scholarly journals An amino acid at position 142 in nitrilase from Rhodococcus rhodochrous ATCC 33278 determines the substrate specificity for aliphatic and aromatic nitriles

2008 ◽  
Vol 415 (3) ◽  
pp. 401-407 ◽  
Author(s):  
Soo-Jin Yeom ◽  
Hye-Jung Kim ◽  
Jung-Kul Lee ◽  
Dong-Eun Kim ◽  
Deok-Kun Oh
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Hydrophobic Interactions ◽  
Electron System ◽  
Rhodococcus Rhodochrous ◽  
Aromatic Nitriles ◽  
Charged Amino Acids ◽  
Aromatic Substrates ◽  
In The Wild ◽  
Hydrolysis Of

Nitrilase from Rhodococcus rhodochrous ATCC 33278 hydrolyses both aliphatic and aromatic nitriles. Replacing Tyr-142 in the wild-type enzyme with the aromatic amino acid phenylalanine did not alter specificity for either substrate. However, the mutants containing non-polar aliphatic amino acids (alanine, valine and leucine) at position 142 were specific only for aromatic substrates such as benzonitrile, m-tolunitrile and 2-cyanopyridine, and not for aliphatic substrates. These results suggest that the hydrolysis of substrates probably involves the conjugated π-electron system of the aromatic ring of substrate or Tyr-142 as an electron acceptor. Moreover, the mutants containing charged amino acids such as aspartate, glutamate, arginine and asparagine at position 142 displayed no activity towards any nitrile, possibly owing to the disruption of hydrophobic interactions with substrates. Thus aromaticity of substrate or amino acid at position 142 in R. rhodochrous nitrilase is required for enzyme activity.

scholarly journals Arabidopsis Heat Stress-Induced Proteins Are Enriched in Electrostatically Charged Amino Acids and Intrinsically Disordered Regions

2018 ◽  
Vol 19 (8) ◽  
pp. 2276 ◽  
Author(s):  
David Alvarez-Ponce ◽  
Mario Ruiz-González ◽  
Francisco Vera-Sirera ◽  
Felix Feyertag ◽  
Miguel Perez-Amador ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
High Temperatures ◽  
Hydrophobic Interactions ◽  
Intrinsic Disorder ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Charged Amino Acids ◽  
Induced Proteins ◽  
Disordered Regions

Comparison of the proteins of thermophilic, mesophilic, and psychrophilic prokaryotes has revealed several features characteristic to proteins adapted to high temperatures, which increase their thermostability. These characteristics include a profusion of disulfide bonds, salt bridges, hydrogen bonds, and hydrophobic interactions, and a depletion in intrinsically disordered regions. It is unclear, however, whether such differences can also be observed in eukaryotic proteins or when comparing proteins that are adapted to temperatures that are more subtly different. When an organism is exposed to high temperatures, a subset of its proteins is overexpressed (heat-induced proteins), whereas others are either repressed (heat-repressed proteins) or remain unaffected. Here, we determine the expression levels of all genes in the eukaryotic model system Arabidopsis thaliana at 22 and 37 °C, and compare both the amino acid compositions and levels of intrinsic disorder of heat-induced and heat-repressed proteins. We show that, compared to heat-repressed proteins, heat-induced proteins are enriched in electrostatically charged amino acids and depleted in polar amino acids, mirroring thermophile proteins. However, in contrast with thermophile proteins, heat-induced proteins are enriched in intrinsically disordered regions, and depleted in hydrophobic amino acids. Our results indicate that temperature adaptation at the level of amino acid composition and intrinsic disorder can be observed not only in proteins of thermophilic organisms, but also in eukaryotic heat-induced proteins; the underlying adaptation pathways, however, are similar but not the same.

scholarly journals Charged Amino Acids Conserved in the Aromatic Acid/H+ Symporter Family of Permeases Are Required for 4-Hydroxybenzoate Transport by PcaK from Pseudomonas putida

2002 ◽  
Vol 184 (5) ◽  
pp. 1444-1448 ◽  
Author(s):  
Jayna L. Ditty ◽  
Caroline S. Harwood
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Pseudomonas Putida ◽  
Essential Amino Acid ◽  
Major Facilitator Superfamily ◽  
Aromatic Acid ◽  
Transmembrane Segment ◽  
Amino Acid Motif ◽  
Charged Amino Acids ◽  
Major Facilitator

ABSTRACT Charged amino acids in the predicted transmembrane portion of PcaK, a permease from Pseudomonas putida that transports 4-hydroxybenzoate (4-HBA), were required for 4-HBA transport, and they were also required for P. putida to have a chemotactic response to 4-HBA. An essential amino acid motif (DGXD) containing aspartate residues is located in the first transmembrane segment of PcaK and is conserved in the aromatic acid/H+ symporter family of the major facilitator superfamily of transporters.

scholarly journals THE AMINO ACID COMPOSITION OF HYPERTENSIN II AND ITS BIOCHEMICAL RELATIONSHIP TO HYPERTENSIN I

1956 ◽  
Vol 104 (2) ◽  
pp. 183-191 ◽  
Author(s):  
Kenneth E. Lentz ◽  
Leonard T. Skeggs ◽  
Kenneth R. Woods ◽  
Joseph R. Kahn ◽  
Norman P. Shumway
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Ion Exchange ◽  
Amino Acid Composition ◽  
Acid Content ◽  
Amino Acid Content ◽  
Converting Enzyme ◽  
Terminal Sequence ◽  
Carboxyl Terminal ◽  
Hydrolysis Of

Preparations of hypertensin II, obtained from the treatment of hypertensin I by the action of the hypertensin converting enzyme of plasma and purified by countercurrent distribution, were quantitatively analyzed for their amino acid content. Chromatography on ion exchange columns showed the presence of equimolar amounts of aspartic acid, proline, valine, isoleucine, tyrosine, phenylalanine, histidine, and arginine. Hypertensin I was found to contain one mole of leucine and one mole of histidine in addition to the amino acids of hypertensin II. These two amino acids were isolated from the conversion products of hypertensin I and identified as the peptide histidylleucine. Carboxypeptidase digestion of hypertensin I showed the carboxyl terminal sequence of amino acids to be residue-phenylalanyl-histidylleucine. Similar studies of hypertensin II demonstrated residue-phenylalanine. It was concluded that the conversion of hypertensin I by the plasma hypertensin converting enzyme involved hydrolysis of the phenylalanyl-histidine bond to form hypertensin II and histidylleucine. The further removal by carboxypeptidase of phenylalanine from hypertensin II destroyed all of the vasoconstrictor activity.

scholarly journals iDPGK: characterization and identification of lysine phosphoglycerylation sites based on sequence-based features

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Kai-Yao Huang ◽  
Fang-Yu Hung ◽  
Hui-Ju Kao ◽  
Hui-Hsuan Lau ◽  
Shun-Long Weng
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Training Dataset ◽  
Post Translational Modification ◽  
Web Based ◽  
Charged Amino Acids ◽  
Pair Composition ◽  
Weighted Matrix ◽  
Svm Model ◽  
Effective Performance

Abstract Background Protein phosphoglycerylation, the addition of a 1,3-bisphosphoglyceric acid (1,3-BPG) to a lysine residue of a protein and thus to form a 3-phosphoglyceryl-lysine, is a reversible and non-enzymatic post-translational modification (PTM) and plays a regulatory role in glucose metabolism and glycolytic process. As the number of experimentally verified phosphoglycerylated sites has increased significantly, statistical or machine learning methods are imperative for investigating the characteristics of phosphoglycerylation sites. Currently, research into phosphoglycerylation is very limited, and only a few resources are available for the computational identification of phosphoglycerylation sites. Result We present a bioinformatics investigation of phosphoglycerylation sites based on sequence-based features. The TwoSampleLogo analysis reveals that the regions surrounding the phosphoglycerylation sites contain a high relatively of positively charged amino acids, especially in the upstream flanking region. Additionally, the non-polar and aliphatic amino acids are more abundant surrounding phosphoglycerylated lysine following the results of PTM-Logo, which may play a functional role in discriminating between phosphoglycerylation and non-phosphoglycerylation sites. Many types of features were adopted to build the prediction model on the training dataset, including amino acid composition, amino acid pair composition, positional weighted matrix and position-specific scoring matrix. Further, to improve the predictive power, numerous top features ranked by F-score were considered as the final combination for classification, and thus the predictive models were trained using DT, RF and SVM classifiers. Evaluation by five-fold cross-validation showed that the selected features was most effective in discriminating between phosphoglycerylated and non-phosphoglycerylated sites. Conclusion The SVM model trained with the selected sequence-based features performed well, with a sensitivity of 77.5%, a specificity of 73.6%, an accuracy of 74.9%, and a Matthews Correlation Coefficient value of 0.49. Furthermore, the model also consistently provides the effective performance in independent testing set, yielding sensitivity of 75.7% and specificity of 64.9%. Finally, the model has been implemented as a web-based system, namely iDPGK, which is now freely available at http://mer.hc.mmh.org.tw/iDPGK/.

scholarly journals The isolation of a product of hydrolysis of the proteins hitherto undescribed

1925 ◽  
Vol 98 (687) ◽  
pp. 58-65 ◽  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Free Amino Acid ◽  
Convenient Method ◽  
Free Amino ◽  
Barium Carbonate ◽  
Present Communication ◽  
Hydrolysis Products ◽  
Hydrolysis Of

Some time ago, two of the authors of the present communication, in seeking a method for the separation of the amino-acids from the carbohydrates, found that under certain conditions the former could be readily separated in the form of the barium salts of their carbamates, a class of compounds originally described by Siegfried. As these carbamates, on heating with water, are readily decomposed into barium carbonate and the free amino-acid, it was suggested that a convenient method might be evolved, using the formation of these compounds as a basis, for the separation of the hydrolysis products of the proteins.* This suggestion was followed up, and a method was subsequently elaborated and applied to the separation of the hydrolysis products of gelatin by one of the authors in conjunction with Miss H. L. Kingston. Since the publication of the two papers just quoted, the researches on the use of the “carbamate method,” as it may be conveniently called, have been continued, and promise results, which may ultimately lead to a satisfactory separation of most of the hydrolysis products of the proteins when only relatively small amounts of material are available for investigation. During the course of this work the base, which is the chief subject discussed in this paper, was discovered.

Substrate Preferences for Antiplasmin Cleaving Enzyme Hydrolysis of Peptides Derived from the α2-Antiplasmin Sequence.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1704-1704
Author(s):  
Kenneth W. Jackson ◽  
Victoria J. Christiansen ◽  
Kyung N. Lee ◽  
Christina F. Mason ◽  
Patrick A. McKee
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Enzyme Hydrolysis ◽  
Peptide Sequence ◽  
Peptide Hydrolysis ◽  
Cleavage Rate ◽  
Amino Terminal ◽  
Substrate Preferences ◽  
Polymorphic Position ◽  
Hydrolysis Of

Abstract Antiplasmin cleaving enzyme (APCE) is a proteinase that specifically, but slowly cleaves the Pro-Asn bond in long-form α2-antiplasmin (Met-α2AP) in human plasma. This slow cleavage produces a steady-state plasma mixture of Met-α2AP and an N-terminally shortened form of antiplasmin, Asn-α2AP. The Asn-α2AP form crosslinks to fibrin ~13-fold faster than Met-α2AP. A faster crosslink rate causes a greater number of antiplasmin molecules to become bound during fibrin formation, thereby enhancing resistance to fibrinolysis. Inhibition of plasma APCE may decrease the number of antiplasmin molecules crosslinked and result in clots that are more easily removed during fibrinolysis. Therefore, an inhibitor specific for APCE could potentially be used to regulate fibrinolysis. Human Met-α2AP exists in two polymorphic forms at position six in the mature sequence, with arginine predominant, and tryptophan accounting for a lesser percentage. We have determined the relative cleavage rates of synthetic peptides from a peptide library that span the cleavage site. The peptides contained all common amino acids except cysteine in the polymorphic position (P7 position). Arg was the optimal amino acid in this position with a relative cleavage rate ~5–10-fold faster than other amino acids except Lys, which was ~70% of the Arg rate. The P7 position Arg enhancement was also observed when Arg was in the P6 or P5 position, but no enhancement was observed when Arg was moved to positions P8, P4, P3 or P2. It was also determined that APCE is preferentially an endoproteinase rather than an aminodipeptidase, with a 10-fold greater rate of hydrolysis of the internal Pro-Asn bond in the Met-α2AP 1–17 peptide sequence MEPLGRQLTSGP-NQEQV over the Pro-Asn bond penultimate to the amino-terminal bond in the Met-α2AP 11–27 peptide sequence GP-NQEQVSPLTLLKLGN in peptide hydrolysis experiments. We conclude that APCE inhibitors designed with a positive charge placed upstream of the Pro-X scissile bond equivalent to five to seven amino acid residues may prove to be highly potent and specific. In addition, such inhibitors should also prove useful for blocking the activity of the closely related enzyme fibroblast activation protein. This work was supported by NIH grant HL072995.

Comparison on Nutrient Composition and Amino Acid and Fatty Acid Profile of Muscle in Wild and Farmed Prawn, Penaeus japonicu

2011 ◽  
Vol 140 ◽  
pp. 286-290 ◽  
Author(s):  
Xing Hong Xu ◽  
Bin Lun Yan ◽  
Jia Tao Xu
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Amino Acid ◽  
Unsaturated Fatty Acids ◽  
Essential Amino Acids ◽  
Department Of Health ◽  
Penaeus Japonicus ◽  
In The Wild ◽  
Amino Acid Score ◽  
Wild Group

Penaeus japonicus is an important marine shrimps resource in China. In order to evaluate the nutritional value, the contents of general nutritional compositions, amino acids and fatty acids in muscle were compared between wild and farmed P. japonicus. The contents of muscle moisture and crude protein, fat and ash in wild P. japonicus were 77.16%, 17.74%, 2.08% and 1.79％, and those in farmed P. japonicus were 78.02%, 17.26%, 2.04% and 1.63％, respectively. The essential amino acids (EAA) in wild and farmed P. japonicus were 23.25％ and 22.43％, respectively. The amino acid score of essential amino acids were higher than 100 except Leu and Trp, so the protein of P. japonicus has a well-balanced amino acid composition. Wild P. japonicus has more unsaturated fatty acids (64.05％) than farmed group (60.34％). Higher n-3 polyunsaturated fatty acids (PUFAs), eicosapentainoic acids (EPA, 20:5 n-3), docosahexaenoic acids (DHA, 22:6 n-3) contents and lower C16:0, C20:0, C18:1, C18:2, C18:3 levels were detected in the wild group. Values of n-6/n-3 in muscle of farmed and wild P. japonicus were 0.30 and 0.23 respectively, which were both significantly lower than the maximum value (4.0) recommended by UK Department of Health (HMSO, 1994), while Values of the PUFA/SFA ratio of two groups were 0.60 and 0.74 higher than the minimum value (0.45) recommended by HMSO. Thus the muscle of farmed and wild P. japonicus are both healthy and safe, and the the muscle of wild P. japonicus is more beneficial to human health.

scholarly journals Partial amino acid sequence and mRNA analysis of cytosolic pyridoxine-beta-d-glucoside hydrolase from porcine intestinal mucosa: proposed derivation from the lactase-phlorizin hydrolase gene

2004 ◽  
Vol 380 (1) ◽  
pp. 211-218 ◽  
Author(s):  
Chi-Wah TSEUNG ◽  
Laura G. McMAHON ◽  
Jorge VÁZQUEZ ◽  
Jan POHL ◽  
Jesse F. GREGORY
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Northern Blot ◽  
Sequence Data ◽  
Cdna Probe ◽  
Protein Mass ◽  
Sds Page ◽  
Mrna Analysis ◽  
Hydrolysis Of

We have previously identified and purified a novel β-glucosidase, designated PNGH (pyridoxine-5´-β-d-glucoside hydrolase), from the cytosolic fraction of pig intestinal mucosal. PNGH catalyses the hydrolysis of PNG (pyridoxine-5´-β-d-glucoside), a plant derivative of vitamin B6 that exhibits partial nutritional bioavailability in humans and animals. Preliminary amino acid sequence analysis indicated regions of close similarity of PNGH to the precursor form of LPH (lactase–phlorizin hydrolase), the β-glucosidase localized to the brush-border membrane. We report in the present study amino acid sequence data for PNGH and results of Northern blot analyses, upon which we propose a common genomic origin of PNGH and LPH. Internal Edman sequencing of the PNGH band isolated by SDS/PAGE yielded data for 16 peptides, averaging 10.8 amino acids in length. These peptides from PNGH (approx. 140 kDa) were highly similar to sequences existing over most of the length of the >200 kDa precursor of rabbit LPH; however, we found no PNGH sequences that corresponded to approx. 350 amino acids between positions 463 and 812 of the LPH precursor, a region encoded by exon 7 of the LPH precursor gene (amino acids 568–784), and no sequences that corresponded to regions near the N-terminus. MS analysis of tryptic peptides yielded 25 peptides, averaging 15 amino acids, with masses that matched segments of the rabbit LPH precursor. Northern blot analysis of pig and human small intestinal polyadenylated mRNA using a non-specific LPH cDNA probe showed an expected approx. 6 kb transcript of the LPH precursor, but also an approx. 4 kb transcript that was consistent with the size predicted from the PNGH protein mass. Using a probe specific to the region encoded by exon 7, hybridization occurred only with the 6 kb transcript. Based on these observations, we propose that both PNGH and LPH enzymes have the same genomic origin, but differ in transcriptional and, possibly, post-translational processing.

Evaluation of Deformation Mechanisms at Mineral-Protein Composite Interface Using Steered Molecular Dynamics Simulations

2004 ◽  
Vol 844 ◽  
Author(s):  
Dinesh R. Katti ◽  
Pijush Ghosh ◽  
Kalpana Katti
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Amino Acid ◽  
Steered Molecular Dynamics ◽  
Clay Nanocomposites ◽  
Strain Behavior ◽  
New Class ◽  
Charged Amino Acids ◽  
Tension And Compression ◽  
Dynamics Simulations

AbstractIn the area of clay-polymer nanocomposites, recently montmorillonite is extensively used because of its unique characteristics of swelling. In this work, steered molecular dynamics is used to evaluate the mechanical behavior of a new class of nanocomposites, using amino acids to intercalate clay interlayers. Two positively charged amino acids, lysine and arginine, are used here. Our simulation indicates that both the amino acids have preferred orientation inside the clay interlayer. Our simulations also indicate that the clay-amino acid interlayer is about three times stiffer under tension as compared to under compression. On the other hand, dry montmorillonite shows similar stiffness under tension and compression. The fundamental mechanism of deformation during tension and compression is intrinsically different in the amino acid-clay composite. The stress-strain behavior of this clay-amino acid interlayer is predominantly linear until a stress of 1.5 GPa. This study is a first step towards the potential use of biomacromolecules as modifiers in clay nanocomposites.

scholarly journals Hydrolysis of the Peptide Bond and Amino Acid Modification with Hydriodic Acid

1971 ◽  
Vol 24 (4) ◽  
pp. 1235 ◽  
Author(s):  
AS Inglis ◽  
PW Nicholls ◽  
CM Roxburgh
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Boiling Point ◽  
Amino Acid Analysis ◽  
Peptide Bond ◽  
Hydriodic Acid ◽  
Acid Modification ◽  
Amino Acid Modification ◽  
Hydrolysis Of

Reaction of hydriodic acid with peptides and proteins has been studied. At the boiling point, hydrolysis of the peptide bond, particularly stable bonds linking valine and isoleucine residues, is facile. Several amino acids react with constantboiling hydriodic acid but the only reactions detrimental to the amino acid analysis are the reduction of serine with concomitant formation of alanine, and the destruction of tryptophan. Gentler conditions of hydrolysis with diluted hydriodic acid are required for analysis of serine. Good results for analysis of proteins for amino acids may be obtained after a 6-hr hydrolysis period.

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