Rapid determination of parvalbumin amino acid sequence from Rana catesbeiana (pI 4.78) by combination of ESI mass spectrometry, protein sequencing, and amino acid analysis

The complete amino acid sequence of beta-type parvalbumin (PA) from bullfrog Rana catesbeiana (pI 4.78) was determined by tandem mass spectrometry in combination with amino acid analysis and peptide sequencing following Arg-C and V(8) protease digestion. The primary structure of the protein was compared with that of beta-type PA from R. esculenta (pI 4.50), with which it is highly homologous. Compared with R. esculenta beta-type PA4.50, R. catesbeiana beta-type parvalbumin (PA 4.78) differed in 15 out of 108 amino acid residues (14% displacement), PA4.78 had Cys at residue 64 and was acetylated at the amino terminus, but 25 residues of the carboxyl terminus were completely conserved. Several amino acid displacements were found between residues 51 and 80 (30% displacement), although the functionally important sequence of PA was completely conserved. The amino acids residues of putative calcium-binding sites were Asp-51, Asp-53, Ser-55, Phe-57, Glu-59, Glu-62, Asp-90, Asp-92, Asp-94, Lys-96, and Glu-101, which were conserved in all a and b-types of R. catesbeiana as well as other parvalbumins. In addition, Arg-75 and Glu-81, which are thought to form a salt bridge located in the interior of the molecule [Coffee, C.J. et al. (1976) Biochim. Biophys. Acta 453, 67-80], were also conserved in PA4.78.     

A new double-labelling procedure for determination of amino acid composition: application to bacteriorhodopsin

A new double-labelling procedure for amino acid analysis which requires only routine chromatographic equipment is described. When 1-fluoro-2,4-dinitro[3H]benzene is reacted with a mixture of 14C-labelled amino acids followed by reaction with the same 14C-labelled amino acid mixture diluted with an unlabelled sample of amino acids, the 3H:14C ratio in the resulting 2,4-dinitrophenyl (DNP) amino acid derivatives of the diluted sample will be increased in proportion to the quantity of unlabelled amino acid in the diluted sample. This procedure gave reliable results when applied to the known proteins insulin and lysozyme. The procedure is most advantageous when applied to amino acids which are unstable during acid hydrolysis or present in low molar fractions. When applied to the analysis of the bacteriorhodopsin in Halobacterium cutirubrum, this procedure showed the presence of one histidine residue and four tryptophan residues per mole protein but no cystine or cysteine; in general, the analyses obtained were consistent with those originally reported by Oesterhelt, D. and Stoeckenius, W. (1971) (Nature (London) New Biol. 233, 149-152) for bacteriorhodopsin of H. halobium.     

Synthesis of novel protected Nalpha(omega-thioalkyl) amino acid building units and their incorporation in backbone cyclic disulfide and thioetheric bridged peptides.

General methods for the preparation of protected Nalpha(omega-thioalkyl) amino acids building units for backbone cyclization using reductive alkylation and on-resin preparation are described. The synthesis of non-Gly Fmoc-protected S-functionalized N-alkylated amino acids is based on the reaction of readily prepared protected omega-thio aldehyde with the appropriate amino acid. Preparation of Fmoc-protected S-functionalized N-alkylated Gly building units was carried out using two methods: reaction of glyoxylic acid with Acm-thioalkylamine and an on-resin reaction of bromoacetyl resin with Trt-thioalkylamines. Three model peptides were prepared using these building units. The GlyS2 building unit was incorporated into a backbone cyclic analog of somatostatin that contains a disulfide bridge. Formation of the disulfide bridge was performed by on-resin oxidation using 12 or Tl(CF3COO-)3. Both methods resulted in the desired product in a high degree of purity in the crude. The AspS3 building unit was also successfully incorporated into a model peptide. In addition, the in situ generation of sulfur containing Gly building units was demonstrated on a Substance P backbone cyclic analog containing a thioether bridge.     

Mechanisms of amino acid partitioning in cationic reversed micelles

The aim of this work is to discuss the mechanisms involved in amino acidsolubilization in cationic reversed micelles. A simple mechanism was assumedin which the amino acid solubilization is mediated by an ion-exchangeprocess between the amino acid and the surfactant counter ion neglecting theeffect of the reversed micellar structure. Based on this mechanism a simplemodel to predict equilibrium was developed and applied to the solubilizationof amino acids with different structures. It was found that solubilizationof hydrophilic and slightly hydrophobic amino acids can be described by anion-exchange mechanism and the amino acid equilibrium concentration can bedetermined for different experimental conditions using this model. However,solubilization of hydrophobic amino acids can not be described by a simpleion-exchange model. In this case hydrophobic contributions play an importantrole in amino acid solubilization and must be considered in the overallsolubilization process. This hydrophobic contribution was evaluated bydetermination of an interfacial partition coefficient. The overall aminoacid extraction was determined using distribution coefficients of all theamino acid forms and considering their dependence on ionic strength.     

High-sensitivity amino acid analysis: methodology for the determination of amino acid compositions with less than 100 picomoles of peptides

Highly sensitive methodology is described for the determination of amino acid compositions of picomole quantities of peptides using an automated fluorescence amino acid analyzer with o-phthalaldehyde as the detection agent. All commonly occurring amino acids, including cystine, proline, and tryptophan, can be quantitated. High sensitivity is primarily achieved by using simple procedures which effectively and reliably reduce the level of interfering contamination present in buffers and reagents or introduced during sample handling. Accurate and reproducible amino acid compositions are obtained with 50 pmol or less peptide.     

Qualitative determination of N-terminal amino acids of peptides and proteins with cobalt(III) chelates

1. A method of N-terminal peptide-bond hydrolysis with the cis-beta-hydroxyaquo(triethylenetetramine)cobalt(III) ion, i.e. beta-[Co(trien)(OH)(OH(2))](2+), is reported. The method has been demonstrated with 22 small peptides and ten proteins. 2. The procedure is rapid (an N-terminal amino acid determination can be made easily in one day), it involves no acid hydrolysis step and thus no destruction of labile amino acids, and it involves the use of easily prepared inexpensive reagents. 3. The released N-terminal amino acids can be identified as their cobalt(III) derivatives, or directly as the amino acid or as their dansylated derivatives. 4. The method is to treat 1 mumol of peptide or protein with beta-[Co(trien)(OH)(OH(2))](2+) reagent at pH8.0, 45 degrees C for 3h. Addition of 0.5m-phosphate buffer, pH10.5 at 45 degrees C for 10min cleaves the N-terminal bidentate amino acid-cobalt complex, which can be identified directly. For greater sensitivity with 10nmol of peptide) the free amino acid is prepared from the complex by treatment (with NaCN (0.1m, 40 degrees C, 30min), or H(2)S or NaBH(4) (25 degrees C, 5min), dried, dansylated and the dansyl-amino acid identified by high-voltage electrophoresis. The method is unaffected by the presence of 4-8m-urea, but will not cleave blocked N-terminal acids.     

An automatic analyzer for the specific determination of amino sugars

The techniques previously employed for the extraction and determination of amino acids from different matrices are not necessarily optimal for the determination of the amino sugars. An analytical system is described which is a hybrid between the conventional amino acid analyzer and the liquid chromatographic system for the detection of reducing sugars. The major, naturally occurring amino sugars are separated in about 40 min, with sensitivites lying under the nanomole range, without interference from other co-extracted compounds such as amino acids and sugars. The reagent employed is noncorrosive and stable over long periods of time. The amino sugar analyzer can be readily constructed by simple modification of a conventional phenylketonuria or amino acid analyzer.     

Determination of polypeptide amino acid sequences from the carboxyl terminus using angiotensin I converting enzyme

A method for sequence analysis of polypeptides starting at the carboxyl terminus is described that utilizes degradation of the polypeptide into dipeptides with angiotensin I converting enzyme. Dipeptides were identified by gas chromatography-mass spectroscopy. Dipeptide alignment was achieved by replicate digestion of the polypeptide after modification at the carboxyl terminus either by chemical or enzymatic removal of one residue or by addition of a single residue. The addition reaction involved coupling of L-alpha-aminobutyric acid under conditions described herein which yielded essentially complete conversions. Unlike sequence determination methods that commence from the polypeptide amino terminus, this procedure does not require that a polypeptide have a free amino terminus for successful application. A number of polypeptides with varying chain lengths (up to 49 residues), containing among them most of the common amino acids, have been successfully analyzed in amounts as low as 5 nmol.     

Snorkeling preferences foster an amino acid composition bias in transmembrane helices

By analyzing transmembrane (TM) helices in known structures, we find that some polar amino acids are more frequent at the N terminus than at the C terminus. We propose the asymmetry occurs because most polar amino acids are better able to snorkel their polar atoms away from the membrane core at the N terminus than at the C terminus. Two findings lead us to this proposition: (1) side-chain conformations are influenced strongly by the N or C-terminal position of the amino acid in the bilayer, and (2) the favored snorkeling direction of an amino acid correlates well with its N to C-terminal composition bias. Our results suggest that TM helix predictions should incorporate an N to C-terminal composition bias, that rotamer preferences of TM side-chains are position-dependent, and that the ability to snorkel influences the evolutionary selection of amino acids for the helix N and C termini.     

A sensitive and accurate method for amino acid analysis using isotopic double labeling with fluorodinitrobenzene

A double-labeling procedure for amino acid analysis using ³H-labeled 1-fluoro-2,4-dinitrobenzene and ¹⁴C-labeled amino acids as internal standards is described. The procedure was tested by analyzing lysozyme and insulin B chain, and the results obtained were in good agreement with their accepted amino acid compositions. Analysis of samples containing from 100 pmol of each amino acid can be achieved at an accuracy comparable to that obtained by conventional automated amino acid analysis methods, many of which require considerably more material. An important advantage is that amino acids present in low molar proportions can be separated and measured more readily than by column chromatography.     

利用气相色谱-质谱联机测定土壤氨基酸手性异构体13C富集比例

氨基酸手性异构体的转化与更新程度在表征土壤有机质的循环转化机制方面具有重要意义.为有效区分土壤中原有的和利用外加碳源新合成的氨基酸,本文建立了稳定同位素培养 气相色谱/质谱联机测定土壤氨基酸手性异构体¹³C富集比例的方法.由于培养过程中加入的¹³C葡萄糖被迅速利用形成氨基酸碳骨架,因而利用质谱技术可检测同位素的富集强度的变化.外加葡萄糖直接合成氨基酸的比例可利用质谱碎片(F+n)的相对强度变化来评价（n为质谱碎片F中含有的碳原子数目）;而源于葡萄糖的¹³C同位素在氨基酸分子中的富集程度是所有同位素峰相对强度变化的总和.¹³C在目标化合物中的富集比例用原子百分超（APE）评价,D 氨基酸的APE还需进一步利用水解诱导的外消旋化系数校正.¹³C在目标化合物中的富集程度可反映各氨基酸手性异构体的碳循环速率大小,是研究土壤氨基酸动态变化的有力工具.     

Isolation and structural characterization of a new crosslinking amino acid, cyclopentenosine, from the acid hydrolysate of elastin.

A novel polyfunctional crosslinking amino acid, which was developed slower than lysinonorleucine and faster than desmosine on thin layer chromatography, was isolated from the hydrolysate of bovine aorta elastin. Its proposed structure was verified by ultraviolet spectroscopy, fast atom bombardment mass spectroscopy, and nuclear magnetic resonance spectroscopy. The data indicated it to be a trifunctional amino acid with a cyclopentene structure. The mass spectral analysis indicated a parent compound with a mass of 381 (C18H27N3O6). The proposed structure is one derived from the condensation of three allysine residues. Based on the names of other crosslinking amino acids found in elastin, the trivial name of cyclopentenosine is given to this compound.     

The 43-kilodalton protein of Torpedo nicotinic postsynaptic membranes: purification and determination of primary structure

The primary structure of the 43-kilodalton peripheral membrane protein (43-kDa protein) of Torpedo nicotinic postsynaptic membrane has been determined. The 43-kDa protein, which was isolated by preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis, has an amino terminus resistant to Edman degradation, while the sequence at the carboxyl terminus is Tyr-Val. An amino acid sequence of 405 residues was obtained by NH2-terminal sequence analysis of complementary peptides generated by digestion with trypsin, chymotrypsin, Staphylococcus aureus V8 protease, and endoproteinase Lys-C, as well as by chemical cleavage at methionine. This sequence of molecular mass 45,618 daltons lacks the amino terminus but extends to the carboxyl terminus of the 43-kDa protein. Unusual structural features of the 43-kDa protein include two regions of approximately 80 residues, each containing 10% cysteine, as well as stretches predicted to exist as amphipathic alpha-helices. Other than the group blocking the amino terminus, no evidence was found for posttranslational modification of amino acids. The 43-kDa protein may represent a novel protein family because a computer search of this sequence with the National Biomedical Research Foundation data base (Release 12.0) did not reveal any significant homology to known protein sequences.     

Phospholipid transfer protein: full-length cDNA and amino acid sequence in maize. Amino acid sequence homologies between plant phospholipid transfer proteins

We have determined the primary structure of a phospholipid transfer protein (PLTP) isolated from maize seeds. This protein consists of 93 amino acids and shows internal homology originating in the repetition of (do)decapeptides. By using antibodies against maize PLTP, we have isolated from a cDNA library one positive clone (6B6) which corresponds to the incomplete nucleotide sequence. Another cDNA clone (9C2) was obtained by screening a size-selected library with 6B6. Clone 9C2 (822 base pairs) corresponds to the full-length cDNA of the phospholipid-transfer protein whose mRNA contains 0.8 kilobase. Southern blot analysis shows that the maize genome may contain several PLTP genes. In addition, the deduced amino acid sequence of clone 9C2 reveals the presence of a signal peptide. The significance of this signal peptide (27 amino acids) might be related to the function of the phospholipid-transfer protein. The amino acid sequence of maize PLTP was compared to those isolated from spinach leaves or castor bean seeds which exhibit physicochemical properties close to those of the maize protein. A high homology was observed between the three sequences. Three domains can be distinguished: a highly charged central core (around 40-60), a very hydrophobic N-terminal sequence characteristic of polypeptide-membrane interaction, and a hydrophilic C terminus. A model for plant phospholipid-transfer proteins is proposed in which the phospholipid molecule is embedded within the protein with its polar moiety interacting with the central hydrophilic core of the protein, whereas the N-terminal region plunges within the membrane in the transfer process.     

Amino acid sequence of a novel calmodulin from Paramecium tetraurelia that contains dimethyllysine in the first domain

A class of Paramecium behavioral mutants called pantophobiacs have a deficiency in calcium-dependent potassium efflux, and this deficiency can be corrected by the microinjection of wild-type Paramecium calmodulin (Hinrichsen, R. D., Burgess-Cassler, A., Soltvelt, B. C., Hennessey, T., and Kung, C. (1986) Science 232, 503-506). As a starting point in investigations of which features allow wild-type Paramecium calmodulin to fully restore this behavior while other calmodulins are inactive or poorly effective, we elucidated the amino acid sequence of the wild-type calmodulin. We utilized an approach that combined Edman chemistry with mass spectrometry. This approach resulted in the identification of a new post-translational modification in calmodulin: N epsilon,N epsilon-dimethyllysine at residue 13. This particular modification has not been described for calmodulins studied previously. The only other first-domain modification that has been described for any calmodulin is acetylation of the amino terminus (Watterson, D. M., Sharief, F., and Vanaman, T. C. (1980) J. Biol. Chem. 255, 962-975). These results along with analyses of pantophobiac calmodulin and calmodulin binding proteins will provide insight into calmodulin's role in a well-defined behavioral mutant.     

Sequence determination of the Sendai virus HN gene and its comparison to the influenza virus glycoproteins

The nucleotide sequence of the Sendai virus (SV) HN (hemagglutinin-neuraminidase) gene was determined. The deduced primary structure of the protein showed only one hydrophobic domain likely to represent the transmembrane region, but at its N terminus. Since the SV F protein is anchored in the membrane at its C terminus, the two SV glycoproteins are thus membrane-anchored in opposite orientations, similar to the two influenza virus (FLU) glycoproteins. Amino acid sequence comparisons of the SV HN and the FLU HA and NA proteins revealed homologies between 100 amino acids of the hemagglutinin region of the FLU HA protein and the C terminus of the SV HN, and between 200 amino acids of the neuraminidase region of the FLU NA and the central region of SV HN. Alignment of the neuraminidase, hemagglutinin, and fusion regions shared by these glycoproteins suggest the structure of a possible ancestral gene.     

Remote protein homology detection using recurrence quantification analysis and amino acid physicochemical properties

Remote homology detection refers to the detection of structure homology in evolutionarily related proteins with low sequence similarity. Supervised learning algorithms such as support vector machine (SVM) are currently the most accurate methods. In most of these SVM-based methods, efforts have been dedicated to developing new kernels to better use the pairwise alignment scores or sequence profiles. Moreover, amino acids’ physicochemical properties are not generally used in the feature representation of protein sequences. In this article, we present a remote homology detection method that incorporates two novel features: (1) a protein's primary sequence is represented using amino acid's physicochemical properties and (2) the similarity between two proteins is measured using recurrence quantification analysis (RQA). An optimization scheme was developed to select different amino acid indices (up to 10 for a protein family) that are best to characterize the given protein family. The selected amino acid indices may enable us to draw better biological explanation of the protein family classification problem than using other alignment-based methods. An SVM-based classifier will then work on the space described by the RQA metrics. The classification scheme is named as SVM-RQA. Experiments at the superfamily level of the SCOP1.53 dataset show that, without using alignment or sequence profile information, the features generated from amino acid indices are able to produce results that are comparable to those obtained by the published state-of-the-art SVM kernels. In the future, better prediction accuracies can be expected by combining the alignment-based features with our amino acids property-based features. Supplementary information including the raw dataset, the best-performing amino acid indices for each protein family and the computed RQA metrics for all protein sequences can be downloaded from http://ym151113.ym.edu.tw/svm-rqa.     

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.     

Automated fluorometric amino acid analysis: the determination of proline and hydroxyproline.

A fluorometric method for the automated determination of the imino acids proline and hydroxyproline has been developed. The assay is based on the postcolumn reaction of the imino acids with alkaline sodium hypochlorite, which yields oxidation products amenable to detection with fluorogenic amine reagents. The method is simple and can be adapted readily to high-sensitivity amino acid analyzers which use o-phthalaldehyde for detection. As little as 10 pmol proline and 20 pmol hydroxyproline can be determined accurately. Thus the full array of natural imino and amino acids can now be determined on a high-sensitivity amino acid analyzer using o-phthalaldehyde.