scholarly journals Simultaneous Ligand and Receptor Tracking through NMR Spectroscopy Enabled by Distinct 19F Labels

2019 ◽  
Vol 20 (15) ◽  
pp. 3658 ◽  
Author(s):  
Jeffrey R. Simmons ◽  
Alexandre Murza ◽  
Michael D. Lumsden ◽  
Calem Kenward ◽  
Éric Marsault ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Environmental Changes ◽  
Chemical Shifts ◽  
Spin Dynamics ◽  
Conformational Sampling ◽  
Unambiguous Tracking ◽  
Binding Preference ◽  
Binding Event ◽  
Highly Sensitive ◽  
Α Helix

To probe ligand-receptor binding at the atomic-level, a frequent approach involves multidimensional nuclear magnetic resonance (NMR) spectroscopy experiments relying on 13C- and/or 15N-enrichment alongside 1H. Alternatively, the lack of fluorine in biomolecules may be exploited through specific incorporation of 19F nuclei into a sample. The 19F nucleus is highly sensitive to environmental changes and allows for one-dimensional NMR spectroscopic study, with perturbation to chemical shift and spin dynamics diagnostic of structural change, ligand binding, and modified conformational sampling. This was applied to the apelinergic system, which comprises a rhodopsin-like G protein-coupled receptor (the apelin receptor (AR)/APJ) and two families of cognate ligands, the apelin and apela (ELABELA/toddler) peptides. Specifically, AR fragments consisting of either the N-terminal tail and first transmembrane (TM) α-helix (AR55) or the first three transmembrane α-helices (TM1-3) were prepared with biosynthetic fluorotryptophan incorporation. Interactions of each AR fragment with a high-affinity, 2,4,5-trifluorophenylalanine labeled apelin analogue were compared by 19F NMR. Distinct ranges of 19F chemical shifts for ligand and receptor provide unambiguous tracking of both species, with distinct binding behaviour observed for each AR fragment implying that AR55 is not sufficient to recapitulate the physiological binding event. Site-specific perturbation was also apparent for the apelin analogue as a function of substitution site, indicating an orientational binding preference. As a whole, this strategy of distinctive 19F labelling for ligand and receptor provides a relatively fast (i.e., employing 1D NMR experiments) and highly sensitive method to simultaneously and definitively track binding in both species.

scholarly journals Structure of Nanobody Nb23

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3567
Author(s):  
Mathias Percipalle ◽  
Yamanappa Hunashal ◽  
Jan Steyaert ◽  
Federico Fogolari ◽  
Gennaro Esposito
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Solution Structure ◽  
Chemical Shifts ◽  
Molecular Size ◽  
Side Chain ◽  
3D Nmr ◽  
Target Antigen ◽  
Internuclear Distances ◽  
2D And 3D

Background: Nanobodies, or VHHs, are derived from heavy chain-only antibodies (hcAbs) found in camelids. They overcome some of the inherent limitations of monoclonal antibodies (mAbs) and derivatives thereof, due to their smaller molecular size and higher stability, and thus present an alternative to mAbs for therapeutic use. Two nanobodies, Nb23 and Nb24, have been shown to similarly inhibit the self-aggregation of very amyloidogenic variants of β2-microglobulin. Here, the structure of Nb23 was modeled with the Chemical-Shift (CS)-Rosetta server using chemical shift assignments from nuclear magnetic resonance (NMR) spectroscopy experiments, and used as prior knowledge in PONDEROSA restrained modeling based on experimentally assessed internuclear distances. Further validation was comparatively obtained with the results of molecular dynamics trajectories calculated from the resulting best energy-minimized Nb23 conformers. Methods: 2D and 3D NMR spectroscopy experiments were carried out to determine the assignment of the backbone and side chain hydrogen, nitrogen and carbon resonances to extract chemical shifts and interproton separations for restrained modeling. Results: The solution structure of isolated Nb23 nanobody was determined. Conclusions: The structural analysis indicated that isolated Nb23 has a dynamic CDR3 loop distributed over different orientations with respect to Nb24, which could determine differences in target antigen affinity or complex lability.

scholarly journals Resolving Entangled JH-H-Coupling Patterns for Steroidal Structure Determinations by NMR Spectroscopy

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2643
Author(s):  
Danni Wu ◽  
Kathleen Joyce Carillo ◽  
Jiun-Jie Shie ◽  
Steve S.-F. Yu ◽  
Der-Lii M. Tzou
Keyword(s):  
Nmr Spectroscopy ◽  
1H Nmr Spectroscopy ◽  
Chemical Shifts ◽  
Atomic Level ◽  
Molecular Structures ◽  
Naturally Occurring ◽  
Structure Determinations ◽  
Ligand Interactions ◽  
Synthetic Steroids ◽  
The Individual

For decades, high-resolution 1H NMR spectroscopy has been routinely utilized to analyze both naturally occurring steroid hormones and synthetic steroids, which play important roles in regulating physiological functions in humans. Because the 1H signals are inevitably superimposed and entangled with various JH–H splitting patterns, such that the individual 1H chemical shift and associated JH–H coupling identities are hardly resolved. Given this, applications of thess information for elucidating steroidal molecular structures and steroid/ligand interactions at the atomic level were largely restricted. To overcome, we devoted to unraveling the entangled JH–H splitting patterns of two similar steroidal compounds having fully unsaturated protons, i.e., androstanolone and epiandrosterone (denoted as 1 and 2, respectively), in which only hydroxyl and ketone substituents attached to C3 and C17 were interchanged. Here we demonstrated that the JH–H values deduced from 1 and 2 are universal and applicable to other steroids, such as testosterone, 3β, 21-dihydroxygregna-5-en-20-one, prednisolone, and estradiol. On the other hand, the 1H chemical shifts may deviate substantially from sample to sample. In this communication, we propose a simple but novel scheme for resolving the complicate JH–H splitting patterns and 1H chemical shifts, aiming for steroidal structure determinations.

Installation of a Rigid EDTA-Like Motif into a Protein α-Helix for Paramagnetic NMR Spectroscopy with Cobalt(II) Ions

2015 ◽  
Vol 22 (4) ◽  
pp. 1228-1232 ◽  
Author(s):  
James D. Swarbrick ◽  
Phuc Ung ◽  
Matthew L. Dennis ◽  
Michael D. Lee ◽  
Sandeep Chhabra ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Paramagnetic Nmr ◽  
Α Helix

Reversal of order of chemical shifts. Differential solvent effects in the hydrogen shifts of toluene,m-xylene ando-xylene as determined by 320 MHz tritium NMR spectroscopy

1984 ◽  
Vol 22 (10) ◽  
pp. 665-667 ◽  
Author(s):  
Mervyn A. Long ◽  
John K. Saunders ◽  
Philip G. Williams ◽  
Allan L. Odell ◽  
R. Wayne Martin
Keyword(s):  
Nmr Spectroscopy ◽  
Solvent Effects ◽  
Chemical Shifts ◽  
Tritium Nmr ◽  
Hydrogen Shifts

scholarly journals 19F NMR Spectroscopy as a Highly Sensitive Method for the Direct Monitoring of Confined Crystallization within Nanoporous Materials

2016 ◽  
Vol 55 (31) ◽  
pp. 8904-8908 ◽  
Author(s):  
Karol P. Nartowski ◽  
Diksha Malhotra ◽  
Lucy E. Hawarden ◽  
Juraj Sibik ◽  
Dinu Iuga ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Nanoporous Materials ◽  
19F Nmr ◽  
19F Nmr Spectroscopy ◽  
Confined Crystallization ◽  
Highly Sensitive ◽  
Sensitive Method

27Al-MAS-NMR-Untersuchungen des thermischen Abbaus von NH4Al(SO4)2·12H2O / 27Al-MAS-NMR Studies on the Thermolysis of NH4Al(SO4)2· 12H2O

1991 ◽  
Vol 46 (11) ◽  
pp. 1515-1518 ◽  
Author(s):  
Gerhard Wegner ◽  
Gert Blumenthal ◽  
Dirk Müller ◽  
Dirk-Henning Menz ◽  
Antje Schmalstieg
Keyword(s):  
Nmr Spectroscopy ◽  
Structural Changes ◽  
Chemical Shifts ◽  
Mas Nmr ◽  
Nmr Studies ◽  
High Stage ◽  
27Al Mas Nmr ◽  
High Resolution Nmr ◽  
First Time

Products of the thermolysis of NH4Al-alum were prepared under dried air and characterized by X-ray powder diffraction, thermogravimetry, and for the first time by solid-state 27Al-MAS-NMR spectroscopy. It was found, that high resolution NMR spectroscopy is applicable to follow up the thermal decomposition and to indicate even minor structural changes. 27Al-MAS-NMR spectra show peaks with characteristic chemical shifts for octahedral Al-units up to a high stage of thermolysis. During the decomposition of Al2(SO4)3 to γ-Al2O3 we again observed three-peak spectra with the specific signal at ≈ 35 ppm for penta-coordinated Al ions as recently proved for the thermolysis of AlCl3 · 6 H2O.

Preparation, 1H and 13C NMR, and ab initio/IGLO study of mono-O-protonated deltic acid and theoretical investigation of di-, tri-, and tetra-O-protonated deltic acids

1999 ◽  
Vol 77 (5-6) ◽  
pp. 525-529 ◽  
Author(s):  
GK Surya Prakash ◽  
Golam Rasul ◽  
George A Olah ◽  
Ronghua Liu ◽  
Thomas T Tidwell
Keyword(s):  
Nmr Spectroscopy ◽  
Ab Initio ◽  
Theoretical Investigation ◽  
13C Nmr ◽  
Chemical Shifts ◽  
1H And 13C Nmr ◽  
Nmr Chemical Shifts ◽  
Molar Solution ◽  
Protonated Species ◽  
C Nmr

The hitherto elusive mono-O-protonated deltic acid C3O3H3+ was prepared by protolysis of di-tert-butoxy deltate in FSO3H-SO2ClF and in FSO3H:SbF5 (Magic Acid; 1:1 molar solution) in SO2ClF as solvent at -78°C and was characterized by 1H and 13C NMR spectroscopy. The structure and NMR chemical shifts were also calculated by the ab initio/IGLO method. No NMR evidence was found for persistent di-O-protonated deltic acid under these conditions, although a limited equilibrium with the mono-O-protonated species can be involved. Di-, tri-, and tetra-O-protonated deltic acids were also studied by ab initio/IGLO method.Key words: protonated deltic acid, aromaticity, superacids, NMR spectroscopy, ab initio and IGLO calculations.

Hexaethyl-2,4-dicarba-nido-hexaborane(8), Deprotonation and Complexation Studied by NMR Spectroscopy and Density Functional Theory (DFT) Calculations

2004 ◽  
Vol 59 (6) ◽  
pp. 685-691 ◽  
Author(s):  
Bernd Wrackmeyer ◽  
Hans-Jörg Schanz
Keyword(s):  
Density Functional Theory ◽  
Nmr Spectroscopy ◽  
Density Functional ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Analogous Reaction ◽  
Sandwich Complex ◽  
Dft Methods ◽  
Functional Theory ◽  
Nmr Data

Deprotonation of hexaethyl-2,4-dicarba-nido-borane(8) 2 leads first to the hexaethyl-2,4-dicarbanido- borate(1−) 3, and further deprotonation, using BuLi/KOtBu, gives the hexaethyl-2,4-dicarbanido- hexaborate(2−) 4. The reaction of 3 with FeCl2 affords the commo-ferracarborane [Fe(Et6-2,4- C2B4H)2] 5, and the analogous reaction of 4 leads to the anionic sandwich complex [Fe(Et6-2,4- C2B4)2]2− 6 which can be protonated to give 5. The complex 5 contains two hydrido ligands, each bridging the iron and two boron atoms. Reactions were monitored and the products were characterised by 11B NMR spectroscopy in solution. The geometries of the carboranes, the borates (all unsubstituted and permethyl-substituted) and the iron complexes (all unsubstituted) were optimised by DFT methods [B3LYP/6-311+G(d,p) or B3LYP/6-31+G(d)], and the relevant NMR data [chemical shifts δ11B, δ13C, δ57Fe, and coupling constants 1J(13C,1H), 1J(11B,1H), 1J(57Fe,1H), 1J(57Fe,11B)] were calculated at the same level of theory.

Sign in / Sign up

Export Citation Format

Share Document