scholarly journals LAIPT: Lysine Acetylation Site Identification with Polynomial Tree

2018 ◽  
Vol 20 (1) ◽  
pp. 113 ◽  
Author(s):  
Wenzheng Bao ◽  
Bin Yang ◽  
Zhengwei Li ◽  
Yong Zhou
Keyword(s):  
Amino Acid ◽  
Chemical Properties ◽  
Classification Model ◽  
Lysine Acetylation ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Acetylation Site ◽  
Site Identification ◽  
Physical And Chemical ◽  
Peptide Segments

Post-translational modification plays a key role in the field of biology. Experimental identification methods are time-consuming and expensive. Therefore, computational methods to deal with such issues overcome these shortcomings and limitations. In this article, we propose a lysine acetylation site identification with polynomial tree method (LAIPT), making use of the polynomial style to demonstrate amino-acid residue relationships in peptide segments. This polynomial style was enriched by the physical and chemical properties of amino-acid residues. Then, these reconstructed features were input into the employed classification model, named the flexible neural tree. Finally, some effect evaluation measurements were employed to test the model’s performance.

scholarly journals Peptide reagent design based on physical and chemical properties of amino acid residues

2007 ◽  
Vol 28 (12) ◽  
pp. 2043-2050 ◽  
Author(s):  
Qi-Shi Du ◽  
Ri-Bo Huang ◽  
Yu-Tuo Wei ◽  
Cheng-Hua Wang ◽  
Kuo-Chen Chou
Keyword(s):  
Amino Acid ◽  
Chemical Properties ◽  
Physical And Chemical Properties ◽  
Amino Acid Residues ◽  
Physical And Chemical ◽  
And Chemical Properties

Sequence Analysis of Potato α-Amylase Gene amyA2

2013 ◽  
Vol 643 ◽  
pp. 56-59 ◽  
Author(s):  
Yong Gang Wang ◽  
Jian Zhong Ma ◽  
Xue Qing Ma ◽  
Jin Ge Liu ◽  
Ming Jun Yang
Keyword(s):  
Amino Acid ◽  
Catalytic Domain ◽  
Amino Acid Level ◽  
Chemical Properties ◽  
Amino Acid Residues ◽  
Accession Number ◽  
Amylase Gene ◽  
Reading Frame ◽  
Beta Barrel ◽  
Physical And Chemical

The sequences of Potato α-Amylase Gene amyA2 was analysised by Bioinformatics, including its codon usage bias, physical and chemical properties, subcellular localization, and conserved structures. The results showed that the cDNA had a 1218 bp open reading frame and was referred to as amyA2, which encodes for an α-amylase with 405 amino acid residues (GenBank accession number: GU134783), and shared 98% identity with a published potato α-amylase (GenBank accession number: M79328.1) at the amino acid level. The amino sequences contains a catalytic domain (PF00128、SM00624) between 20 to 348 and a C-terminal beta-sheet domain between 349-407, which are similar to ones of the amylase family 13. Eight-stranded alpha/beta barrel was also found in the enzyme, which was thought as an active site of α-amylase.

Rabbit Cardiac Myosin. II. Proteolytic Fragmentation with Insolubilized Papain

1975 ◽  
Vol 53 (2) ◽  
pp. 175-188 ◽  
Author(s):  
William T. Wolodko ◽  
Cyril M. Kay
Keyword(s):  
Amino Acid ◽  
Chemical Properties ◽  
Single Type ◽  
Myosin Molecule ◽  
Cardiac Myosin ◽  
Dialdehyde Starch ◽  
Parent Molecule ◽  
Documented Information ◽  
Physical And Chemical ◽  
Helical Molecules

The substructure of the cardiac myosin molecule was examined by the limited proteolytic digestion of the parent molecule with (dialdehyde starch)-methylenedianiline–mercuripapain, S-MDA–mercuripapain, at low temperatures and neutral pH, using moderate enzyme to myosin ratios. Pertinent properties of the insoluble enzyme complex were also examined. Kinetic, ultracentrifugal, and chromatographic observations of the fragmentation process revealed that a single type of lytic reaction occurs during the early stages, predominantly releasing heavy meromyosin subfragment 1 (HMM-S1) and myosin rods. With further time of digestion, the rods are additionally cleaved yielding light meromyosin and HMM-S2, and HMM-S1 is found to be partially degraded. The major proteolytic subfragments were isolated, purified, and characterized with respect to their enzymatic, optical, amino acid, and physicochemical properties. Only HMM-S1 exhibited Ca2+-activated ATPase activity, and at a level three- to fourfold higher than that of native myosin. Moreover, its hydrodynamic properties suggest that it is globular in structure. On the other hand, light meromyosin-A (LMM-A) (which consists mainly of rods), and HMM-S2 appear to be highly asymmetric, rigid, α-helical molecules devoid of the amino acid proline. Strong similarities were evident in all aspects upon comparison of these results with documented information concerning the skeletal system. On the basis of the physical and chemical properties of the proteolytic subfragments relative to that of native myosin, it was further concluded that the cardiac myosin molecule is a double-stranded, α-helical rod ending in two subfragment 1 globules, of which only one may be enzymatically active at a time.

scholarly journals Synthesis and Evaluation of Cyclic Acetals of Serine Hydroxylamine for Amide-Forming KAHA Ligations

Synthesis ◽  
2019 ◽  
Vol 51 (05) ◽  
pp. 1273-1283 ◽  
Author(s):  
Simon Baldauf ◽  
Jeffrey Bode
Keyword(s):  
Amino Acid ◽  
Amino Acid Residue ◽  
Amino Acid Residues ◽  
High Demand ◽  
Cyclic Acetals ◽  
Ligation Product ◽  
Canonical Amino Acid ◽  
The Stability ◽  
Peptide Segments ◽  
Derivatives Of

The α-ketoacid–hydroxylamine (KAHA) ligation allows the coupling of unprotected peptide segments. The most widely used variant employs a 5-membered cyclic hydroxylamine that forms a homoserine ester as the primary ligation product. While very effective, monomers that give canonical amino acid residues are in high demand. In order to preserve the stability and reactivity of cyclic hydroxylamines, but form a canonical amino acid residue upon ligation, we sought to prepare cyclic derivatives of serine hydroxylamine. An evaluation of several cyclization strategies led to cyclobutanone ketals as the leading structures. The preparation, stability, and amide-forming ligation of these serine-derived ketals are described.

scholarly journals Evidence that glutathione S-transferases B1B1 and B2B2 are the products of separate genes and that their expression in human liver is subject to inter-individual variation. Molecular relationships between the B1 and B2 subunits and other Alpha class glutathione S-transferases

1989 ◽  
Vol 264 (2) ◽  
pp. 437-445 ◽  
Author(s):  
J D Hayes ◽  
L A Kerr ◽  
A D Cronshaw
Keyword(s):  
Amino Acid ◽  
Human Liver ◽  
Sequence Data ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Amino Acid Sequence Analysis ◽  
Cdna Sequences ◽  
Glutathione S Transferases ◽  
Molecular Relationships ◽  
The Relationship

The Alpha class glutathione S-transferases (GSTs) in human liver are composed of polypeptides of Mr 25,900. These enzymes are dimeric, and two immunochemically distinct subunits, B1 and B2, have been described that combine to form GSTs B1B1, B1B2 and B2B2 [Stockman, Beckett & Hayes (1985) Biochem. J. 227, 457-465]. Gradient affinity elution from GSH-Sepharose has been used to resolve the three Alpha class GSTs, and this method has been applied to demonstrate marked inter-individual differences in the hepatic content of GSTs B1B1, B1B2 and B2B2. The B1 and B2 subunits can be resolved by reverse-phase h.p.l.c., and their elution positions suggest that they are equivalent to the alpha chi and alpha y h.p.l.c. peaks described by Ketterer and his colleagues [Ostlund Farrants, Meyer, Coles, Southan, Aitken, Johnson & Ketterer (1987) Biochem. J. 245, 423-428]. The B1 and B2 subunits have now been cleaved with CNBr and the fragments subjected to automated amino acid sequence analysis. The sequence data show that B1 and B2 subunits do not arise from post-translational modification, as had been previously believed for the hepatic Alpha class GSTs, but are instead the products of separate genes; B1 and B2 subunits were found to contain different amino acid residues at positions 88, 110, 111, 112, 116, 124 and 127. The relationship between the B1 and B2 subunits and the cloned GTH1 and GTH2 cDNA sequences [Rhoads, Zarlengo & Tu (1987) Biochem. Biophys. Res. Commun. 145, 474-481] is discussed.

Capillary Gas Chromatographic Analysis of Amino Acids by Enantiomer Labeling

1987 ◽  
Vol 70 (2) ◽  
pp. 234-240
Author(s):  
Ernst Bayer ◽  
Hartmut Frank ◽  
Jürgen Gerhardt ◽  
Graeme Nicholson
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Sea Water ◽  
Biological Fluids ◽  
Chemical Properties ◽  
Internal Standard ◽  
Optical Isomers ◽  
Internal Standards ◽  
Sample Enrichment ◽  
Physical And Chemical

Abstract The optical isomers of amino acids can be easily separated by gas chromatography using capillary columns coated with the chiral polysiloxane peptide, Chirasil-Val. Quantitative trace amino acid analysis in complex mixtures such as biological fluids, sea water, or protein hydrolysates can be achieved by enantiomer labeling: The D-amino acid enantiomers, which do not occur naturally, are added to the sample prior to analysis as internal standards. Because the D-enantiomers show the same physical and chemical properties as the natural L-enantiomers, they are ideal standard references. In routine analysis, the derivatization is achieved with a new automated derivatization robot. The D-standard serves as overall internal standard for the whole analytical procedure from sample enrichment to derivatization, chromatography, and response of the detector.

scholarly journals Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope in Saccharomyces cerevisiae

2012 ◽  
Vol 11 (11) ◽  
pp. 1510-1522 ◽  
Author(s):  
Peter Henriksen ◽  
Sebastian A. Wagner ◽  
Brian T. Weinert ◽  
Satyan Sharma ◽  
Giedrė Bačinskaja ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Synthesis ◽  
High Resolution Mass Spectrometry ◽  
Budding Yeast ◽  
Large Fraction ◽  
Model Organism ◽  
Bioinformatic Analysis ◽  
Lysine Acetylation ◽  
Post Translational Modification ◽  
Acetylation Site

Post-translational modification of proteins by lysine acetylation plays important regulatory roles in living cells. The budding yeast Saccharomyces cerevisiae is a widely used unicellular eukaryotic model organism in biomedical research. S. cerevisiae contains several evolutionary conserved lysine acetyltransferases and deacetylases. However, only a few dozen acetylation sites in S. cerevisiae are known, presenting a major obstacle for further understanding the regulatory roles of acetylation in this organism. Here we use high resolution mass spectrometry to identify about 4000 lysine acetylation sites in S. cerevisiae. Acetylated proteins are implicated in the regulation of diverse cytoplasmic and nuclear processes including chromatin organization, mitochondrial metabolism, and protein synthesis. Bioinformatic analysis of yeast acetylation sites shows that acetylated lysines are significantly more conserved compared with nonacetylated lysines. A large fraction of the conserved acetylation sites are present on proteins involved in cellular metabolism, protein synthesis, and protein folding. Furthermore, quantification of the Rpd3-regulated acetylation sites identified several previously known, as well as new putative substrates of this deacetylase. Rpd3 deficiency increased acetylation of the SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex subunit Sgf73 on K33. This acetylation site is located within a critical regulatory domain in Sgf73 that interacts with Ubp8 and is involved in the activation of the Ubp8-containing histone H2B deubiquitylase complex. Our data provides the first global survey of acetylation in budding yeast, and suggests a wide-ranging regulatory scope of this modification. The provided dataset may serve as an important resource for the functional analysis of lysine acetylation in eukaryotes.

scholarly journals An Activated Glutamate Residue Identified in Photosystem II at the Interface between the Manganese-stabilizing Subunit and the D2 Polypeptide

2007 ◽  
Vol 282 (38) ◽  
pp. 27802-27809 ◽  
Author(s):  
Sascha Rexroth ◽  
Catherine C. L. Wong ◽  
Jessica H. Park ◽  
John R. Yates ◽  
Bridgette A. Barry
Keyword(s):  
Amino Acid ◽  
Photosystem Ii ◽  
Oxygenic Photosynthesis ◽  
Photosynthetic Oxygen Evolution ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Steady State Rate ◽  
Reactive Groups ◽  
Psii Subunits

Photosystem II (PSII) catalyzes the oxidation of water during oxygenic photosynthesis. PSII is composed both of intrinsic subunits, such as D1, D2, and CP47, and extrinsic subunits, such as the manganese-stabilizing subunit (MSP). Previous work has shown that amines covalently bind to amino acid residues in the CP47, D1, and D2 subunits of plant and cyanobacterial PSII, and that these covalent reactions are prevented by the addition of chloride in plant preparations depleted of the 18- and 24-kDa extrinsic subunits. It has been proposed that these reactive groups are carbonyl-containing, post-translationally modified amino acid side chains (Ouellette, A. J. A., Anderson, L. B., and Barry, B. A. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 2204–2209 and Anderson, L. B., Ouellette, A. J. A., and Barry, B. A. (2000) J. Biol. Chem. 275, 4920–4927). To identify the amino acid binding site in the spinach D2 subunit, we have employed a biotin-amine labeling reagent, which can be used in conjunction with avidin affinity chromatography to purify biotinylated peptides from the PSII complex. Multidimensional chromato-graphic separation and multistage mass spectrometry localizes a novel post-translational modification in the D2 subunit to glutamate 303. We propose that this glutamate is activated for amine reaction by post-translational modification. Because the modified glutamate is located at a contact site between the D2 and manganese-stabilizing subunits, we suggest that the modification is important in vivo in stabilizing the interaction between these two PSII subunits. Consistent with this conclusion, mutations at the modified glutamate alter the steady-state rate of photosynthetic oxygen evolution.

Using Small Peptide Segments of Amyloid-β and Humanin to Examine their Physical Interactions

2019 ◽  
Vol 26 (7) ◽  
pp. 502-511 ◽  
Author(s):  
Deborah L. Heyl ◽  
Brandon Iwaniec ◽  
Daniel Esckilsen ◽  
Deanna Price ◽  
Prathyusha Guttikonda ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amyloid Fibrils ◽  
Amyloid Β ◽  
Full Length ◽  
Binding Kinetics ◽  
Amino Acid Residues ◽  
Aβ Peptides ◽  
Physical Interactions ◽  
Peptide Segments ◽  
Kinetics Of

Background: Amyloid fibrils in Alzheimer’s disease are composed of amyloid-β (Aβ) peptides of variant lengths. Humanin (HN), a 24 amino acid residue neuroprotective peptide, is known to interact with the predominant Aβ isoform in the brain, Aβ (1-40). Methods: Here, we constructed smaller segments of Aβ and HN and identified residues in HN important for both HN-HN and HN-Aβ interactions. Peptides corresponding to amino acid residues 5- 15 of HN, HN (5-15), HN (5-15, L11S), where Leu11 was replaced with Ser, and residues 17-28 of Aβ, Aβ (17-28), were synthesized and tested for their ability to block formation of the complex between HN and Aβ (1-40). Results: Co-immunoprecipitation and binding kinetics showed that HN (5-15) was more efficient at blocking the complex between HN and Aβ (1-40) than either HN (5-15, L11S) or Aβ (17-28). Binding kinetics of these smaller peptides with either full-length HN or Aβ (1-40) showed that HN (5- 15) was able to bind either Aβ (1-40) or HN more efficiently than HN (5-15, L11S) or Aβ (17-28). Compared to full-length HN, however, HN (5-15) bound Aβ (1-40) with a weaker affinity suggesting that while HN (5-15) binds Aβ, other residues in the full length HN peptide are necessary for maximum interactions. Conclusion: L11 was more important for interactions with Aβ (1-40) than with HN. Aβ (17-28) was relatively ineffective at binding to either Aβ (1-40) or HN. Moreover, HN, and the smaller HN (5-15), HN (5-15 L11S), and Aβ (17-28) peptides, had different effects on regulating Aβ (1-40) aggregation kinetics.

scholarly journals Non-Protein Amino Acids: A Review of the Biosynthesis and Taxonomic Significance

2008 ◽  
Vol 3 (1) ◽  
pp. 1934578X0800300 ◽  
Author(s):  
E. Arthur Bell ◽  
Alison A. Watson ◽  
Robert J. Nash
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Biosynthetic Pathway ◽  
Amino Acid Residues ◽  
Taxonomic Significance ◽  
Post Translational Modification ◽  
Protein Amino Acid ◽  
Ancestral Form ◽  
Higher Taxa ◽  
Protein Amino Acids

The non-protein amino acids, with which we are concerned here, are not incorporated into the proteins of the organisms that synthesize them nor are their residues formed by the post-translational modification of protein amino acid residues. Non-protein amino acids are of value in the study of relationships between species and higher taxa of organisms because most of them are of restricted distribution. If a particular non-protein amino acid is only known to occur in a limited group of species which are related in other respects then it is probable that these species have all arisen from a common ancestral form in which the biosynthetic pathway to that particular non-protein amino acid already existed.

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