1H 3D NOE-NOE spectrum of met-cyanomyoglobin: The first 3D NMR spectrum of a paramagnetic protein

Reaction of 3β-acetoxy-21,22-dioxo-18α,19βH-ursan-28,20β-olide (IIIa) and 20β,28-epoxy-21,22-dioxo-19α,19βH-ursan-3β-yl acetate (IIIb) with diazomethane afforded derivatives XII-XIV with spiroepoxide group in position 21 or 22, which were further converted into hydroxy derivatives XV and XVII. Ethylene ketals VIII-X were also prepared. In connection with the determination of position and configuration of the functional groups at C(21) and C(22), the 1H and 13C NMR spectral data of the prepared compounds are discussed. Complete analysis of two four-spin systems in the 1H NMR spectrum of bisethylenedioxy derivative Xb led to the proton-proton coupling constants from which the structure with two 1,4-dioxane rings condensed with ring E, and their conformation, was derived.

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Structure of Nanobody Nb23

Molecules ◽

10.3390/molecules26123567 ◽

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.

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Biotin-Containing Third Generation Glucoheptoamidated Polyamidoamine Dendrimer for 5-Aminolevulinic Acid Delivery System

International Journal of Molecular Sciences ◽

10.3390/ijms22041982 ◽

2021 ◽

Vol 22 (4) ◽

pp. 1982 ◽

Cited By ~ 1

Author(s):

Aleksandra Kaczorowska ◽

Małgorzata Malinga-Drozd ◽

Wojciech Kałas ◽

Marta Kopaczyńska ◽

Stanisław Wołowiec ◽

...

Keyword(s):

Reactive Oxygen Species ◽

Aminolevulinic Acid ◽

Reactive Oxygen ◽

Pamam Dendrimer ◽

Variable Number ◽

Amide Bond ◽

Oxygen Species ◽

Nmr Spectrum ◽

Guest Molecules ◽

Amine Groups

Polyamidoamine PAMAM dendrimer generation 3 (G3) was modified by attachment of biotin via amide bond and glucoheptoamidated by addition of α-D-glucoheptono-1,4-lacton to obtain a series of conjugates with a variable number of biotin residues. The composition of conjugates was determined by detailed 1-D and 2-D NMR spectroscopy to reveal the number of biotin residues, which were 1, 2, 4, 6, or 8, while the number of glucoheptoamide residues substituted most of the remaining primary amine groups of PAMAM G3. The conjugates were then used as host molecules to encapsulate the 5-aminolevulinic acid. The solubility of 5-aminolevulinic acid increased twice in the presence of the 5-mM guest in water. The interaction between host and guest was accompanied by deprotonation of the carboxylic group of 5-aminolevulinic acid and proton transfer into internal ternary nitrogen atoms of the guest as evidenced by a characteristic chemical shift of resonances in the 1H NMR spectrum of associates. The guest molecules were most likely encapsulated inside inner shell voids of the host. The number of guest molecules depended on the number of biotin residues of the host, which was 15 for non-biotin-containing glucoheptoamidated G3 down to 6 for glucoheptoamidated G3 with 8 biotin residues on the host surface. The encapsulates were not cytotoxic against Caco-2 cells up to 200-µM concentration in the dark. All encapsulates were able to deliver 5-aminolevulinic acid to cells but aqueous encapsulates were more active in this regard. Simultaneously, the reactive oxygen species were detected by staining with H2DCFDA in Caco-2 cells incubated with encapsulates. The amount of PpIX was sufficient for induction of reactive oxygen species upon 30-s illumination with a 655-nm laser beam.

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Protein–Ligand Binding Volume Determined from a Single 2D NMR Spectrum with Increasing Pressure

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.1c02917 ◽

2021 ◽

Author(s):

Gediminas Skvarnavičius ◽

Zigmantas Toleikis ◽

Vilma Michailovienė ◽

Christian Roumestand ◽

Daumantas Matulis ◽

...

Keyword(s):

Ligand Binding ◽

2D Nmr ◽

Nmr Spectrum

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Structural studies of phosphorylation-dependent interactions between the V2R receptor and arrestin-2

Nature Communications ◽

10.1038/s41467-021-22731-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Qing-Tao He ◽

Peng Xiao ◽

Shen-Ming Huang ◽

Ying-Li Jia ◽

Zhong-Liang Zhu ◽

...

Keyword(s):

Crystal Structures ◽

Conformational Changes ◽

Nmr Spectrum ◽

H Nmr ◽

Interaction Sites ◽

Receptor Interactions ◽

Remote Sites ◽

Genetic Code Expansion ◽

G Protein Coupled ◽

Interaction Change

AbstractArrestins recognize different receptor phosphorylation patterns and convert this information to selective arrestin functions to expand the functional diversity of the G protein-coupled receptor (GPCR) superfamilies. However, the principles governing arrestin-phospho-receptor interactions, as well as the contribution of each single phospho-interaction to selective arrestin structural and functional states, are undefined. Here, we determined the crystal structures of arrestin2 in complex with four different phosphopeptides derived from the vasopressin receptor-2 (V2R) C-tail. A comparison of these four crystal structures with previously solved Arrestin2 structures demonstrated that a single phospho-interaction change results in measurable conformational changes at remote sites in the complex. This conformational bias introduced by specific phosphorylation patterns was further inspected by FRET and 1H NMR spectrum analysis facilitated via genetic code expansion. Moreover, an interdependent phospho-binding mechanism of phospho-receptor-arrestin interactions between different phospho-interaction sites was unexpectedly revealed. Taken together, our results provide evidence showing that phospho-interaction changes at different arrestin sites can elicit changes in affinity and structural states at remote sites, which correlate with selective arrestin functions.

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Homopiperazine (Hexahydro-1,4-diazepine)

Molbank ◽

10.3390/m1200 ◽

2021 ◽

Vol 2021 (2) ◽

pp. M1200

Author(s):

R. Alan Aitken ◽

Dheirya K. Sonecha ◽

Alexandra M. Z. Slawin

Keyword(s):

13C Nmr ◽

Title Compound ◽

Coupling Constants ◽

15N Nmr ◽

Time Data ◽

Nmr Spectrum ◽

X Ray ◽

First Time

The X-ray structure of the title compound has been determined for the first time. Data on its 1H–13C-NMR coupling constants and 15N-NMR spectrum are also given.

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