scholarly journals Characterization of the Structural Diversity and Structure-Specific Behavior of Oxidized Phospholipids by LC-MS/MS

2021 ◽  
Vol 69 (10) ◽  
pp. 953-961
Author(s):  
Ryohei Aoyagi ◽  
Takahiro Yamamoto ◽  
Yuuki Furukawa ◽  
Makoto Arita
Keyword(s):  
Structural Diversity ◽  
Oxidized Phospholipids ◽  
Specific Behavior

scholarly journals Unravelling the Skin Secretion Peptides of the Gliding Leaf Frog, Agalychnis spurrelli (Hylidae)

Biomolecules ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 667 ◽  
Author(s):  
Carolina Proaño-Bolaños ◽  
Ailín Blasco-Zúñiga ◽  
José Rafael Almeida ◽  
Lei Wang ◽  
Miguel Angel Llumiquinga ◽  
...  
Keyword(s):  
Inhibitory Concentration ◽  
Structural Diversity ◽  
Biologically Active ◽  
Biological Characterization ◽  
Skin Secretion ◽  
Peptide Profile ◽  
Active Chemical ◽  
Molecular Masses ◽  
Skin Secretions

Frog skin secretions contain medically-valuable molecules, which are useful for the discovery of new biopharmaceuticals. The peptide profile of the skin secretion of Agalychnis spurrelli has not been investigated; therefore, the structural and biological characterization of its compounds signify an inestimable opportunity to acquire new biologically-active chemical scaffolds. In this work, skin secretion from this amphibian was analysed by molecular cloning and tandem mass spectrometry. Although the extent of this work was not exhaustive, eleven skin secretion peptides belonging to five peptide families were identified. Among these, we report the occurrence of two phyllokinins, and one medusin-SP which were previously reported in other related species. In addition, eight novel peptides were identified, including four dermaseptins, DRS-SP2 to DRS-SP5, one phylloseptin-SP1, and three orphan peptides. Phylloseptin-SP1 and dermaseptins-SP2 were identified in HPLC fractions based on their molecular masses determined by MALDI-TOF MS. Among the antimicrobial peptides, dermaseptin-SP2 was the most potent, inhibiting Escherichia coli, Staphylococcus aureus, and ORSA with a minimum inhibitory concentration (MIC) of 2.68 μM, and Candida albicans with an MIC of 10.71 μM, without haemolytic effects. The peptides described in this study represent but a superficial glance at the considerable structural diversity of bioactive peptides produced in the skin secretion of A. spurrelli.

Structural diversity of thiodiacetate compounds of group II metals: Synthesis and X-ray characterization of 2D coordination polymers of calcium and strontium

2007 ◽  
Vol 10 (10) ◽  
pp. 1125-1128 ◽  
Author(s):  
Abdessamad Grirrane ◽  
Antonio Pastor ◽  
Eleuterio Álvarez ◽  
Raquel Moyano ◽  
Agustín Galindo
Keyword(s):  
Coordination Polymers ◽  
Structural Diversity ◽  
X Ray ◽  
Group Ii

scholarly journals BIOFACQUIM: A Mexican Compound Database of Natural Products

Biomolecules ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 31 ◽  
Author(s):  
B. Pilón-Jiménez ◽  
Fernanda Saldívar-González ◽  
Bárbara Díaz-Eufracio ◽  
José Medina-Franco
Keyword(s):  
Natural Products ◽  
Drug Discovery ◽  
Physicochemical Properties ◽  
Chemical Space ◽  
Structural Diversity ◽  
Proof Of Concept ◽  
Molecular Fingerprints ◽  
The Public ◽  
Compound Database

Compound databases of natural products have a major impact on drug discovery projects and other areas of research. The number of databases in the public domain with compounds with natural origins is increasing. Several countries, Brazil, France, Panama and, recently, Vietnam, have initiatives in place to construct and maintain compound databases that are representative of their diversity. In this proof-of-concept study, we discuss the first version of BIOFACQUIM, a novel compound database with natural products isolated and characterized in Mexico. We discuss its construction, curation, and a complete chemoinformatic characterization of the content and coverage in chemical space. The profile of physicochemical properties, scaffold content, and diversity, as well as structural diversity based on molecular fingerprints is reported. BIOFACQUIM is available for free.

Crystallographic evidence for structural diversity in cationic (tripyrrinato)cobalt(II) complexes

2005 ◽  
Vol 09 (10) ◽  
pp. 683-690 ◽  
Author(s):  
Martin Bröring ◽  
Carsten D. Brandt ◽  
Silke Köhler ◽  
Maximilian Sieber
Keyword(s):  
Single Crystals ◽  
Anion Exchange ◽  
Structural Diversity ◽  
Complete Characterization ◽  
Donor Ligands ◽  
Highly Sensitive ◽  
Weakly Coordinating ◽  
Weakly Coordinating Anion ◽  
Coordinate Structures

Cobalt(II) complexes of tripyrrin ligands can be transformed into cations by anion exchange using NaBAr F , a salt of a weakly coordinating anion. The complete characterization of these highly sensitive cations (probably solvate complexes) could not be achieved, but the coordination to donor ligands like nitriles or trialkylphosphanes stabilizes the cations sufficiently for the isolation of some single crystals. As the structural analyses of these donor-stabilized cobalt(II) tripyrrins reveal, either four- or five coordinate structures are formed depending on the type and size of ligand used.

scholarly journals Evaluation of the Extent of Haptoglobin Glycosylation Using Orthogonal Intact-Mass MS Approaches

2021 ◽  
Author(s):  
Yang Yang ◽  
Jake W. Pawlowski ◽  
Ian J. Carrick ◽  
Igor Kaltashov
Keyword(s):  
Disulfide Bonds ◽  
Heterogeneous Systems ◽  
Structural Diversity ◽  
Mass Range ◽  
Protein Characterization ◽  
Charge Reduction ◽  
Average Mass ◽  
Significant Difference ◽  
Intact Mass

Intact-mass measurements are becoming an increasingly popular in mass spectrometry (MS) based protein characterization, as they allow the entire complement of proteoforms to be evaluated within a relatively short time. However, applications of this approach are currently limited to systems exhibiting relatively modest degrees of structural diversity, as the high extent of heterogeneity frequently prevents straightforward MS measurements. Incorporation of limited charge reduction into electrospray ionization (ESI) MS measurements provides an elegant way to obtain meaningful information on most heterogeneous systems, yielding not only the average mass of the protein, but also the mass range populated by various proteoforms. Application of this approach to characterization of two different phenotypes of haptoglobin (1-1 and 2-1) provides evidence of a significant difference in their extent of glycosylation, with the glycan load of phenotype 2-1 being notably lighter. More detailed characterization of their glycosylation patterns is enabled by the recently introduced crosspath reactive chromatography (XP-RC) with on-line MS detection, a technique that combines chromatographic separation with in-line reduction of disulfide bonds to generate metastable haptoglobin subunits. Application of XP-RC to both haptoglobin phenotypes confirms that no modifications are present within their light chains, and provides a wealth of information on glycosylation patterns of the heavy chains. The haptoglobin 1-1 glycans are mature fully sialylated biantennary structures that exhibit high degrees of fucosylation. In contrast, phenotype 2-1 contains a significant fraction of incomplete biantennary structures and exhibit significantly lower levels of sialylation and fucosylation. The glycosylation patterns deduced from the XP-RC/MS measurements are in agreement with the conclusions of haptoglobin analysis by limited charge reduction, suggesting that the latter can be employed in situations when a fast assessment of a protein heterogeneity is needed (e.g., comparability studies of biopharmaceutical products). <br>

scholarly journals Biochemical and Structural Characterization of Two Cif-Like Epoxide Hydrolases from Burkholderia cenocepacia

2021 ◽  
Author(s):  
Noor M. Taher ◽  
Kelli L. Hvorecny ◽  
Cassandra M. Burke ◽  
Morgan S.A. Gilman ◽  
Gary E. Heussler ◽  
...  
Keyword(s):  
Structural Characteristics ◽  
Structural Diversity ◽  
Burkholderia Cenocepacia ◽  
Epoxide Ring ◽  
The Novel ◽  
Epoxide Hydrolases ◽  
Cellular Processes ◽  
Vicinal Diols ◽  
Quaternary Structures

AbstractEpoxide hydrolases catalyze the conversion of epoxides to vicinal diols in a range of cellular processes such as signaling, detoxification, and virulence. These enzymes typically utilize a pair of tyrosine residues to orient the substrate epoxide ring in the active site and stabilize the hydrolysis intermediate. A new subclass of epoxide hydrolases that utilize a histidine in place of one of the tyrosines was established with the discovery of the CFTR Inhibitory Factor (Cif) from Pseudomonas aeruginosa. Although the presence of such Cif-like epoxide hydrolases was predicted in other opportunistic pathogens based on sequence analyses, only Cif and its homologue aCif from Acinetobacter nosocomialis have been characterized. Here we report the biochemical and structural characteristics of Cfl1 and Cfl2, two Cif-like epoxide hydrolases from Burkholderia cenocepacia. Cfl1 is able to hydrolyze xenobiotic as well as biological epoxides that might be encountered in the environment or during infection. In contrast, Cfl2 shows very low activity against a diverse set of epoxides. The crystal structures of the two proteins reveal quaternary structures that build on the well-known dimeric assembly of the α/β hydrolase domain, but broaden our understanding of the structural diversity encoded in novel oligomer interfaces. Analysis of the interfaces reveals both similarities and key differences in sequence conservation between the two assemblies, and between the canonical dimer and the novel oligomer interfaces of each assembly. Finally, we discuss the effects of these higher-order assemblies on the intra-monomer flexibility of Cfl1 and Cfl2 and their possible roles in regulating enzymatic activity.

scholarly journals Kinetic and Structural Characterization of the First B3 Metallo-β-Lactamase with an Active Site Glutamic Acid

2021 ◽  
Author(s):  
Liam A. Wilson ◽  
Esmée G. Knaven ◽  
Marc T. Morris ◽  
Marcelo Monteiro Pedroso ◽  
Christopher J. Schofield ◽  
...  
Keyword(s):  
Glutamic Acid ◽  
Structural Characterization ◽  
Active Site ◽  
Structural Diversity ◽  
Kinetic Properties ◽  
Design Studies ◽  
Degrading Bacterium ◽  
Active Site Motif ◽  
Wide Range

The structural diversity in metallo-β-lactamases (MBLs), especially in the vicinity of the active site, has been a major hurdle in the development of clinically effective inhibitors. Representatives from three variants of the B3 MBL subclass, containing either the canonical HHH/DHH active site motif (present in the majority of MBLs in this subclass) or the QHH/DHH (B3-Q) or HRH/DQK (B3-RQK) variations were reported previously. Here, we describe the structure and kinetic properties of the first example (SIE-1) of a fourth variant containing the EHH/DHH active site motif (B3-E). SIE-1 was identified in the hexachlorocyclohexane-degrading bacterium Sphingobium indicum , and kinetic analyses demonstrate that although it is active against a wide range of antibiotics its efficiency is lower than that of other B3 MBLs, but with improved efficiency towards cephalosporins relative to other β-lactam substrates. The overall fold of SIE-1 is characteristic of the MBLs; the notable variation is observed in the Zn1 site due to the replacement of the canonical His116 by a glutamate. The unusual preference of SIE-1 for cephalosporins and its occurrence in a widespread environmental organism suggests scope for increased MBL-mediated β-lactam resistance. It is thus relevant to include SIE-1 into MBL inhibitor design studies to widen the therapeutic scope of much needed anti-resistance drugs.

scholarly journals Synthesis and Characterization of Various Amino Acid Derived Thiohydantoins

Proceedings ◽  
2018 ◽  
Vol 9 (1) ◽  
pp. 37
Author(s):  
Petar Stanić ◽  
Marija Živković ◽  
Biljana Šmit
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Allyl Isothiocyanate ◽  
Structural Diversity ◽  
Biologically Active ◽  
Reaction Conditions ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sulfur Containing

Hydantoins and their sulfur containing analogues, thiohydantoins, are cyclic ureides that have attracted huge attention ever since their discovery. Most of them are biologically active compounds and several points of structural diversity have made them very synthetically attractive. Although substituents can be introduced to the hydantoin nucleus, most substituted hydantoins are synthesized from substrates already containing these groups, while forming the hydantoin nucleus. This is a common route to the synthesis of hydantoins and one of them is employed in this study. A series of 3-allyl-2-thiohydantoins is synthesized from various α-amino acids in a reaction with allyl isothiocyanate. The substitution of the acquired thiohydantoin depends on the structure of the starting α-amino acid. The residual group of the α-amino acid becomes the substituent at the C5-position, while N-monosubstituted amino acids give rise to a substituent in the N1-position. The reaction is carried out in a two-step process and the reaction conditions generally depend on the nature of the amino acid itself. All thiohydantoins are obtained in a good yield and fully characterized by NMR and IR spectroscopy, as well as X-ray crystallography.

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