New Antibiotic Uperin Peptides From the Dorsal Glands of the Australian Toadlet Uperoleia mjobergii

1996 ◽  
Vol 49 (12) ◽  
pp. 1325 ◽  
Author(s):  
AM Bradford ◽  
JH Bowie ◽  
MJ Tyler ◽  
JC Wallace
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Related Species ◽  
Antibiotic Activity ◽  
Amino Acid Sequences ◽  
The Other ◽  
Cationic Peptides ◽  
Amino Acid Residues ◽  
Skin Glands ◽  
Edman Sequencing

The dorsal glandular extract of the toadlet Uperoleia mjobergii contains more than 20 peptides. We report the amino acid sequences of the seven major peptides: these were determined by a combination of mass spectrometry and automated Edman sequencing. Three of these peptides have 19 amino acid residues and belong to the uperin 2 group of peptides [e.g. uperin 2.6, Gly Ile Leu Asp Ile Ala Lys Lys Leu Val Gly Gly Ile Arg Asn Val Leu Gly Ile (OH)], while the other four have 17 residues and are classified as uperins 3 [e.g. Uperin 3.4, Gly Val Gly Asp Leu Ile Arg Lys Ala Val Ala Ala Ile Lys Asn Ile Val (NH2)]. Several of these cationic peptides have been synthesized in order for bioassays to be carried out: they show significant antibiotic activity against a range of Gram-positive microorganisms. A major skin peptide from the related species Uperoleia inundata is a powerful neuropeptide named uperin 1.1 ([Ala2] uperolein ): no corresponding neuropeptide is detected in the skin glands of Uperoleia mjobergii.

Isolation of Two Bovine Amelogenin Peptides and Their Amino Acid Sequences

1987 ◽  
Vol 1 (2) ◽  
pp. 276-281 ◽  
Author(s):  
J.-H. Yeh ◽  
T. Takagi ◽  
S. Sasaki
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Gel Electrophoresis ◽  
Polyacrylamide Gel Electrophoresis ◽  
Amino Acid Sequences ◽  
Polyacrylamide Gel ◽  
The Other ◽  
Edman Degradation ◽  
Amino Acid Residues ◽  
Peptide Fractions

Two peptide fractions of bovine amelogenin having a highly aggregative property to form polymers were purified by chromatography, SDS-polyacrylamide gel electrophoresis, and HPLC. Amino acid sequences of purified peptides were determined by automated Edman degradation. One peptide was found to be composed of 63 amino acid residues having a molecular weight of 7105, and the other of 86 residues having that of 9683. The sequence of the smaller peptide was identical to the C-terminal 63 residues of the amelogenin molecule of 170 residues previously reported, but the larger contained eight residues which are absent in the amelogenin sequence. There is a possibility that the latter peptide might be synthesized independently from mRNA spliced at different positions.

Novel Uperin Peptides From the Dorsal Glands of the Australian Floodplain Toadlet Uperoleia inundata

1996 ◽  
Vol 49 (4) ◽  
pp. 475 ◽  
Author(s):  
AM Bradford ◽  
MJ Raftery ◽  
JH Bowie ◽  
MJ Tyler ◽  
JC Wallace ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Amino Acid Sequences ◽  
Host Defence ◽  
Edman Sequencing ◽  
Antibiotic Peptides

The dorsal glandular extract of the floodplain toadlet Uperoleia inundata contains more than 50 peptides: we report the amino acid sequences and bioactivity data of 13 of these. The peptides have been sequenced by using a combination of mass spectrometry and automated Edman sequencing. Ten of the peptides have been synthesized in order to confirm their structures, and to enable bioassays to be carried out. Ten peptides are host- defence agents, including ( i ) a powerful new neuropeptide of the tachykinin family which we name uperin 1.1 [ pGlu Ala Asp Pro Asn Ala Phe Tyr Gly Leu Met (NH2)], and (ii) nine antibiotic peptides including five uperins 2 [e.g. uperin 2.1, Gly Ile Val Asp Phe Ala Lys Lys Val Val Gly Gly Ile Arg Asn Ala Leu Gly Ile (OH)], three uperins 3 [e.g. uperin 3.1, Gly Val Leu Asp Ala Phe Arg Lys Ile Ala Thr Val Val Lys Asn Val Val (NH2)] and uperin 4.1 [ Gly Val Gly Ser Phe Ile His Lys Val Val Ser Ala Ile Lys Asn Val Ala (NH2)]. The function of the three other characterized peptides in the amphibian integument is not known, viz. ( i ) uperin 5.1 [ Phe Gln Phe Val Asn Pro Ser Asp Ile Val Phe Gly Ser (OH)] and (ii) the two uperins 6 [e.g. uperin 6.1, Gly Leu Ala Gly Ala Ile Ser Ser Ala Leu Asp Lys Leu Lys Gln Ser Gln Leu Ile Lys Asn Tyr Ala Lys Lys Leu Gly Tyr Pro Arg (OH)].

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

Computational Analysis of Therapeutic Enzyme Uricase from Different Source Organisms

2020 ◽  
Vol 17 (1) ◽  
pp. 59-77
Author(s):  
Anand Kumar Nelapati ◽  
JagadeeshBabu PonnanEttiyappan
Keyword(s):  
Uric Acid ◽  
Amino Acid ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Protein Sequences ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Multiple Sequence ◽  
Physiochemical Properties ◽  
Pharmaceutical Industries

Background:Hyperuricemia and gout are the conditions, which is a response of accumulation of uric acid in the blood and urine. Uric acid is the product of purine metabolic pathway in humans. Uricase is a therapeutic enzyme that can enzymatically reduces the concentration of uric acid in serum and urine into more a soluble allantoin. Uricases are widely available in several sources like bacteria, fungi, yeast, plants and animals.Objective:The present study is aimed at elucidating the structure and physiochemical properties of uricase by insilico analysis.Methods:A total number of sixty amino acid sequences of uricase belongs to different sources were obtained from NCBI and different analysis like Multiple Sequence Alignment (MSA), homology search, phylogenetic relation, motif search, domain architecture and physiochemical properties including pI, EC, Ai, Ii, and were performed.Results:Multiple sequence alignment of all the selected protein sequences has exhibited distinct difference between bacterial, fungal, plant and animal sources based on the position-specific existence of conserved amino acid residues. The maximum homology of all the selected protein sequences is between 51-388. In singular category, homology is between 16-337 for bacterial uricase, 14-339 for fungal uricase, 12-317 for plants uricase, and 37-361 for animals uricase. The phylogenetic tree constructed based on the amino acid sequences disclosed clusters indicating that uricase is from different source. The physiochemical features revealed that the uricase amino acid residues are in between 300- 338 with a molecular weight as 33-39kDa and theoretical pI ranging from 4.95-8.88. The amino acid composition results showed that valine amino acid has a high average frequency of 8.79 percentage compared to different amino acids in all analyzed species.Conclusion:In the area of bioinformatics field, this work might be informative and a stepping-stone to other researchers to get an idea about the physicochemical features, evolutionary history and structural motifs of uricase that can be widely used in biotechnological and pharmaceutical industries. Therefore, the proposed in silico analysis can be considered for protein engineering work, as well as for gout therapy.

Oxytocin analogues with non-coded amino acid residues in position 8: [8-Neopentylglycine]oxytocin and [8-cycloleucine]oxytocin

1987 ◽  
Vol 52 (9) ◽  
pp. 2317-2325 ◽  
Author(s):  
Jan Hlaváček ◽  
Jan Pospíšek ◽  
Jiřina Slaninová ◽  
Walter Y. Chan ◽  
Victor J. Hruby
Keyword(s):  
Amino Acid ◽  
Solid Phase Synthesis ◽  
Solid Phase ◽  
The Other ◽  
Amino Acid Residues ◽  
Phase Synthesis ◽  
Other Hand ◽  
Fragment Condensation

[8-Neopentylglycine]oxytocin (II) and [8-cycloleucine]oxytocin (III) were prepared by a combination of solid-phase synthesis and fragment condensation. Both analogues exhibited decreased uterotonic potency in vitro, each being about 15-30% that of oxytocin. Analogue II also displayed similarly decreased uterotonic potency in vivo and galactogogic potency. On the other hand, analogue III exhibited almost the same potency as oxytocin in the uterotonic assay in vivo and in the galactogogic assay.

Resolution of a protein sequence ambiguity by X-ray crystallographic and mass spectrometric methods

1992 ◽  
Vol 25 (2) ◽  
pp. 205-210 ◽  
Author(s):  
L. J. Keefe ◽  
E. E. Lattman ◽  
C. Wolkow ◽  
A. Woods ◽  
M. Chevrier ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Electron Density ◽  
Mass Spectrometric ◽  
Amino Acid Sequences ◽  
Data Matrix ◽  
Protein Crystal ◽  
Insertion Mutant ◽  
Laser Desorption Mass Spectrometry ◽  
X Ray

Ambiguities in amino acid sequences are a potential problem in X-ray crystallographic studies of proteins. Amino acid side chains often cannot be reliably identified from the electron density. Many protein crystal structures that are now being solved are simple variants of a known wild-type structure. Thus, cloning artifacts or other untoward events can readily lead to cases in which the proposed sequence is not correct. An example is presented showing that mass spectrometry provides an excellent tool for analyzing suspected errors. The X-ray crystal structure of an insertion mutant of Staphylococcal nuclease has been solved to 1.67 Å resolution and refined to a crystallographic R value of 0.170 [Keefe & Lattman (1992). In preparation]. A single residue has been inserted in the C-terminal α helix. The inserted amino acid was believed to be an alanine residue, but the final electron density maps strongly indicated that a glycine had been inserted instead. To confirm the observations from the X-ray data, matrix-assisted laser desorption mass spectrometry was employed to verify the glycine insertion. This mass spectrometric technique has sufficient mass accuracy to detect the methyl group that distinguishes glycine from alanine and can be extended to the more common situation in which crystallographic measurements suggest a problem with the sequence, but cannot pinpoint its location or nature.

Development of a derivatisation method for the analysis of aldehyde modified amino acid residues in proteins by Fourier transform mass spectrometry

2009 ◽  
Vol 633 (2) ◽  
pp. 216-222 ◽  
Author(s):  
Mostafa Pournamdari ◽  
Ahmed Saadi ◽  
Elizabeth Ellis ◽  
Ruth Andrew ◽  
Brian Walker ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Fourier Transform ◽  
Amino Acid ◽  
Fourier Transform Mass Spectrometry ◽  
Amino Acid Residues

scholarly journals A novel giant secretion polypeptide in Chironomus salivary glands: implications for another Balbiani ring gene.

1985 ◽  
Vol 101 (3) ◽  
pp. 1044-1051 ◽  
Author(s):  
W Y Kao ◽  
S T Case
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Salivary Glands ◽  
Cyanogen Bromide ◽  
Tryptic Peptide ◽  
Amino Acid Sequences ◽  
The Other ◽  
Balbiani Ring ◽  
Sequence Organization ◽  
Peptide Maps

Chironomus salivary glands contain a family of high Mr (approximately 1,000 X 10(3)) secretion polypeptides thought to consist of three components: sp-Ia, sp-Ib, and sp-Ic. The use of a new extraction protocol revealed a novel high Mr component, sp-Id. Results of a survey of individual salivary glands indicated that sp-Id was widespread in more than a dozen strains of C. tentans and C. pallidivittatus. Sp-Id was phosphorylated at Ser residues, and a comparison of cyanogen bromide and tryptic peptide maps of 32P-labeled polypeptides suggested that sp-Ia, sp-Ib, and sp-Id are comprised of similar but nonidentical tandemly repeated amino acid sequences. We concluded that sp-Id is encoded by an mRNA whose size and nucleotide sequence organization are similar to Balbiani ring (BR) mRNAs that code for the other sp-I components. Furthermore, parallel repression of sp-Ib and sp-Id synthesis by galactose led us to hypothesize that both of their genes exist within Balbiani ring 2.

scholarly journals Bile-pigment formation from different leghaemoglobins. Methine-bridge specificity of coupled oxidation

1978 ◽  
Vol 176 (2) ◽  
pp. 359-364 ◽  
Author(s):  
Päivi Lehtovaara ◽  
Ulla Perttilä
Keyword(s):  
Amino Acid ◽  
Polypeptide Chain ◽  
Broad Bean ◽  
Amino Acid Sequences ◽  
Second Step ◽  
Bile Pigment ◽  
Site Specificity ◽  
Amino Acid Residues ◽  
Reaction Step ◽  
Pigment Formation

The coupled oxidation of leghaemoglobins with O2 and ascorbate yielded oxyleghaemoglobin in the first reaction step, and the second step was the degradation of haem characterized by an A675 increase. Leghaemoglobins were degraded to biliverdin isomers specifically, depending on the structure of the protein. The main leghaemoglobin components of Glycine (soya bean) and Phaseolus (kidney bean) were degraded to biliverdin mixtures containing about 50% of the β-form, about 30% of the α-form and about 20% of the δ-isomer, whereas the leghaemoglobin I components of Vicia (broad bean) and Pisum (pea) were degraded almost exclusively to the β-isomer, with traces of the α-isomer. The amino acid sequences of Glycine and Phaseolus leghaemoglobins resemble each other, as do those of Vicia and Pisum. The site specificity of bile-pigment formation from leghaemoglobins can be tentatively explained by specific differences in the amino acid sequences at those regions of the polypeptide chain that are in the vicinity of the appropriate methine bridges. The ligand-binding site in different leghaemoglobins may be outlined on the basis of the present results, supposing that the haem is degraded when a reduction product of haem-bound O2 reacts with a methine bridge of the haem, and that the bridge specificity is regulated by hindering amino acid residues that determine the location of the bound O2. The residue phenylalanine-CD1 appears to be further away from the haem plane or in a markedly more flexible position in leghaemoglobins than in mammalian globins. The haem-bound oxygen atom B, in Fe–O(A)–O(B), seems to be free to rotate in all directions except that of the γ-bridge in Glycine and Phaseolus leghaemoglobins, but its position in Vicia and Pisum leghaemoglobin I might be restricted to the direction of the β-methine bridge.

scholarly journals Molecular cloning of two human liver 3 α-hydroxysteroid/dihydrodiol dehydrogenase isoenzymes that are identical with chlordecone reductase and bile-acid binder

1994 ◽  
Vol 299 (2) ◽  
pp. 545-552 ◽  
Author(s):  
Y Deyashiki ◽  
A Ogasawara ◽  
T Nakayama ◽  
M Nakanishi ◽  
Y Miyabe ◽  
...  
Keyword(s):  
Bile Acid ◽  
Amino Acid ◽  
Human Liver ◽  
Polyclonal Antibodies ◽  
Amino Acid Sequences ◽  
Cdna Clones ◽  
Amino Acid Residues ◽  
Human Bile ◽  
Coding Regions ◽  
Computer Based

Human liver contains two dihydrodiol dehydrogenases, DD2 and DD4, associated with 3 alpha-hydroxysteroid dehydrogenase activity. We have raised polyclonal antibodies that cross-reacted with the two enzymes and isolated two 1.2 kb cDNA clones (C9 and C11) for the two enzymes from a human liver cDNA library using the antibodies. The clones of C9 and C11 contained coding sequences corresponding to 306 and 321 amino acid residues respectively, but lacked 5′-coding regions around the initiation codon. Sequence analyses of several peptides obtained by enzymic and chemical cleavages of the two purified enzymes verified that the C9 and C11 clones encoded DD2 and DD4 respectively, and further indicated that the sequence of DD2 had at least additional 16 residues upward from the N-terminal sequence deduced from the cDNA. There was 82% amino acid sequence identity between the two enzymes, indicating that the enzymes are genetic isoenzymes. A computer-based comparison of the cDNAs of the isoenzymes with the DNA sequence database revealed that the nucleotide and amino acid sequences of DD2 and DD4 are virtually identical with those of human bile-acid binder and human chlordecone reductase cDNAs respectively.

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