Determination of sulfur-containing amino acid residues in proteins by pyrolysis-gas chromatography with flame photometric detection

Summary A new method for the determination of sulfur-containing amino acid residues, cysteine (Cys) and methionine (Met) in proteins has been developed with pyrolysis-gas chromatography. Characteristic sulfur compounds among the complicated pyrolysis products formed from protein samples were separated by using a high resolution fused silica capillary column and selectively detected by flame photometric detector (FPD). In order to improve the reproducibility, an internal standard substance, benzothiophene, was pyrolyzed at 600 °C together with the protein samples. Thus the observed pyrograms were interpreted in terms of the compositional analysis. On the basis of the relative peak intensities of CH₃SH and H₂S, the simultaneous determinations of Cys and Met residues in various enzyme proteins were successfully carried out with 10–12% and 5–6% of relative standard deviations, respectively.

---

Bestimmung von schwefelhaltigen Aminosäureresten in Proteinen durch Pyrolyse-GC mit flammenphotometrischer Detektion

     

Distinct molecular surfaces and hydrophobicity of amino acid residues in proteins

Hydrophobicity is a useful concept to rationalize the role played by amino acid residues in terms of buried or exposed conformation with regard to the aqueous environment in proteins. The relationship of this concept with distinct approaches to represent the molecular surface is analyzed by computing reliable surface areas for three definitions namely the van der Waals, solvent-accessible, and solvent-excluded molecular surfaces. The surface areas are obtained for all of the naturally occurring amino acids by first setting a proper reference standard state and then calculating their values for a database of proteins containing a total of 4297 residues. Despite the great differences in these molecular surfaces, proper indexes are here defined for handling the information of interest to study the hydrophobic behavior of amino acids provided by such surfaces.     

Amino acid end-group in commercial heparin. III. Determination of the number of amino groups of amino acid and hexosamine residues per heparin molecule

The reactions of heparin with 2,4,6-trinitrobenzenesulfonic acid (TNBS) were studied spectrometrically. Seven different commercial heparins were used in this study. The amino groups react with TNBS to form equimolar amounts of trinitrophenylated (TNP) amino groups and bisulfite ions. The TNP-amino groups further react with bisulfite ions to form the monosubstituted anionic sigma complex. The absorption spectrum with two maxima at approximately 350 nm and approximately 420 nm, characteristic of either the TNP-amino groups or the complex, was analyzed for the reaction of TNBS with heparin. It was shown that the reactivities of TNBS with amino groups from α-amino acid and hexosamine residues are greatly different. By combining the results of the reaction kinetics and the reaction of heparin with Sanger's reagent, the number of the α-amino groups and the free amino groups in hexosamine residues were determined. These data have been performed with a range of heparins from different commercial sources, of different activities and physical characteristics. No correlation was found between the free amino contents of these heparins and biological potency. © 1993 John Wiley & Sons, Inc.     

Determination of the cystine and cysteine contents of proteins with the aid of an amino acid analyzer

A method is proposed which permits the determination of the amounts of cystine an cysteine in the form pf systeic acid in various proteins of animal and plant origin — even in those in which, on the analysis of standard hydrolysates, the peaks of cysteine are not detected because of their low concentration.Institute of Chemistry, Academy of Sciences of the Tadzhik SSR, Dushanbe. Translated from Khimiya Prirodnykh Soedinenii, No. 4, pp. 551–554, July–August, 1985.     

Determination of the cystine and cysteine contents of proteins with the aid of an amino acid analyzer

A method is proposed which permits the determination of the amounts of cystine an cysteine in the form pf systeic acid in various proteins of animal and plant origin — even in those in which, on the analysis of standard hydrolysates, the peaks of cysteine are not detected because of their low concentration.     

Efficient copper-catalyzed synthesis of poly-N-heterocycles containing amino acid residues

An efficient copper-catalyzed method has been developed for the synthesis of poly-N-heterocycles containing amino acid residues. The protocol uses readily available 2-halobenzamides containing amino acids and their methyl esters, substituted phenylacetonitriles, and malononitrile as the starting materials and the reactions were performed well under mild conditions. The method should provide a novel and useful strategy for synthesis of N-heterocyclic compounds.     

Effect of isomerization of amino acid residues on the structure of aquaporin

The effect of isomerization of amino acid residues on the structure and water permeability of aquaporin has been investigated. It was established that the equilibrium configuration of the model D isomer is energetically less favorable than that of its natural L isomer. It is shown that the model D isomer of aquaporin is waterproof.     

A compilation of amino acid analyses of proteins

The amino acid analyses of 183 proteins, as residues per 1000 residues, are given. In addition the carbohydrate content and the content of any noncommon amino acids are also given. The sources of all proteins are presented.     

A compilation of amino acid analyses of proteins

The amino acid analyses of 213 proteins, as residues per 1000 residues, are given. In addition, the carbohydrate content, the content of any noncommon amino acids, the sources of all proteins, and the necessary literature citations are given.     

A compilation of amino acid analyses of proteins

The amino acid analyses of 186 proteins are given as residues per 1000 residues. Additional information as carbohydrate composition, content of uncomon amino acids, and sources of all proteins are also presented.     

Development of a derivatisation method for the analysis of aldehyde modified amino acid residues in proteins by Fourier transform mass spectrometry

A method was developed for the analysis of amino acids within bovine serum albumin (BSA) which had been modified by reaction with different enals. BSA was reacted with the aldehydes and the reaction products were stabilised by reaction with NaBH₄. The protein was then hydrolysed with 6N HCl and the hydrolysis products were analysed by liquid chromatography-mass spectrometry (LC-MS). The modified amino acids were derivatised with propylchloroformate. High resolution mass spectrometry carried out using an LTQ-Orbitrap instrument which was able to characterise a wide range of adducts. In addition double adducts were observed to be formed with 4-hydroxynonenal (HNE) and lysine or lysine + histidine. Qualitatively it was possible to consistently observe a pyridinium adduct formed between lysine and pentenal in human plasma from normal subjects.     

Fractional and amino acid compositions of micromycete proteins

A comparative study has been made of the fractional and amino acid compositions of the proteins of the biomasses ofTrichoderma harzianum, Fusarium moniliforme, and the hybrid culture FT-2. It has been established that the micromycete strains investigated are high-protein cultures containing from 36.0to 49.7% of protein. A study of the amino acid compositions of the micromycetes showed that the hybrid culture FT-2 possessed the largest amount of amino acids among the water-soluble proteins of the biomass (61.3 g/100g of biomass protein).Institute of Microbiology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, fax (3712) 41 71 29. Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 428–431, May–June, 1997.     

Calix[4]resorcinols functionalized with amino acid residues

By the Mannich reaction in ternary systems calix[4]resorcinol-amino acid (amino acid ester, amino acid ester hydrochloride)-formaldehyde calix[4]resorcinols were obtained functionalized on the upper molecule rim by amino acid residues.     

Prediction of solvent accessibility of amino acid residues: critical aspects

For predicting solvent accessibility from the sequence of amino acids in proteins, we use a logistic function trained on a non-redundant protein database. Using a principal component analysis, we find that the prediction can be considered, in a good approximation, as a monofactorial problem: a crossed effect of the burial propensity of amino acids and of their locations at positions flanking the amino acid of interest. Complementary effects depend on the presence of certain amino acids (mostly P, G and C) at given positions. We have refined the predictive model (1) by adding supplementary input data, (2) by using a strategy of prediction correction and (3) by adapting the decision rules according to the amino acid type. We obtain a best score of 77.6% correct prediction for a relative accessibility of 9%. However, compared to trivial strategy only based upon the frequencies of buried or exposed residues, the gain is less than 4%. Received: 4 June 1998 / Accepted: 17 September 1998 / Published online: 10 December 1998     

Synthesis and specific biodegradation of novel polyesteramides containing amino acid residues

Novel polyesteramides were synthesized from p‐nitrophenyl esters of sebacic or adipic acids and diamines containing α‐amino acid ester groups. The optimal polymerization condition was 60 °C in N,N‐dimethylformamide. The structures of these polymers were confirmed by IR and NMR. The number‐average molecular weights of these polyesteramides ranged from 2280 to 23,600 (except for the polymers containing glycine residues), depending on the nature of the amino acid used. The biodegradability of the polyesteramides was investigated by in vitro hydrolysis with proteases and a lipase as catalysts in borate buffer solutions. The results indicated that the polymers containing L ‐phenylalanine were hydrolyzed most effectively by α‐chymotrypsin, subtilisin Carlsberg, and subtilisin BPN′. The polyesteramides containing other amino acid residues also underwent hydrolysis to different extents, reflecting the substrate specificity of the proteases. Lipase had almost no effect on the hydrolytic degradation of these polyesteramides. The polymers containing glycine residues were hardly decomposed by any of the enzymes used. © 2001 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 1318–1328, 2001     

Toward amino acid typing for proteins in FFLUX

Continuing the development of the FFLUX, a multipolar polarizable force field driven by machine learning, we present a modern approach to atom‐typing and building transferable models for predicting atomic properties in proteins. Amino acid atomic charges in a peptide chain respond to the substitution of a neighboring residue and this response can be categorized in a manner similar to atom‐typing. Using a machine learning method called kriging, we are able to build predictive models for an atom that is defined, not only by its local environment, but also by its neighboring residues, for a minimal additional computational cost. We found that prediction errors were up to 11 times lower when using a model specific to the correct group of neighboring residues, with a mean prediction of ∼0.0015 au. This finding suggests that atoms in a force field should be defined by more than just their immediate atomic neighbors. When comparing an atom in a single alanine to an analogous atom in a deca‐alanine helix, the mean difference in charge is 0.026 au. Meanwhile, the same difference between a trialanine and a deca‐alanine helix is only 0.012 au. When compared to deca‐alanine models, the transferable models are up to 20 times faster to train, and require significantly less ab initio calculation, providing a practical route to modeling large biological systems. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.