Toward Expanded Diversity of Host-Guest Interactions via Synthesis and Characterization of Cyclodextrin Derivatives

2018 ◽  
Author(s):  
Kathryn Kellett ◽  
Samuel A. Kantonen ◽  
Brendan M. Duggan ◽  
Michael K. Gilson
Keyword(s):  
Standard Free Energy ◽  
Binding Constants ◽  
Aqueous Solubility ◽  
Amic Acid ◽  
Model Systems ◽  
Side Chain ◽  
Titration Calorimetry ◽  
One Pot ◽  
Cross Correlations

Researchers developing software to predict the binding constants of small molecules for proteins have, in recent years, turned to host-guest systems as simple, computationally tractable model systems to test and improve these computational methods. However, taking full advantage of this strategy requires aqueous host-guest systems that probe a greater diversity of chemical interactions. Here, we advance the development of an experimental platform to generate such systems by building on the cyclodextrin (CD) class of hosts. The secondary face derivative mono-3-carboxypropionamido-β-cyclodextrin (CP-β-CD) was synthesized in a one-pot strategy with 87% yield, and proved to have much greater aqueous solubility than native β-CD. The complexation of anionic CP-β-CD with the cationic drug rimantadine hydrochloride was explored using one and two-dimensional nuclear magnetic resonance (NMR); NOESY analysis showed secondary face binding of the ammonium moiety of the guest, based on cross-correlations between the amic acid functionality and the side-chain of rimantadine. Isothermal titration calorimetry was furthermore used to determine the standard free energy and enthalpy for this binding reaction, and the results were compared with those of rimantadine with native β-CD.

Toward Expanded Diversity of Host-Guest Interactions via Synthesis and Characterization of Cyclodextrin Derivatives

2018 ◽  
Author(s):  
Kathryn Kellett ◽  
Samuel A. Kantonen ◽  
Brendan M. Duggan ◽  
Michael K. Gilson
Keyword(s):  
Standard Free Energy ◽  
Binding Constants ◽  
Aqueous Solubility ◽  
Amic Acid ◽  
Model Systems ◽  
Side Chain ◽  
Titration Calorimetry ◽  
One Pot ◽  
Cross Correlations

Researchers developing software to predict the binding constants of small molecules for proteins have, in recent years, turned to host-guest systems as simple, computationally tractable model systems to test and improve these computational methods. However, taking full advantage of this strategy requires aqueous host-guest systems that probe a greater diversity of chemical interactions. Here, we advance the development of an experimental platform to generate such systems by building on the cyclodextrin (CD) class of hosts. The secondary face derivative mono-3-carboxypropionamido-β-cyclodextrin (CP-β-CD) was synthesized in a one-pot strategy with 87% yield, and proved to have much greater aqueous solubility than native β-CD. The complexation of anionic CP-β-CD with the cationic drug rimantadine hydrochloride was explored using one and two-dimensional nuclear magnetic resonance (NMR); NOESY analysis showed secondary face binding of the ammonium moiety of the guest, based on cross-correlations between the amic acid functionality and the side-chain of rimantadine. Isothermal titration calorimetry was furthermore used to determine the standard free energy and enthalpy for this binding reaction, and the results were compared with those of rimantadine with native β-CD.

scholarly journals Genome-wide characterization of LTR retrotransposons in the non-model deep-sea annelid Lamellibrachia luymesi

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Oluchi Aroh ◽  
Kenneth M. Halanych
Keyword(s):  
Deep Sea ◽  
Long Terminal Repeat Retrotransposons ◽  
Marine Organisms ◽  
Model Systems ◽  
Ltr Retrotransposons ◽  
Genome Wide ◽  
Lamellibrachia Luymesi ◽  
Vestimentiferan Tubeworm ◽  
Retrotransposon Activity

Abstract Background Long Terminal Repeat retrotransposons (LTR retrotransposons) are mobile genetic elements composed of a few genes between terminal repeats and, in some cases, can comprise over half of a genome’s content. Available data on LTR retrotransposons have facilitated comparative studies and provided insight on genome evolution. However, data are biased to model systems and marine organisms, including annelids, have been underrepresented in transposable elements studies. Here, we focus on genome of Lamellibrachia luymesi, a vestimentiferan tubeworm from deep-sea hydrocarbon seeps, to gain knowledge of LTR retrotransposons in a deep-sea annelid. Results We characterized LTR retrotransposons present in the genome of L. luymesi using bioinformatic approaches and found that intact LTR retrotransposons makes up about 0.1% of L. luymesi genome. Previous characterization of the genome has shown that this tubeworm hosts several known LTR-retrotransposons. Here we describe and classify LTR retrotransposons in L. luymesi as within the Gypsy, Copia and Bel-pao superfamilies. Although, many elements fell within already recognized families (e.g., Mag, CSRN1), others formed clades distinct from previously recognized families within these superfamilies. However, approximately 19% (41) of recovered elements could not be classified. Gypsy elements were the most abundant while only 2 Copia and 2 Bel-pao elements were present. In addition, analysis of insertion times indicated that several LTR-retrotransposons were recently transposed into the genome of L. luymesi, these elements had identical LTR’s raising possibility of recent or ongoing retrotransposon activity. Conclusions Our analysis contributes to knowledge on diversity of LTR-retrotransposons in marine settings and also serves as an important step to assist our understanding of the potential role of retroelements in marine organisms. We find that many LTR retrotransposons, which have been inserted in the last few million years, are similar to those found in terrestrial model species. However, several new groups of LTR retrotransposons were discovered suggesting that the representation of LTR retrotransposons may be different in marine settings. Further study would improve understanding of the diversity of retrotransposons across animal groups and environments.

scholarly journals A Concerted Action of UBA5 C-Terminal Unstructured Regions Is Important for Transfer of Activated UFM1 to UFC1

2021 ◽  
Vol 22 (14) ◽  
pp. 7390
Author(s):  
Nicole Wesch ◽  
Frank Löhr ◽  
Natalia Rogova ◽  
Volker Dötsch ◽  
Vladimir V. Rogov
Keyword(s):  
Cellular Localization ◽  
Molecular Mechanisms ◽  
Biochemical Characterization ◽  
Effective Interaction ◽  
Regulatory Region ◽  
Titration Calorimetry ◽  
Enzymatic Reactions ◽  
Cellular Processes ◽  
Mechanism Of Interaction

Ubiquitin fold modifier 1 (UFM1) is a member of the ubiquitin-like protein family. UFM1 undergoes a cascade of enzymatic reactions including activation by UBA5 (E1), transfer to UFC1 (E2) and selective conjugation to a number of target proteins via UFL1 (E3) enzymes. Despite the importance of ufmylation in a variety of cellular processes and its role in the pathogenicity of many human diseases, the molecular mechanisms of the ufmylation cascade remains unclear. In this study we focused on the biophysical and biochemical characterization of the interaction between UBA5 and UFC1. We explored the hypothesis that the unstructured C-terminal region of UBA5 serves as a regulatory region, controlling cellular localization of the elements of the ufmylation cascade and effective interaction between them. We found that the last 20 residues in UBA5 are pivotal for binding to UFC1 and can accelerate the transfer of UFM1 to UFC1. We solved the structure of a complex of UFC1 and a peptide spanning the last 20 residues of UBA5 by NMR spectroscopy. This structure in combination with additional NMR titration and isothermal titration calorimetry experiments revealed the mechanism of interaction and confirmed the importance of the C-terminal unstructured region in UBA5 for the ufmylation cascade.

Biophysical characterization of polymyxin b interaction with LPS aggregates and membrane model systems

Biopolymers ◽  
2012 ◽  
Vol 98 (4) ◽  
pp. 338-344 ◽  
Author(s):  
Marco M. Domingues ◽  
Rita G. Inácio ◽  
José M. Raimundo ◽  
Miguel Martins ◽  
Miguel A. R. B. Castanho ◽  
...  
Keyword(s):  
Polymyxin B ◽  
Model Systems ◽  
Membrane Model ◽  
Biophysical Characterization

scholarly journals One-Pot Bi-Enzymatic Cascade Synthesis of Novel Ganoderma Triterpenoid Saponins

Catalysts ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 580
Author(s):  
Te-Sheng Chang ◽  
Chien-Min Chiang ◽  
Tzi-Yuan Wang ◽  
Yu-Li Tsai ◽  
Yu-Wei Wu ◽  
...  
Keyword(s):  
High Performance ◽  
Aqueous Solubility ◽  
Major Product ◽  
Cyclodextrin Glucanotransferase ◽  
Bioactive Constituents ◽  
Ganoderic Acid ◽  
One Pot ◽  
Triterpenoid Saponins ◽  
Medicinal Fungus ◽  
Triterpenoid Glycosides

Ganoderma lucidum is a medicinal fungus whose numerous triterpenoids are its main bioactive constituents. Although hundreds of Ganoderma triterpenoids have been identified, Ganoderma triterpenoid glycosides, also named triterpenoid saponins, have been rarely found. Ganoderic acid A (GAA), a major Ganoderma triterpenoid, was synthetically cascaded to form GAA-15-O-β-glucopyranoside (GAA-15-G) by glycosyltransferase (BtGT_16345) from Bacillus thuringiensis GA A07 and subsequently biotransformed into a series of GAA glucosides by cyclodextrin glucanotransferase (Toruzyme® 3.0 L) from Thermoanaerobacter sp. The optimal reaction conditions for the second-step biotransformation of GAA-15-G were found to be 20% of maltose; pH 5; 60 °C. A series of GAA glucosides (GAA-G2, GAA-G3, and GAA-G4) could be purified with preparative high-performance liquid chromatography (HPLC) and identified by mass and nucleic magnetic resonance (NMR) spectral analysis. The major product, GAA-15-O-[α-glucopyranosyl-(1→4)-β-glucopyranoside] (GAA-G2), showed over 4554-fold higher aqueous solubility than GAA. The present study demonstrated that multiple Ganoderma triterpenoid saponins could be produced by sequential actions of BtGT_16345 and Toruzyme®, and the synthetic strategy that we proposed might be applied to many other Ganoderma triterpenoids to produce numerous novel Ganoderma triterpenoid saponins in the future.

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