Automated Resonance Assignment of Proteins Using Heteronuclear 3D NMR. 2. Side Chain and Sequence-Specific Assignment

1997 ◽  
Vol 37 (3) ◽  
pp. 467-477 ◽  
Author(s):  
Kuo-Bin Li ◽  
B. C. Sanctuary
Keyword(s):  
Resonance Assignment ◽  
Side Chain ◽  
3D Nmr ◽  
Sequence Specific Assignment ◽  
Automated Resonance Assignment ◽  
Specific Assignment

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.

NMR study of non-structural proteins—part I: 1H, 13C, 15N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV)

2014 ◽  
Vol 9 (1) ◽  
pp. 191-195 ◽  
Author(s):  
Efstathios Melekis ◽  
Aikaterini C. Tsika ◽  
Julie Lichière ◽  
Christos T. Chasapis ◽  
Irene Margiolaki ◽  
...  
Keyword(s):  
Resonance Assignment ◽  
Structural Proteins ◽  
Side Chain ◽  
Nmr Study ◽  
Chain Resonance ◽  
Macro Domain ◽  
Side Chain Resonance ◽  
Side Chain Resonance Assignment ◽  
Mayaro Virus

Automated resonance assignment of the 21 kDa stereo-array isotope labeled thioldisulfide oxidoreductase DsbA

2014 ◽  
Vol 249 ◽  
pp. 88-93 ◽  
Author(s):  
Elena Schmidt ◽  
Teppei Ikeya ◽  
Mitsuhiro Takeda ◽  
Frank Löhr ◽  
Lena Buchner ◽  
...  
Keyword(s):  
Resonance Assignment ◽  
Automated Resonance Assignment

Optimized 3D-NMR sampling for resonance assignment of partially unfolded proteins

2007 ◽  
Vol 186 (1) ◽  
pp. 142-149 ◽  
Author(s):  
Nicolas Pannetier ◽  
Klaartje Houben ◽  
Laurence Blanchard ◽  
Dominique Marion
Keyword(s):  
Resonance Assignment ◽  
3D Nmr ◽  
Unfolded Proteins ◽  
Partially Unfolded
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