroxyacids by epimastigotes of Trypanosoma cruzi, and its possible role in NADH reoxidation

Abstract Epimastigotes of Trypanosoma cruzi in culture produce and excrete into the medium small amounts of phenyllactic acid and p -hydrocyphenyllactic acids, presumbly arising from the catabolism of the aromatic amino acids phenylalanine and tyrosine, respectively. This production might constitute a minor pathway for the reoxidation of cytosolic NADH, through the concerted action of tyrosine aminotransferase and aromatic α-hydroxyacid dehydrogenase.     

Evolution of the biosynthesis of the branched-chain amino acids

The origin of the biosynthetic pathways for the branched-chain amino acids cannot be understood in terms of the backwards development of the present acetolactate pathway because it contains unstable intermediates. We propose that the first biosynthesis of the branched-chain amino acids was by the reductive carboxylation of short branched chain fatty acids giving keto acids which were then transaminated. Similar reaction sequences mediated by nonspecific enzymes would produce serine and threonine from the abundant prebiotic compounds glycolic and lactic acids. The aromatic amino acids may also have first been synthesized in this way, e.g. tryptophan from indole acetic acid. The next step would have been the biosynthesis of leucine from -ketoisovaleric acid. The acetolactate pathway developed subsequently. The first version of the Krebs cycle, which was used for amino acid biosynthesis, would have been assembled by making use of the reductive carboxylation and leucine biosynthesis enzymes, and completed with the development of a single new enzyme, succinate dehydrogenase. This evolutionary scheme suggests that there may be limitations to inferring the origins of metabolism by a simple back extrapolation of current pathways.     

氨基酸生产和海洋生物的氨基酸资源开发

氨基酸在医药、食品、饲料等领域有着极为重要和广泛的用途,世界上氨基酸总需求量以５～１０％递增,市场竞争十分激烈。生物资源提取、化学合成、生物合成和综合法是生产氨基酸的４种技术,目前的发展趋势为生物合成和综合法,特别是将现代生物工程技术应用于氨基酸生产。另外,氨基酸生产领域另一个新的倾向是海洋生物氨基酸资源的开发和应用,尤其是海洋生物所产生的特殊氨基酸、肽及其衍生物的开发,同时,综合利用海产品加工后的废弃物来生产氨基酸也受到重视。     

Rapid reversed-phase high-performance liquid chromatographic method with double derivatization for the assay of urinary hydroxyproline

An HPLC method with two derivatizations, the first with o-phthaldehyde in order to eliminate interferences due to some primary amino acids eluting with retention times similar to those of hydroxyproline and the second with dabsyl chloride, was developed and evaluated. Calibration graph linearity, influence of agitation and temperature on the preparation of the first derivative and the influence of the detection wavelength were assessed. The analysis time is shorter in comparison with other available methods, and therefore this method is suitable for laboratories that analyse both small and large series of samples.     

Polyene fatty acid interactions with recombinant intestinal and liver fatty acid-binding proteins. Spectroscopic studies

Binding and proximity relationships of fatty acids with recombinant rat liver fatty acid-binding protein (L-FABP) and intestinal fatty acid-binding protein (I-FABP) were studied with absorption and fluorescence spectroscopy. Protein aromatic amino acids were examined in the absence and presence of bound fatty acid. Second derivative absorbance spectroscopy of the apo- and holoproteins suggested that fatty acid binding altered the conformation of L-FABP, but not of I-FABP. Fatty acid binding also blocked the accessibility of L-FABP tyrosine and I-FABP tryptophan to Stern-Volmer quenching by acrylamide, indicating that these amino acids were present in the fatty acid-binding pocket. Forster energy transfer from I-FABP tryptophan to bound cis-parinaric acid resulted in quenching of tryptophan lifetime and appearance of sensitized lifetime of bound cis-parinaric acid. The calculated donor-acceptor distances were 16.9 +/- 0.6 and 19.2 +/- 0.3 A for I-FABP and L-FABP, respectively. Absorbance spectral shifts and ratios of fluorescence excitation maxima indicated that the parinaric acid microenvironment in the fatty acid-binding site of I-FABP was much less polar than that of L-FABP. Parinaric acids displayed similar rotational correlation time and limiting anisotropy when bound to I-FABP and to L-FABP. These results are consistent with a close proximity of bound fatty acids to the tyrosine and tryptophan residues and with immobilization of the polyene fatty acids in the fatty acid-binding site(s) of L-FABP and I-FABP. The two proteins differ in that only L-FABP has two fatty acid-binding sites and appears to undergo significant conformational change upon fatty acid binding.     

Colorimetric assay for methanesulfinic acid in biological samples

We describe a simple colorimetric method to measure 30 to 300 microM concentrations of sulfinic acids in biologic samples. The procedure employs the coupling reaction of an aromatic diazonium salt (Ar--N = N+) with the sulfinic acids (RSOOH) to produce a colored diazosulfone derivative (Ar-N = N-SOOR), which can be selectively extracted into an organic solvent. Linearity as well as noninterference by liver homogenate, phenols, amines, and thousandfold or greater excesses of sulfate, thiol, and dimethyl sulfoxide is demonstrated. Sensitivity of the method is about 10 nmol per sample. Because methanesulfinic acid is the principal product of the action of hydroxyl radicals upon dimethyl sulfoxide, and because intact animals can tolerate dimethyl sulfoxide in millimolar concentrations, the method may prove widely useful for detecting the involvement of hydroxyl radicals in pathologic processes in vivo.     

Ultraviolet resonance Raman study of drug binding in dihydrofolate reductase, gyrase, and catechol O-methyltransferase.

This paper presents a study of the use of ultraviolet resonance Raman (UVRR) spectroscopic methods as a means of elucidating aspects of drug-protein interactions. Some of the RR vibrational bands of the aromatic amino acids tyrosine and tryptophan are sensitive to the microenvironment, and the use of UV excitation radiation allows selective enhancement of the spectral features of the aromatic amino acids, enabling observation specifically of their change in microenvironment upon drug binding. The three drug-protein systems investigated in this study are dihydrofolate reductase with its inhibitor trimethoprim, gyrase with novobiocin, and catechol O-methyltransferase with dinitrocatechol. It is demonstrated that UVRR spectroscopy has adequate sensitivity to be a useful means of detecting drug-protein interactions in those systems for which the electronic absorption of the aromatic amino acids changes because of hydrogen bonding and/or possible dipole-dipole and dipole-polarizability interactions with the ligand.     

Selenotyrosine and related phenylalanine derivatives.

A new series of Se-substituted phenylalanine derivatives has been synthesized having the para position of the phenyl ring substituted by selenocyanate (-SeCN), seleninic acid (-SeO(2)H), or selenol (-SeH) functional groups. The starting material for synthesis was 4'-aminophenylalanine, which is readily available in DL- or L- forms. Selenium was incorporated into the ring by reacting the unprotected amino acid with nitrous acid, followed by reaction of the diazotized aromatic amine with potassium selenocyanate at pH 4-5 to give phenylalanine selenocyanate. The selenocyanate derivative was converted to the selenol directly by reduction with sodium borohydride, or oxidized to the seleninic acid, which was then reduced to the selenol. Alkylation of the selenol ('selenotyrosine') gave the selenoether derivatives of phenylalanine [(Phe-SeR), R=methyl or allyl], and air oxidation of the selenol gave the diselenide. Mild oxidation of the selenoether 4'-(MeSe)Phe with peroxide gave the selenoxide derivative, 4'-[Se(O)Me]. Because of their stability and useful redox properties, aromatic selenoamino acids can be used as synthetic analogues to increase chemical functionality in proteins or peptides, and have potential pharmaceutical or nutritional applications. The possibility that aromatic selenoamino acids could be formed metabolically through reactions of reactive selenium intermediates with aromatic amino acid residues is discussed.     

Transport of Aromatic Amino Acids by Pseudomonas aeruginosa

Kinetic studies of the transport of aromatic amino acids by Pseudomonas aeruginosa revealed the existence of two high-affinity transport systems which recognized the three aromatic amino acids. From competition data and studies on the exchange of preformed aromatic amino acid pools, the first transport system was found to be functional with phenylalanine, tyrosine, and tryptophan (in order of decreasing activity), whereas the second system was active with tryptophan, phenylalanine, and tyrosine. The two systems also transported a number of aromatic amino acid analogues but not other amino acids. Mutants defective in each of the two and in both transport systems were isolated and described. When the amino acids were added at low external concentrations to cells growing logarithmically in glucose minimal medium, the tryptophan pool very quickly became saturated. Under identical conditions, phenylalanine and tyrosine each accumulated in the intracellular pool of P. aeruginosa at a concentration which was 10 times greater than that of tryptophan.     

Chemometric methods for simultaneous quantification of lactic,malic and fumaric acids

Lactic, fumaric and malic acids are commonly used in food and pharmaceutical industries. During microbial production of these compounds, it is important to determine their concentrations in the fermentation broth with a rapid and sensitive method. Spectrophotometry is commonly used. However, UV‐spectral overlap between these organic acids makes it difficult to determine each of them individually from the mixture. In order to overcome this problem, statistical methods, namely principal component regression (PCR) and partial least squares‐1 methods, were tested and compared with conventional HPLC techniques. The absorbance data matrix was obtained by measuring the absorbances of 21 ternary mixtures of lactic, fumaric and malic acids in a wavelength range of 210–260 nm. Calibration and validation were performed by using the data obtained in a mixture of these organic acids. The prediction abilities of the methods were tested by applying them to fermentation broths. The precision of the PCR method was better than that of the partial least squares‐1 method. In the PCR method, the correlation coefficients between actual and predicted concentrations of the organic acids were calculated as 0.970 for lactic acid and 0.996 for fumaric acid in fermentation broths. The concentration of malic acid was not detected due to its low concentration in samples. These results show that the PCR method can be applied for simultaneous determination of lactic, fumaric and malic acids in fermentation broths.