PSSP: Protein splice site prediction algorithm using Bayesian approach

This study aimed to introduce an algorithm and identify intein motif and blocks involved in protein splicing, and explore the underlying methods in the development of detection of protein motifs. Inteins are mobile protein splicing elements capable of self-splicing post-translationally. They exist in viruses and bacteriophage, notwithstanding this broad phylogenetic distribution, all inteins apportion common structural features. A method was developed to predict intein in a raw sequence, using a ranking and scoring scheme based on amino acid [Formula: see text] value tables. This method aided in the identification and assessment of patterns characterizing the intein sequences. New intein conserved properties are revealed and the known ones are described and localized. We have computed the [Formula: see text] value of each amino acid at block A positions [Formula: see text] to [Formula: see text], block B positions [Formula: see text] to [Formula: see text] and block G positions [Formula: see text]7 to [Formula: see text] for the three categories. The consensus amino acids thus found are listed at the end of each row. We gave statistics for the distance between the blocks, block A to B, block B to F, and block F to G with the average being 66.1, 294, and 10.2 amino acids, respectively. The actual blocks A, B, and G of the one intein found in vacuolar membrane ATPase subunit, a precursor protein, are ranked 1. The results indicate all of the block sequences that are found in nine proteins are ranked at top of the list. The intein sequence is used to search the databases for intein-like proteins. Understanding the functional, structural, and dynamical aspects of inteins is important for intein engineering and the betterment of intein database.

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MATHEMATICAL MODELS FOR THE SYNTHESIS OF PLANT-BASED COMPOSITIONS WITH IMPROVED AMINO ACID COMPOSITION

10.32008/geolinks2021/b1/v3/12 ◽

2021 ◽

Author(s):

Irina Gaivoronskaya ◽

Valenitna Kolpakova

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Mathematical Models ◽

Functional Properties ◽

Amino Nitrogen ◽

Essential Amino Acids ◽

Major Allergen ◽

Structural Features ◽

Covalent Bonds ◽

Pea Protein

The aim of the work was to optimize the process of obtaining multicomponent protein compositions with high biological value and higher functional properties than the original vegetable protein products. Was realized studies to obtain biocomposites on the base of pea protein-oat protein and pea protein-rice protein. Developed composites were enriched with all limited amino acids. For each of the essential amino acids, the amino acid score was 100% and higher. Protein products used in these compositions are not in major allergen list, which allows to use these compositions in allergen-free products and specialized nutrition. To determine biosynthesis parameters for compositions from pea protein and various protein concentrates with the use of transglutaminase enzyme, was studied effect of concentration and exposition time on the amount of amino nitrogen released during the reaction. Decreasing of amino nitrogen in the medium indicated the occurrence of a protein synthesis reaction with the formation of new covalent bonds. Were determined optimal parameters of reaction: the hydromodule, the exposure time, the concentration of EP of the preparation, were obtained mathematical models. Studies on the functional properties of composites, the physicochemical properties of the proteins that make up their composition, and structural features will make it possible to determine the uses in the manufacture of food products based on their ability to bind fat, water, form foam, gels, and etc.

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Isolation and characterization of some novel genes of the apolipoprotein A-I family in Japanese eel, Anguilla japonica

Open Life Sciences ◽

10.2478/s11535-011-0042-8 ◽

2011 ◽

Vol 6 (4) ◽

pp. 545-557 ◽

Cited By ~ 2

Author(s):

Malay Choudhury ◽

Takahiro Oku ◽

Shoji Yamada ◽

Masaharu Komatsu ◽

Keita Kudoh ◽

...

Keyword(s):

Amino Acids ◽

Molecular Weight ◽

Amino Acid ◽

Consensus Sequence ◽

Structural Features ◽

Lipid Binding ◽

Japanese Eel ◽

Amino Acid Sequences ◽

Novel Genes ◽

Isolation And Characterization

AbstractApolipoproteins such as apolipoprotein (apo) A-I, apoA-IV, and apoE are lipid binding proteins synthesized mainly in the liver and the intestine and play an important role in the transfer of exogenous or endogenous lipids through the circulatory system. To investigate the mechanism of lipid transport in fish, we have isolated some novel genes of the apoA-I family, apoIA-I (apoA-I isoform) 1–11, from Japanese eel by PCR amplification. Some of the isolated genes of apoIA-I corresponded to 28kDa-1 cDNAs which had already been deposited into the database and encoded an apolipoprotein with molecular weight of 28 kDa in the LDL, whereas others seemed to be novel genes. The structural organization of all apoIA-Is consisted of four exons separated by three introns. ApoIA-I10 had a total length of 3232 bp, whereas other genes except for apoIA-I9 ranged from 1280 to 1441 bp. The sequences of apoIA-Is at the exon-intron junctions were mostly consistent with the consensus sequence (GT/AG) at exon-intron boundaries, whereas the sequences of 3′ splice acceptor in intron 1 of apoIA-I1-7 were (AC) but not (AG). The deduced amino acid sequences of all apoIA-Is contained a putative signal peptide and a propeptide of 17 and 5 amino acid residues, respectively. The mature proteins of apoIA-I1-3, 7, and 8 consisted of 237 amino acids, whereas those of apoIA-I4-6 consisted of 239 amino acids. The mature apoIA-I10 sequence showed 65% identity to amino acid sequence of apoIA-I11 which was associated with an apolipoprotein with molecular weight of 23 kDa in the VLDL. All these mature apoIA-I sequences satisfied the common structural features depicted for the exchangeable apolipoproteins such as apoA-I, apoA-IV, and apoE but apoIA-I11 lacked internal repeats 7, 8, and 9 when compared with other members of apoA-I family. Phylogenetic analysis showed that these novel apoIA-Is isolated from Japanese eel were much closer to apoA-I than apoA-IV and apoE, suggesting new members of the apoA-I family.

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Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1920097117 ◽

2020 ◽

Vol 117 (20) ◽

pp. 10806-10817 ◽

Cited By ~ 6

Author(s):

Michael P. Torrens-Spence ◽

Ying-Chih Chiang ◽

Tyler Smith ◽

Maria A. Vicent ◽

Yi Wang ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Convergent Evolution ◽

Structural Features ◽

Divergent Evolution ◽

Structural Basis ◽

Acid Decarboxylase ◽

Substrate Selectivity ◽

Amino Acid Decarboxylase ◽

Catalytic Mechanisms

Radiation of the plant pyridoxal 5′-phosphate (PLP)-dependent aromatic l-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic l-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.

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Creation of a Broad-Range and Highly Stereoselectived-Amino Acid Dehydrogenase for the One-Step Synthesis ofd-Amino Acids

Journal of the American Chemical Society ◽

10.1021/ja0603960 ◽

2006 ◽

Vol 128 (33) ◽

pp. 10923-10929 ◽

Cited By ~ 84

Author(s):

Kavitha Vedha-Peters ◽

Manjula Gunawardana ◽

J. David Rozzell ◽

Scott J. Novick

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Acid Dehydrogenase ◽

Amino Acid Dehydrogenase ◽

One Step ◽

The One

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Separation of two forms of rabbit metallothionein by isoelectric focusing

Biochemical Journal ◽

10.1042/bj1260491 ◽

1972 ◽

Vol 126 (3) ◽

pp. 491-498 ◽

Cited By ~ 186

Author(s):

G F Nordberg ◽

M. Nordberg ◽

M. Piscator ◽

O. Vesterberg

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Isoelectric Focusing ◽

Amino Acid Analysis ◽

Cadmium Chloride ◽

Small Difference ◽

Isoelectric Points ◽

Main Protein ◽

Structural Changes in Prothrombin during Activation: A Theory

Thrombosis and Haemostasis ◽

10.1055/s-0038-1654116 ◽

1970 ◽

Vol 23 (01) ◽

pp. 026-036 ◽

Cited By ~ 5

Author(s):

Walter H. Seegers ◽

Genesio Murano ◽

Lowell McCoy

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Structural Changes ◽

Polypeptide Chain ◽

Disulfide Bridge ◽

Single Chain ◽

Analytical Reagents ◽

Terminal Amino ◽

The One ◽

Autoprothrombin C

SummaryProperties of the thrombin zymogen are quite different when in the form of prothrombin complex, DEAE-prothrombin (prothrombin) or prethrombin. When removed from the prothrombin complex, prothrombin spontaneously became refractory to the two-stage analytical reagents. No new N-terminal amino acids formed in association with this activation. A first step in prothrombin activation might be related to conformation. Repeatedly one mole of alanine was found as N-terminal amino acid for prothrombin and it is thus a single chain protein. Prethrombin did not have this alanine, but lysine and threonine, were found. Prethrombin, like thrombin, thus had two chains. After the conversion of prethrombin to thrombin with purified autoprothrombin C, a new N-terminal alanine amino acid was found attached to a peptide. Additionally peptides with N-terminal serine, lysine, and glycine were found. Threonine and isoleucine were again found as the N-terminal amino acids for 3.7 S thrombin and 3.2 S thrombin. As a working hypothesis, a perspective on the possible structure of prothrombin is outlined on the basis that it contains two moles of thrombin. Prethrombin probably forms when Ala1-peptide splits from a polypeptide chain which forms a loop held together by a disulfide bridge. Proteolysis probably also occurs in this loop. The postulated disulfide bridge would be the one which holds the A and B chains of thrombin together. In the conversion of prethrombin to thrombin, the first mole of thrombin would be set free. Then the Ala2-peptide released might correspond to the Ala1-peptide removed when prethrombin originally formed. Ala2-peptide thus would be related to the second mole of thrombin which could arise by further proteolysis including a split in the loop held together by a disulfide bridge. It is postulated that acidic peptides are attached to the main prothrombin polypeptide chain, to prethrombin, and to 3.7 S thrombin as satellite material.

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The Uniqueness of Tryptophan in Biology: Properties, Metabolism, Interactions and Localization in Proteins

International Journal of Molecular Sciences ◽

10.3390/ijms21228776 ◽

2020 ◽

Vol 21 (22) ◽

pp. 8776 ◽

Cited By ~ 1

Author(s):

Sailen Barik

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Structural Features ◽

Ring Structure ◽

Side Chain ◽

Aromatic Side Chain ◽

Single Ring ◽

Energy Consuming ◽

Animal Diet ◽

Abundant Amino Acid

Tryptophan (Trp) holds a unique place in biology for a multitude of reasons. It is the largest of all twenty amino acids in the translational toolbox. Its side chain is indole, which is aromatic with a binuclear ring structure, whereas those of Phe, Tyr, and His are single-ring aromatics. In part due to these elaborate structural features, the biosynthetic pathway of Trp is the most complex and the most energy-consuming among all amino acids. Essential in the animal diet, Trp is also the least abundant amino acid in the cell, and one of the rarest in the proteome. In most eukaryotes, Trp is the only amino acid besides Met, which is coded for by a single codon, namely UGG. Due to the large and hydrophobic π-electron surface area, its aromatic side chain interacts with multiple other side chains in the protein, befitting its strategic locations in the protein structure. Finally, several Trp derivatives, namely tryptophylquinone, oxitriptan, serotonin, melatonin, and tryptophol, have specialized functions. Overall, Trp is a scarce and precious amino acid in the cell, such that nature uses it parsimoniously, for multiple but selective functions. Here, the various aspects of the uniqueness of Trp are presented in molecular terms.

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Yeast Proteins Originated from the Production of Brazilian Bioethanol Quantification and Content

International Journal of Food Engineering ◽

10.1515/ijfe-2012-0179 ◽

2013 ◽

Vol 9 (1) ◽

pp. 141-146 ◽

Cited By ~ 1

Author(s):

Claudia Steckelberg ◽

Maria da GraÇa Stupiello Andrietta ◽

Silvio Roberto Andrietta ◽

Erika Nogueira Andrade Stupielloé

Keyword(s):

Amino Acids ◽

Amino Acid ◽

High Performance ◽

Cell Mass ◽

Amino Acid Profile ◽

Dry Mass ◽

Sensu Stricto ◽

Process Conditions ◽

Yeast Strains ◽

The One

AbstractThe purpose of this work was to determine the levels of protein and the amino acid distribution in the cell mass of yeast strains (Saccharomyces sensu stricto) originated from Brazilian bioethanol industries. The protein was analyzed with the Kjeldahl method and the amino acids, by using high-performance liquid chromatography (HPLC). The percentages of the protein found ranged from 39 to 49%. The results show that in spite of some variation in numbers between the different yeast strains, all of them presented an amino acid profile similar to the one in the literature for S. cerevisae. The amino acids that have occurred in the largest amounts were: aspartic, glutamic acids and lysine, and those in the lowest amounts were: cysteine and methionine. Although the characteristics of the feedstock used and the process conditions are determinant of the protein values obtained in dry mass, this work elucidates that the intrinsic properties of the yeast strain influence these values.

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Ribosome-binding protein p34 is a member of the leucine-rich-repeat-protein superfamily

Biochemical Journal ◽

10.1042/bj2940465 ◽

1993 ◽

Vol 294 (2) ◽

pp. 465-472 ◽

Cited By ~ 19

Author(s):

T Ohsumi ◽

T Ichimura ◽

H Sugano ◽

S Omata ◽

T Isobe ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Protein Interactions ◽

Tandem Repeats ◽

Structural Similarity ◽

Cytoplasmic Domain ◽

Structural Features ◽

Binding Activity ◽

Leucine Rich Repeat ◽

Ribosome Binding

Protein p34 is a non-glycosylated membrane protein characteristic of rough microsomes and is believed to play a role in the ribosome-membrane association. In the present study we isolated cDNA encoding p34 from a rat liver cDNA library and determined its complete amino acid sequence. p34 mRNA is 3.2 kb long and encodes a polypeptide of 307 amino acids with a molecular mass of about 34.9 kDa. Primary sequence analysis, coupled with biochemical studies on the topology, suggested that p34 is a type II signal-anchor protein; it is composed of a large cytoplasmic domain, a membrane-spanning segment and a 38-amino-acid-long luminally disposed C-terminus. The cytoplasmic domain of p34 has several noteworthy structural features, including a region of 4.5 tandem repeats of 23-24 amino acids. The repeated motif shows structural similarity to the leucine-rich repeat which is found in a variety of proteins widely distributed among eukaryotic cells and which potentially functions in mediating protein-protein interactions. The cytoplasmic domain also contains a characteristic hydrophilic region with abundant charged amino acids. These structural regions may be important for the observed ribosome-binding activity of the p34 protein.

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EFFECT OF AMINO ACID CONCENTRATION ON DIET UPTAKE AND PERFORMANCE BY THE PEA APHID, ACYRTHOSIPHON PISUM (HOMOPTERA: APHIDIDAE)

The Canadian Entomologist ◽

10.4039/ent106149-2 ◽

1974 ◽

Vol 106 (2) ◽

pp. 149-156 ◽

Cited By ~ 38

Author(s):

P. N. Srivastava ◽

J. L. Auclair

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Acyrthosiphon Pisum ◽

Sucrose Solution ◽

Average Rate ◽

Pea Aphid ◽

Acid Diet ◽

And Performance ◽

Rate Of Evaporation ◽

The One

AbstractThe average rate of diet uptake by the 1st–3rd instar nymphs of the pea aphid, Acyrthosiphon pisum (Harris), on chemically defined diets containing 0.0–5.0% amino acids varied from 0.08 to 0.23 μl/aphid/24 h and that by 4th instar nymphs to adults varied from 0.15 to 0.74 μl/aphid/24 h. The presence of amino acids increased the acceptability of diets to a great extent, as uptake on such diets was 2–5 times more than that on amino acid free diets. Uptake was lowest on diets lacking amino acids, and highest on those containing 3.5 and 2.5% amino acids by 1st–3rd instar nymphs and 4th instar nymphs to adults respectively. It is suggested that certain amino acids, either alone or in combination, act synergistically with sucrose as phagostimulants. Methionine was slightly phagostimulatory to the pea aphid and enhanced the acceptability of a free amino acid diet and of a sucrose solution.As expected the rate of feeding increased as the aphids grew. Nymphs reached the adult stage, and reproduced on each diet, except on the one lacking amino acids. The longevity on different diets varied from 7 to 37 days. A concentration of 2–4% amino acids, with an optimum at 3.5%, appears to be essential for the growth, survival, and larviposition of the pea aphid.Due to the punctures made in the stretched parafilm by aphids during feeding the rate of evaporation from fed sachets was significantly higher than that from unfed sachets. It is therefore suggested that in experiments where rates of feeding are measured by differential weighings of the sachets, these be renewed at 24-h intervals.

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