scholarly journals D-Amino acid residue in a defensin-like peptide from platypus venom: effect on structure and chromatographic properties

2005 ◽  
Vol 391 (2) ◽  
pp. 215-220 ◽  
Author(s):  
Allan M. Torres ◽  
Chryssanthi Tsampazi ◽  
Dominic P. Geraghty ◽  
Paramjit S. Bansal ◽  
Paul F. Alewood ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Natriuretic Peptide ◽  
Amino Acid Residue ◽  
Tertiary Structure ◽  
Solution Structures ◽  
Isomerase Activity ◽  
New Information ◽  
Structural Template ◽  
Identical Amino Acid Sequence

The recent discovery that the natriuretic peptide OvCNPb (Ornithorhynchus venom C-type natriuretic peptide B) from platypus (Ornithorynchus anatinus) venom contains a D-amino acid residue suggested that other D-amino-acid-containing peptides might be present in the venom. In the present study, we show that DLP-2 (defensin-like peptide-2), a 42-amino-acid residue polypeptide in the platypus venom, also contains a D-amino acid residue, D-methionine, at position 2, while DLP-4, which has an identical amino acid sequence, has all amino acids in the L-form. These findings were supported further by the detection of isomerase activity in the platypus gland venom extract that converts DLP-4 into DLP-2. In the light of this new information, the tertiary structure of DLP-2 was recalculated using a new structural template with D-Met2. The structure of DLP-4 was also determined in order to evaluate the effect of a D-amino acid at position 2 on the structure and possibly to explain the large retention time difference observed for the two molecules in reverse-phase HPLC. The solution structures of the DLP-2 and DLP-4 are very similar to each other and to the earlier reported structure of DLP-2, which assumed that all amino acids were in the L-form. Our results suggest that the incorporation of the D-amino acid at position 2 has minimal effect on the overall fold in solution.

Targeting histidine for developing a new generation of covalent enzyme inhibitors

2021 ◽  
Vol 17 ◽  
Author(s):  
Donald Poirier
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Drug Development ◽  
Chemical Bond ◽  
Amino Acid Residue ◽  
Enzyme Inhibitors ◽  
Irreversible Inhibitors ◽  
Covalent Inhibitors ◽  
Targeted Inhibitors ◽  
New Generation

: Despite the significant number of irreversible inhibitors developed over the years, strong prejudices remain for this type of therapeutic molecule, particularly in the area of drug development. New generations of covalent targeted inhibitors are, however, in development, and interest is increasingly growing. In fact, the new generation of covalent inhibitors has a weakly reactive species (warhead) that is able, in a particular context, to selectively form a chemical bond with a given amino acid residue, which can be irreversible or reversible. In addition to new selective warheads, new amino acids are also targeted. In the following text, we will focus on covalent targeted inhibitors that selectively alkylate histidine.

scholarly journals BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

2019 ◽  
Vol 20 (23) ◽  
pp. 5978 ◽  
Author(s):  
Minkiewicz ◽  
Iwaniak ◽  
Darewicz
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Chronic Diseases ◽  
Bioactive Peptides ◽  
Protein Sequences ◽  
Batch Processing ◽  
Amino Acid Sequences ◽  
Quantitative Parameters ◽  
New Information

The BIOPEP-UWM™ database of bioactive peptides (formerly BIOPEP) has recently become a popular tool in the research on bioactive peptides, especially on these derived from foods and being constituents of diets that prevent development of chronic diseases. The database is continuously updated and modified. The addition of new peptides and the introduction of new information about the existing ones (e.g., chemical codes and references to other databases) is in progress. New opportunities include the possibility of annotating peptides containing D-enantiomers of amino acids, batch processing option, converting amino acid sequences into SMILES code, new quantitative parameters characterizing the presence of bioactive fragments in protein sequences, and finding proteinases that release particular peptides.

scholarly journals α-Amino acid-derived 2-phenylimidazoles with potential antimycobacterial activity

2012 ◽  
Vol 10 (5) ◽  
pp. 1681-1687 ◽  
Author(s):  
Daniel Cvejn ◽  
Věra Klimešová ◽  
Filip Bureš
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Residue ◽  
Phenyl Ring ◽  
Antimycobacterial Activity ◽  
Basic Structure ◽  
Subsequent Treatment ◽  
Imidazole Derivatives ◽  
Structure Activity ◽  
Antimycobacterial Agents

Abstractα-Amino acid-derived 2-phenylimidazole derivatives were designed, synthesized, and further investigated as potential antimycobacterial agents. The synthesis of target imidazole derivatives involved the transformation of Cbz-protected α-amino acids (Ala, Val, Phe, Leu, iLe, and Pro) into α-diazoketones and α-bromoketones, respectively. Subsequent treatment of α-bromoketones with (4-nitro)benzamidine afforded imidazole derivatives bearing α-amino acid residue appended to the imidazole C4 and (4-nitro)phenyl ring in the position C2. Antimycobacterial activities of both series of compounds against M. tuberculosis, M. avium, and M. kansasii were screened and basic structure-activity relationships were further evaluated.

Zur Strahleninaktivierung von Ribonuclease

1968 ◽  
Vol 23 (7) ◽  
pp. 934-943 ◽  
Author(s):  
Horst Jung ◽  
Helga Schüssler
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Low Temperature ◽  
Gamma Radiation ◽  
Enzymatic Activity ◽  
Amino Acid Residue ◽  
Atomic Hydrogen ◽  
Active Components ◽  
Experimental Conditions ◽  
Elution Pattern

Dry ribonuclease was irradiated with 60Co gamma radiation in vacuo, under oxygen atmosphere, and at 77 °K. By chromatography on Sephadex G-50 active ribonuclease was separated from inactive radiation products. From the elution pattern and by ultracentrifugation it was shown that mainly unfolded dimers are formed by gamma irradiation of dry ribonuclease. Amino acid analysis of these various products shows that in all components cystine, methionine, tyrosine, phenylalanine, lysine, and histidine are destroyed with increasing dose whereas glycine shows a small increase. Thus, in ribonuclease irradiated in the dry state the same amino acids are changed as was found after irradiation in aqueous solutions. The radiosensitivity of dry ribonuclease shows an increase by the presence of oxygen of about 2 and a decrease at low temperature in vacuo of about 5. The same factors were also found for the alteration of amino acids, which means that under various experimental conditions amino acid destruction is proportional to loss of enzymatic activity of ribonuclease. The observed selectivity of amino acid destruction may be explained by energy migration or by the attack of atomic hydrogen liberated at random from the molecule. The total number of amino acids destroyed per ribonuclease molecule increases with dose. In enzymatically inactive products this value is always higher by one amino acid residue than in the active components. From this result and from the increase with dose it is concluded that after destruction of one amino acid residue the ribonuclease molecule has a probability (not depending on dose of irradiation) of 0.45 to become inactivated whereas in 55 per cent of all cases the molecule maintains its enzymatic activity.

scholarly journals D-Amino acid residue in the C-type natriuretic peptide from the venom of the mammal,Ornithorhynchus anatinus, the Australian platypus

FEBS Letters ◽  
2002 ◽  
Vol 524 (1-3) ◽  
pp. 172-176 ◽  
Author(s):  
Allan M Torres ◽  
Ian Menz ◽  
Paul F Alewood ◽  
Paramjit Bansal ◽  
Jelle Lahnstein ◽  
...  
Keyword(s):  
Amino Acid ◽  
Natriuretic Peptide ◽  
Amino Acid Residue ◽  
Ornithorhynchus Anatinus

scholarly journals Identification of functional regions on the tail of Acanthamoeba myosin-II using recombinant fusion proteins. II. Assembly properties of tails with NH2- and COOH-terminal deletions.

1990 ◽  
Vol 111 (6) ◽  
pp. 2417-2426 ◽  
Author(s):  
J H Sinard ◽  
D L Rimm ◽  
T D Pollard
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Residue ◽  
Fusion Proteins ◽  
Divalent Cations ◽  
Myosin Ii ◽  
Coiled Coil ◽  
Second Step ◽  
Recombinant Fusion Proteins ◽  
Functional Regions

We used purified fusion proteins containing parts of the Acanthamoeba myosin-II tail to localize those regions of the tail responsible for each of the three steps in the successive dimerization mechanism (Sinard, J. H., W. F. Stafford, and T. D. Pollard. 1989. J. Cell Biol. 107:1537-1547) for Acanthamoeba myosin-II minifiliment assembly. Fusion proteins containing the terminal approximately 90% of the myosin-II tail assemble normally, but deletions within the last 100 amino acids of the tail sequence alter or prevent assembly. The first step in minifilament assembly, formation of antiparallel dimers, requires the COOH-terminal approximately 30 amino acids that are thought to form a nonhelical domain at the end of the coiled-coil. The second step, formation of antiparallel tetramers, requires the last approximately 40 residues in the coiled-coil. The final step, the association of two antiparallel tetramers to form the completed octameric minifilament, requires residues approximately 40-70 from the end of the coiled-coil. A region of the tail near the junction with the heads is important for tight packing of the tails in the minifilaments. Divalent cations induce the lateral aggregation of minifilaments formed from native myosin-II or fusion proteins containing a nonmyosin "head," but under the same conditions fusion proteins composed essentially only of myosin tail sequences with very little nonmyosin sequences form paracrystals. The region of the tail necessary for this paracrystal formation lies NH2-terminal to amino acid residue 1,468 in the native myosin-II sequence.

scholarly journals Predicting protein distance maps according to physicochemical properties

2011 ◽  
Vol 8 (3) ◽  
pp. 158-175
Author(s):  
Gualberto Asencio Cortés ◽  
Jesús A. Aguilar-Ruiz
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Physicochemical Properties ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Protein Structures ◽  
Contact Map ◽  
Acid Properties ◽  
Amino Acid Properties ◽  
3D Surfaces

SummaryThe prediction of protein structures is a current issue of great significance in structural bioinformatics. More specifically, the prediction of the tertiary structure of a protein con- sists in determining its three-dimensional conformation based solely on its amino acid sequence. This study proposes a method in which protein fragments are assembled according to their physicochemical similarities, using information extracted from known protein structures. Many approaches cited in the literature use the physicochemical properties of amino acids, generally hydrophobicity, polarity and charge, to predict structure. In our method, implemented with parallel multithreading, we used a set of 30 physicochemical amino acid properties selected from the AAindex database. Several protein tertiary structure prediction methods produce a contact map. Our proposed method produces a distance map, which provides more information about the structure of a protein than a contact map. We performed several preliminary analysis of the protein physicochemical data distributions using 3D surfaces. Three main pattern types were found in 3D surfaces, thus it is possible to extract rules in order to predict distances between amino acids according to their physicochemical properties. We performed an experimental validation of our method using five non-homologous protein sets and we showed the generality of this method and its prediction quality using the amino acid properties considered. Finally, we included a study of the algorithm efficiency according to the number of most similar fragments considered and we notably improved the precision with the studied proteins sets.

scholarly journals A convenient synthesis of new NSAID esters containing amino acid, urea and amide moieties

2013 ◽  
Vol 63 (3) ◽  
pp. 409-418 ◽  
Author(s):  
Ivana Perković ◽  
Zrinka Rajić Džolić ◽  
Branka Zorc
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Residue ◽  
Acid Chloride ◽  
Amino Acid Derivatives ◽  
Hydroxyl Groups ◽  
Synthetic Method ◽  
Convenient Synthesis ◽  
Preparation Step ◽  
Solvent Free Reaction

Abstract A convenient synthetic method for the preparation of novel NSAID twin esters 6a-i containing amino acid residue, urea and amide moieties has been developed. The synthetic pathway applied for the preparation of target compounds and key intermediates 1-benzotriazolecarboxylic acid chloride (1), NSAID benzotriazolides 2a-c and N-(1-benzotriazolecarbonyl)-amino acids 3a-d involved benzotriazole as a synthetic auxiliary. The final preparation step of esters 6a-i included the solvent-free reaction of compounds 2a-c with amino acid derivatives 5a-g, bearing two hydroxyl groups, one at each terminal, beside urea and amide functionalities.

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