scholarly journals Inhibitory Effect of an Acidic Peptide on the Activity of an Antimicrobial Peptide from the Scorpion Mesobuthus martensii Karsch

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3314 ◽  
Author(s):  
Wanxia Shi ◽  
Pengchen He ◽  
Xian-Chun Zeng ◽  
Weiwei Wu ◽  
Xiaoming Chen
Keyword(s):  
Staphylococcus Aureus ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Coiled Coil ◽  
Inhibitory Effect ◽  
Scorpion Venom ◽  
Amino Acid Residues ◽  
Acidic Peptide ◽  
Venom Glands ◽  
Acidic Peptides

Highly acidic peptides with no disulfide bridges are widely present in the scorpion venoms; however, none of them has been functionally characterized so far. Here, we cloned the full-length cDNA of a short-chain highly acidic peptide (referred to as HAP-1) from a cDNA library made from the venom glands of the Chinese scorpion Mesobuthus martensii Karsch. HAP-1 contains 19 amino acid residues with a predicted IP value of 4.25. Acidic amino residues account for 33.3% of the total residues in the molecule of HAP-1. HAP-1 shows 76–98% identities to some scorpion venom peptides that have not yet been functionally characterized. Secondary structure prediction showed that HAP-1 contains a beta-sheet region (residues 9–17), and two coiled coil regions (residues 1–8 and 18–19) located at the N-terminal and C-terminal regions of the peptide, respectively. Antimicrobial assay showed that HAP-1 does not have any effect on the growth of the bacterium Staphylococcus aureus AB94004. However, it potently inhibits the antimicrobial activity of a 13-mer peptide from M. martensii Karsch against Staphylococcus aureus AB94004. This finding is the first characterization of the function of such highly acidic peptides from scorpions.

HATODAS II – heavy-atom database system with potentiality scoring

2009 ◽  
Vol 42 (3) ◽  
pp. 540-544 ◽  
Author(s):  
Michihiro Sugahara ◽  
Yukuhiko Asada ◽  
Hiroki Shimada ◽  
Hideyuki Taka ◽  
Naoki Kunishima
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Solvent Accessibility ◽  
Heavy Atom ◽  
Database System ◽  
Protein Crystals ◽  
Amino Acid Residues ◽  
Sequence Alignments ◽  
Homologous Proteins

HATODAS II is the second version of HATODAS (the Heavy-Atom Database System), which suggests potential heavy-atom reagents for the derivatization of protein crystals. The present expanded database contains 3103 heavy-atom binding sites, which is four times more than the previous version. HATODAS II has three new criteria to evaluate the feasibility of the search results: (1) potentiality scoring for the predicted heavy-atom reagents, (2) exclusion of the disordered amino acid residues based on the secondary structure prediction and (3) consideration of the solvent accessibility of amino acid residues from a homology model. In the point mutation option, HATODAS II suggests possible mutation sites into reactive amino acid residues such as Met, Cys and His, on the basis of multiple sequence alignments of homologous proteins. These new features allow the user to make a well informed decision as to the possible heavy-atom derivatization experiments of protein crystals.

scholarly journals Cloning and molecular characterization of two novel LMW-m type glutenin genes from Triticum spelta L.

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 141-155
Author(s):  
Ruomei Wang ◽  
Junwei Zhang ◽  
Fei Luo ◽  
Nannan Liu ◽  
Slaven Prodanovic ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Structural Features ◽  
Open Reading Frames ◽  
Wheat Quality ◽  
Amino Acid Residues ◽  
Triticum Spelta ◽  
Spelt Wheat ◽  
A Genome ◽  
Food And Feed

Spelt wheat (Triticum spelta L., 2n=6x=42, AABBDD), as a hexaploid wheat species, is important sources of food and feed in Europe. It also serves as an important genetic resource for improvement of wheat quality and resistance. In this study, two novel m-type low molecularglutenin subunit (LMW-GS) genes, named as TsLMW-m1 and TsLMW-m2 were cloned by allelic specific polymerase chain reaction (AS-PCR)from German spelt wheat cultivars Rochbergers fruher Dinke and Schwabenkorn, respectively. The complete open reading frames (ORFs) of both genes contained 873 bp encoding 290 amino acid residues, and had typical LMW-GS structural features. Two same deletions with 24 bp at the position of 707-730 bp were present in both genes, while TsLMW-m1 had two nonsynonymous single-nucleotide polymorphism (SNP) variations at the positions of 434 bp (C-A transversion) and 857 bp (G-A transition). Phylogenic analysis revealed that both LMW-m genes were closely related to those from wheat A genome, suggesting that both subunits are encoded by the Glu-A3 locus. Secondary structure prediction showed that TsLMW-m1 and TsLMW-m2 subunits had more ?-helices than other wheat LMW-GS including superior quality subunit EU369717, which would benefit to form superior gluten structures and dough properties. The authenticity and expression activity of TsLMW-m1 and TsLMW-m2 genes were verified by prokaryotic expression in E. coli. Our results indicated that two newly cloned TsLMW-m genes could have potential values for wheat quality improvement.

Cloning and Characterization of Three Genes Encoding LMW-GSs from Triticum aestivum, Cultival Cheyenne

2012 ◽  
Vol 554-556 ◽  
pp. 1116-1120 ◽  
Author(s):  
Mei Rong Chen ◽  
Xing Shen ◽  
Lin Li ◽  
Song Qing Hu
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Amino Acid Residues ◽  
Repetitive Domain ◽  
Genebank Accession ◽  
Genes Encoding ◽  
Α Helix ◽  
Β Sheet

Three low molecular weight subunit genes, named LMW-CND1 (GeneBank accession JQ780048), LMW-CND2 (GeneBank accession JQ779840), LMW-CND3 (GeneBank accession JQ779841), with a ORF of 1053 bp, 903 bp, 969 bp, respectively, were isolated from cv. Cheyenne and characterized detailed in molecular level. The proteins encoded by the genes, with 350, 300, 322 amino acid residues respectively, differ only in repetitive domain of sequences due to insertion or deletion of repeats in this domain. Highly similarity in amino-acid sequence between these three subunits and other published LMW-GSs was also observed, showing that all three genes published here are typical LMW-GS genes and closely related to the genes on chromosome 1D. Besides, secondary structure prediction of proteins indicated that, in the three LMW-GSs, random loop accounts for no less than 70 %, α-helix amounts to 26 %, average, and only 1.4 %~1.7 % is β-sheet.

scholarly journals Primary sequence and domain structure of chicken vinculin

1989 ◽  
Vol 259 (2) ◽  
pp. 453-461 ◽  
Author(s):  
G J Price ◽  
P Jones ◽  
M D Davison ◽  
B Patel ◽  
R Bendori ◽  
...  
Keyword(s):  
Amino Acid ◽  
Molecular Mass ◽  
Domain Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Phosphorylation Site ◽  
Cdna Clones ◽  
Amino Acid Residues ◽  
Untranslated Sequence ◽  
Globular Head

We have determined the complete sequence of chick vinculin from two overlapping cDNA clones. The vinculin mRNA consists of 262 bp of 5' untranslated sequence, an open reading frame of 3195 bp (excluding the initiation codon) and a long 3' untranslated sequence (greater than 2 kb). Chick vinculin contains 1066 amino acid residues, and has a deduced molecular mass of 116,933 Da. Analysis of the domain structure of vinculin shows that the molecule can be cleaved by V8 proteinase into a 90 kDa globular head and a 32 kDa tail region, the latter of which could further be cleaved into a 27 kDa polypeptide. The 90 kDa globular head contains the N-terminus of vinculin, three 112-residue repeats (residues 259-589), and extends to approximately residue 850. Gel overlay experiments show that it also contains a binding site for the cytoskeletal protein talin. The talin-binding domain was further localized to the N-terminal 398 amino acid residues of the protein by expression in vitro of this region from a vinculin cDNA cloned into the Bluescript SK+ vector. The head and tail domains are apparently separated by a proline-rich region that contains V8-proteinase-cleavage sites and a candidate tyrosine (822)-phosphorylation site. Secondary-structure prediction suggests that the head and tail domains contain alpha-helical regions separated by short stretches of turn/coil. Comparison of the chick with a partial human sequence reveals that vinculin is a highly conserved protein. In chickens Southern-blot analysis is consistent with a single vinculin gene, and it is therefore likely that vinculin, and its higher-molecular-mass isoform termed metavinculin, arise through alternative splicing.

scholarly journals The Dual α-Amidation System in Scorpion Venom Glands

Toxins ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 425 ◽  
Author(s):  
Gustavo Delgado-Prudencio ◽  
Lourival D. Possani ◽  
Baltazar Becerril ◽  
Ernesto Ortiz
Keyword(s):  
Amino Acid ◽  
Enzymatic Activity ◽  
Biological Function ◽  
Scorpion Venom ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Proprotein Convertases ◽  
Functional Potential ◽  
Recognition Sites ◽  
Venom Glands

Many peptides in scorpion venoms are amidated at their C-termini. This post-translational modification is paramount for the correct biological function of ion channel toxins and antimicrobial peptides, among others. The discovery of canonical amidation sequences in transcriptome-derived scorpion proproteins suggests that a conserved enzymatic α-amidation system must be responsible for this modification of scorpion peptides. A transcriptomic approach was employed to identify sequences putatively encoding enzymes of the α-amidation pathway. A dual enzymatic α-amidation system was found, consisting of the membrane-anchored, bifunctional, peptidylglycine α-amidating monooxygenase (PAM) and its paralogs, soluble monofunctional peptidylglycine α-hydroxylating monooxygenase (PHMm) and peptidyl-α-hydroxyglycine α-amidating lyase (PALm). Independent genes encode these three enzymes. Amino acid residues responsible for ion coordination and enzymatic activity are conserved in these sequences, suggesting that the enzymes are functional. Potential endoproteolytic recognition sites for proprotein convertases in the PAM sequence indicate that PAM-derived soluble isoforms may also be expressed. Sequences potentially encoding proprotein convertases (PC1 and PC2), carboxypeptidase E (CPE), and other enzymes of the α-amidation pathway, were also found, confirming the presence of this pathway in scorpions.

scholarly journals Molecular and Mechanistic Characterization of PddB, the First PLP-Independent 2,4-Diaminobutyric Acid Racemase Discovered in an Actinobacterial D-Amino Acid Homopolymer Biosynthesis

2021 ◽  
Vol 12 ◽  
Author(s):  
Kazuya Yamanaka ◽  
Ryo Ozaki ◽  
Yoshimitsu Hamano ◽  
Tadao Oikawa
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Sequence Similarity ◽  
Structural Difference ◽  
Structural Modeling ◽  
Specific Substrate ◽  
Amino Acid Residues ◽  
Diaminobutyric Acid

We recently disclosed that the biosynthesis of antiviral γ-poly-D-2,4-diaminobutyric acid (poly-D-Dab) in Streptoalloteichus hindustanus involves an unprecedented cofactor independent stereoinversion of Dab catalyzed by PddB, which shows weak homology to diaminopimelate epimerase (DapF). Enzymological properties and mechanistic details of this enzyme, however, had remained to be elucidated. Here, through a series of biochemical characterizations, structural modeling, and site-directed mutageneses, we fully illustrate the first Dab-specific PLP-independent racemase PddB and further provide an insight into its evolution. The activity of the recombinant PddB was shown to be optimal around pH 8.5, and its other fundamental properties resembled those of typical PLP-independent racemases/epimerases. The enzyme catalyzed Dab specific stereoinversion with a calculated equilibrium constant of nearly unity, demonstrating that the reaction catalyzed by PddB is indeed racemization. Its activity was inhibited upon incubation with sulfhydryl reagents, and the site-directed substitution of two putative catalytic Cys residues led to the abolishment of the activity. These observations provided critical evidence that PddB employs the thiolate-thiol pair to catalyze interconversion of Dab isomers. Despite the low levels of sequence similarity, a phylogenetic analysis of PddB indicated its particular relevance to DapF among PLP-independent racemases/epimerases. Secondary structure prediction and 3D structural modeling of PddB revealed its remarkable conformational analogy to DapF, which in turn allowed us to predict amino acid residues potentially responsible for the discrimination of structural difference between diaminopimelate and its specific substrate, Dab. Further, PddB homologs which seemed to be narrowly distributed only in actinobacterial kingdom were constantly encoded adjacent to the putative poly-D-Dab synthetase gene. These observations strongly suggested that PddB could have evolved from the primary metabolic DapF in order to organize the biosynthesis pathway for the particular secondary metabolite, poly-D-Dab. The present study is on the first molecular characterization of PLP-independent Dab racemase and provides insights that could contribute to further discovery of unprecedented PLP-independent racemases.

Effect of human galanin on the response of circulating catecholamines to hypoglycemia in man

1995 ◽  
Vol 133 (6) ◽  
pp. 723-728 ◽  
Author(s):  
Ettore C degli Uberti ◽  
Maria R Ambrosio ◽  
Marta Bondanelli ◽  
Giorgio Transforini ◽  
Alberto Valentini ◽  
...  
Keyword(s):  
Heart Rate ◽  
Healthy Subjects ◽  
Sympathetic Nerve Activity ◽  
Heart Rate Response ◽  
Statistical Significance ◽  
Inhibitory Effect ◽  
Amino Acid Residues ◽  
Nerve Activity ◽  
Receptor Stimulation

degli Uberti EC, Ambrosio MR, Bondanelli M, Trasforini G, Valentini A, Rossi R, Margutti A, Campo M. Effect of human galanin on the response of circulating catecholamines to hypoglycemia in man. Eur J Endocrinol 1995;133:723–8. ISSN 0804–4643 Human galanin (hGAL) is a neuropeptide with 30 amino acid residues that has been found in the peripheral and central nervous system, where it often co-exists with catecholamines. In order to clarify the possible role of hGAL in the regulation of sympathoadrenomedullary function, the effect of a 60 min infusion of hGAL (80 pmol·kg−1 · min−1) on plasma epinephrine and norepinephrine responses to insulin-induced hypoglycemia in nine healthy subjects was investigated. Human GAL administration significantly reduced both the release of basal norepinephrine and the response to insulin-induced hypoglycemia, whereas it attenuated the epinephrine response by 26%, with the hGAL-induced decrease in epinephrine release failing to achieve statistical significance. Human GAL significantly increased the heart rate in resting conditions and clearly exaggerated the heart rate response to insulin-induced hypoglycemia, whereas it had no effect on the blood pressure. We conclude that GAL receptor stimulation exerts an inhibitory effect on basal and insulin-induced hypoglycemia-stimulated release of norepinephrine. These findings provide further evidence that GAL may modulate sympathetic nerve activity in man but that it does not play an important role in the regulation of adrenal medullary function. Ettore C degli Uberti, Chair of Endocrinology, University of Ferrara, Via Savonarola 9, I-44100 Ferrara, Italy

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