scholarly journals Amino Acids Sequence Based in Silico Analysis of RuBisCO (Ribulose-1,5 Bisphosphate Carboxylase Oxygenase) Proteins in Some Carthamus L. ssp.

2017 ◽  
Vol 9 (2) ◽  
pp. 204-208 ◽  
Author(s):  
Emre SEVİNDİK
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Average Length ◽  
3D Structure ◽  
Three Dimensional ◽  
In Silico Analysis ◽  
Bisphosphate Carboxylase ◽  
Molecular Weights ◽  
Acid Ratio ◽  
Important Enzyme

RuBisCO is an important enzyme for plants to photosynthesize and balance carbon dioxide in the atmosphere. This study aimed to perform sequence, physicochemical, phylogenetic and 3D (three-dimensional) comparative analyses of RuBisCO proteins in the Carthamus ssp. using various bioinformatics tools. The sequence lengths of the RuBisCO proteins were between 166 and 477 amino acids, with an average length of 411.8 amino acids. Their molecular weights (Mw) ranged from 18711.47 to 52843.09 Da; the most acidic and basic protein sequences were detected in C. tinctorius (pI = 5.99) and in C. tenuis (pI = 6.92), respectively. The extinction coefficients of RuBisCO proteins at 280 nm ranged from 17,670 to 69,830 M-1 cm-1, the instability index (II) values for RuBisCO proteins ranged from 33.31 to 39.39, while the GRAVY values of RuBisCO proteins ranged from -0.313 to -0.250. The most abundant amino acid in the RuBisCO protein was Gly (9.7%), while the least amino acid ratio was Trp (1.6 %). The putative phosphorylation sites of RuBisCO proteins were determined by NetPhos 2.0. Phylogenetic analysis revealed that RuBisCO proteins formed two main clades. A RAMPAGE analysis revealed that 96.3%-97.6% of residues were located in the favoured region of RuBisCO proteins. To predict the three dimensional (3D) structure of the RuBisCO proteins PyMOL was used. The results of the current study provide insights into fundamental characteristic of RuBisCO proteins in Carthamus ssp.

scholarly journals Sequence and structure of mtr, an amino acid transport gene of Neurospora crassa

Genome ◽  
1991 ◽  
Vol 34 (4) ◽  
pp. 644-651 ◽  
Author(s):  
Kenneth Koo ◽  
W. Dorsey Stuart
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Neurospora Crassa ◽  
Rna Binding ◽  
Signal Sequence ◽  
Average Length ◽  
Open Reading Frame ◽  
Mrna Transcript ◽  
S1 Nuclease ◽  
Reading Frame

The gene product of the mtr locus of Neurospora crassa is required for the transport of neutral aliphatic and aromatic amino acids via the N system. We have previously cloned three cosmids containing Neurospora DNA that complement the mtr-6(r) mutant allele. The cloned DNAs were tightly linked to restriction fragment length polymorphisms that flank the mtr locus. A 2.9-kbp fragment from one cosmid was subcloned and found to complement the mtr-6(r) allele. Here we report the sequence of the fragment that hybridized to a poly(A)+ mRNA transcript of about 2300 nucleotides. We have identified an 845-bp open reading frame (ORF) having a 59-bp intron as the potential mtr ORF. S1 nuclease analysis of the transcript confirmed the transcript size and the presence of the intron. A second open reading frame was found upstream in the same reading frame as the mtr ORF and appears to be present in the mRNA transcript. The mtr ORF is predicted to encode a 261 amino acid polypeptide with a molecular mass of 28 613 Da. The proposed polypeptide exhibits six potential α-helical transmembrane domains with an average length of 23 amino acids, does not have a signal sequence, and contains amino acid sequence homologous to an RNA binding motif.Key words: sequence, membranes, ribonucleoprotein.

scholarly journals Neutralizing Epitopes and Residues Mediating the Potential Antigenic Drift of the Hemagglutinin-Esterase Protein of Influenza C Virus

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 417 ◽  
Author(s):  
Yoko Matsuzaki ◽  
Kanetsu Sugawara ◽  
Yuki Furuse ◽  
Yoshitaka Shimotai ◽  
Seiji Hongo ◽  
...  
Keyword(s):  
Amino Acid ◽  
3D Structure ◽  
Three Dimensional ◽  
Antigenic Site ◽  
Antigenic Drift ◽  
Receptor Binding Site ◽  
Ann Arbor ◽  
Influenza C Virus ◽  
Escape Mutants ◽  
Antigenic Epitopes

We mapped the hemagglutinin-esterase (HE) antigenic epitopes of the influenza C virus on the three-dimensional (3D) structure of the HE glycoprotein using 246 escape mutants that were selected by a panel of nine anti-HE monoclonal antibodies (MAbs), including seven of the C/Ann Arbor/1/50 virus and two of the C/Yamagata/15/2004 virus. The frequency of variant selection in the presence of anti-HE MAbs was very low, with frequencies ranging from 10−4.62 to 10−7.58 for the C/Ann Arbor/1/50 virus and from 10−7.11 to 10−9.25 for the C/Yamagata/15/2004 virus. Sequencing of mutant HE genes revealed 25 amino acid substitutions at 16 positions in three antigenic sites: A-1, A-2, and A-3, and a newly designated Y-1 site. In the 3D structure, the A-1 site was widely located around the receptor-binding site, the A-2 site was near the receptor-destroying enzyme site, and the Y-1 site was located in the loop on the topside of HE. The hemagglutination inhibition reactions of the MAbs with influenza C viruses, circulating between 1947 and 2016, were consistent with the antigenic-site amino acid changes. We also found some amino acid variations in the antigenic site of recently circulating strains with antigenic changes, suggesting that viruses that have the potential to alter antigenicity continue to circulate in humans.

PREDICTION OF THE THREE-DIMENSIONAL STRUCTURE OF THE ENZYMATIC PART OF T-PA

1987 ◽  
Author(s):  
A Heckel ◽  
K M Hasselbach
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Active Site ◽  
Serine Proteases ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Salt Bridges ◽  
Three Dimensional Structure ◽  
Insertions And Deletions

Up to now the three-dimensional structure of t-PA or parts of this enzyme is unknown. Using computer graphical methods the spatial structure of the enzymatic part of t-PA is predicted on the hypothesis, the three-dimensional backbone structure of t-PA being similar to that of other serine proteases. The t-PA model was built up in three steps:1) Alignment of the t-PA sequence with other serine proteases. Comparison of enzyme structures available from Brookhaven Protein Data Bank proved elastase as a basis for modeling.2) Exchange of amino acids of elastase differing from the t-PA sequence. The replacement of amino acids was performed such that backbone atoms overlapp completely and side chains superpose as far as possible.3) Modeling of insertions and deletions. To determine the spatial arrangement of insertions and deletions parts of related enzymes such as chymotrypsin or trypsin were used whenever possible. Otherwise additional amino acid sequences were folded to a B-turn at the surface of the proteine, where all insertions or deletions are located. Finally the side chain torsion angles of amino acids were optimised to prevent close contacts of neigh bouring atoms and to improve hydrogen bonds and salt bridges.The resulting model was used to explain binding of arginine 560 of plasminogen to the active site of t-PA. Arginine 560 interacts with Asp 189, Gly 19 3, Ser 19 5 and Ser 214 of t-PA (chymotrypsin numbering). Furthermore interaction of chromo-genic substrate S 2288 with the active site of t-PA was studied. The need for D-configuration of the hydrophobic amino acid at the N-terminus of this tripeptide derivative could be easily explained.

Comparison of some properties of soil humic acids and synthetic phenolic polymers incorporating amino derivaties

Soil Research ◽  
1966 ◽  
Vol 4 (1) ◽  
pp. 41 ◽  
Author(s):  
JN Ladd ◽  
JHA Butler
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Acid Hydrolysis ◽  
Humic Acids ◽  
Gel Filtration ◽  
Quinone Imine ◽  
Peptide Bonds ◽  
Molecular Weights ◽  
Soil Humic Acids ◽  
Properties Of Soil

Twenty-three model phenolic polymers, either nitrogen-free or incorporating amino acids, peptides, or proteins, have been prepared from p-benzoquinone and catechol under mild oxidative conditions. Two lines of experimentation have demonstrated properties of soil humic acids closely similar to those of polymers incorporating proteins, but different from those of polymers incorporating amino acids: (1) fractionation of humic acids and synthetic polymers by 'Sephadex' gel filtration showed that the percentage of components of molecular weights nominally greater than 100 000 ranged from 52-76 % for eight humic acids tested, 53-59 % for benzoquinone-protein polymers (excluding polymers containing protamine), but less than 20% for all other polymers; (2) acid hydrolysis with 6M HCl resulted in a partial release of polymer nitrogen. Amino acid nitrogen in the hydrolysates accounted for 32.4-51.9 % of humic acid nitrogen, 31.2-56.3 % of the nitrogen of polymers incorporating protein, but less than 10.8% of the nitrogen of polymers incorporating individual amino acids. Experiments with model monomeric N-phenylglycine derivatives and with polymers incorporating simple peptides showed that the bond between the carbon atom of an aromatic ring and the nitrogen atom of an a-amino acid is far more stable to acid hydrolysis than peptide bonds or bonds linking amino acids in humic acids. Glycine is, however, readily released from N-phenylglycine derivatives when conditions favour their oxidation to a quinone-imine intermediate. Incorporation of proteins into phenolic polymers prevented the detection of peptide bonds by the Folin reagent.

scholarly journals A new method for the extraction and purification of K99 pili from enterotoxigenic Escherichia coli and their characterization

1982 ◽  
Vol 201 (3) ◽  
pp. 505-513 ◽  
Author(s):  
K Altmann ◽  
N A Pyliotis ◽  
T K S Mukkur
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Average Length ◽  
Bacterial Species ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Enterotoxigenic Escherichia Coli ◽  
Total Amino Acid ◽  
Apparent Homogeneity

It was found that K99 pili from enterotoxigenic Escherichia coli (of bovine origin) could be extracted by treatment with 3M-KSCN solution. The K99 pili were purified by preparative isoelectric focusing to apparent homogeneity as judged by the presence of a single band on sodium dodecyl sulphate/polyacrylamide-gel electrophoresis; the molecular weight of this component was calculated to be 12 600 +/- 300. This indicated that the K99 pili were composed of a single subunit. On analytical ultracentrifugation, a single boundary with an s20,w of 12.2 S at a concentration of 0.42 mg/ml was observed. The average length of purified pili at zero concentration was approx. 160 nm and the diameter was 7.4 +/- 0.6 nm. Amino acid analysis of the purified K99 pili revealed that sulphur-containing amino acids, cysteine and methionine, were absent. Aromatic amino acids, phenylalanine and tyrosine, previously reported to be absent [Isaacson (1977) Infect. Immun. 15. 272-279], constituted 7.14% of the total amino acid residues present. On immunoelectrophoresis, purified K99 pili migrated towards the cathode and caused mannose-resistant haemagglutination of horse, but not of sheep or guinea-pig, red blood cells. Pili from enterotoxigenic E. coli of porcine and human origin and from another bacterial species, namely Fusiformis nodosus, could also be extracted by the treatment of respective micro-organisms with 3 M-KSCN.

scholarly journals Identification of Genes for Wheat Fungal Resistance Using Bioinformatics Techniques

2018 ◽  
pp. 1-10 ◽  
Author(s):  
Ahmed E. Nassar ◽  
Khaled H. Mousa ◽  
Ahmed A. Madbouly ◽  
Shafik D. Ibrahim ◽  
Alsamman M. Alsamman
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Fungal Pathogens ◽  
Gene Annotation ◽  
Average Length ◽  
Amino Acid Sequences ◽  
Protein Domain ◽  
Fungal Resistance ◽  
Domain Identification ◽  
Cereal Grain

For the majority of world populations, wheat (Triticum aestivum L.) would be the first essential and economic cereal grain crop. Pests and pathogens in both rich and developing countries are constantly threatening wheat production and sustainable development. Multiple gene pathways were recorded to share an association with fungal pathogens with wheat biological resistance. Our aim to use such tools in order to detect and classify fungal resistance genes in wheat through sequence alignment, protein domain identification and phylogenetic analysis. In addition the introduction for restriction fragment length polymorphism (RFLP) for such genes in the new primer database. Approximately 138 sequences of DNA were recovered from the wheat genome by aligning 3845 anti-fungal amino acids through tblastn tool. The NCBI blastn online tool used to detect sequences with functional genes, where 92 genes have been detected. The total number of nucleotides was 48385, where the smallest DNA sequence have 302 bp and the longest contains 977 bp with an average length of 525.9 bp per sequence. The wheat chromosomes 3D, and 4B have the highest number of sequences (9) followed by chromosomes 3B (7) and 3A(6), where wheat genomes A, B and D have 30, 35 and 27 genes, respectively. Five different amino acids motifs have been revealed among studied wheat amino acid sequences. The gene annotation tools used to infer studied amino acid gene annotation. Amino acid sequences belongs to lectin, kinase, tyrosine-protein kinase (STK), thaumatin, and cysteine-rich repeats representing 2, 9, 8, 19, 23 genes respectively, in addition to 31 hypothetical genes. The proteins chemical content have been assessed through 16 different amino acid chemical and physical characteristics.

scholarly journals Extraction and Characterization of “Batuan” [Garcinia binucao (Blco.) Choisy] Seed Protein

2014 ◽  
pp. 89-103 ◽  
Author(s):  
Elizabeth Quevedo ◽  
Marivic Lacsamana ◽  
Antonio Laurena
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Seed Protein ◽  
Seed Proteins ◽  
Essential Amino Acids ◽  
Food Supplement ◽  
Seed Meal ◽  
Molecular Weights ◽  
Hydrophobic Amino Acids ◽  
Amino Acid Score

“Batuan” [Garcinia binucao (Blco.) Choisy], an indigenous, lesser known member of the Gutifferae family with export potential is underutilized and understudied. The present study was carried out to extract and characterize the protein in “batuan” [Garcinia binucao (Blco.) Choisy] seeds for nutritional quality assessment. Protein content of “batuan” seed meal was 8.9 ± 0.59% dry basis. Solubility fractionation of “batuan” seed meal showed globulin and glutelin as the major seed proteins. SDS-PAGE resolved the globulin and glutelin into three groups of polypeptides with molecular weights of about 20 – 54 kDa. Amino acid analysis revealed that seed protein contained all the essential amino acids with leucine as the most abundant while tryptophan, the least. “Batuan” seed proteins were mostly made up of acidic and hydrophobic amino acids with glutamic acid (2.67%) as the highest. Nutritional assessments including E/T (38.4%), amino acid score (1.6%), predicted PER (3.2-3.7) and estimated BV (98.3%) suggested that the seed proteins are of good quality. Hence, “batuan” seeds has a promising potential as an important sources of valuable proteins and amino acids for use as food supplement/enhancing ingredient.

scholarly journals Free Amino Acids and the Amino Acid Ratio of Plasma in Children with Sub-Clinical Protein Deficiency

1973 ◽  
Vol 31 (2) ◽  
pp. 52-56
Author(s):  
Einosuke Tamura ◽  
Nobuo Matsuno ◽  
Masako Iwaya ◽  
Shiro Niizeki ◽  
Hiroshi Wako ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Free Amino Acids ◽  
Free Amino ◽  
Protein Deficiency ◽  
Acid Ratio

scholarly journals Composition and nutritional evaluation of amino acids in Mimai Qu rice wine

2021 ◽  
Vol 33 (2) ◽  
pp. 46-53
Author(s):  
Kaizheng Zhang ◽  
Wenchi Wu ◽  
Wei Zou ◽  
Zhenhui Kang ◽  
Qin Yan ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Nutritional Value ◽  
Principal Component ◽  
Total Amino Acid ◽  
Linear Regression Method ◽  
Rice Wine ◽  
Chinese Rice Wine ◽  
Acid Ratio ◽  
And Control

An amino acid analyzer was used to detect free amino acids (FAA) in Mimai Qu rice wines (SMW and DMW) and control wine samples (Chinese rice wine [CRW] and Japanese sake [JNS]). It was found that CRW had the highest total amino acid (TAA) content (~2814 mg/L), followed by SMW (~2509 mg/L) and DMW (~1474 mg/L), while JNS had the least (~917 mg/L). Amino acid ratio coefficient method (SRCAA), linear regression method, cluster analysis (CA) and principal component analysis (PCA) were used for evaluating the nutritional value of amino acids in wine samples, giving similar results. SMW had the highest nutritional value, followed by CRW and DMW and JNS.

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