Determination of the solution structure of nucleic acid double helices using NOE difference NMR spectroscopy, chemical shift calculations, and computer modeling

2009 ◽  
Vol 28 (S12) ◽  
pp. 183-199
Author(s):  
Goutam Gupta ◽  
Mukti H. Sarma ◽  
Ramaswamy H. Sarma
Keyword(s):  
Nucleic Acid ◽  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Computer Modeling ◽  
Solution Structure ◽  
Double Helices ◽  
Chemical Shift Calculations

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 Determination of 15N Chemical Shift Anisotropy from a Membrane-Bound Protein by NMR Spectroscopy

2012 ◽  
Vol 116 (24) ◽  
pp. 7181-7189 ◽  
Author(s):  
Manoj Kumar Pandey ◽  
Subramanian Vivekanandan ◽  
Shivani Ahuja ◽  
Kumar Pichumani ◽  
Sang-Choul Im ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Chemical Shift Anisotropy ◽  
Membrane Bound

scholarly journals Determination of relative tensor orientations by γ-encoded chemical shift anisotropy/heteronuclear dipolar coupling 3D NMR spectroscopy in biological solids

2010 ◽  
Vol 12 (45) ◽  
pp. 14873 ◽  
Author(s):  
Guangjin Hou ◽  
Sivakumar Paramasivam ◽  
In-Ja L. Byeon ◽  
Angela M. Gronenborn ◽  
Tatyana Polenova
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Dipolar Coupling ◽  
Chemical Shift Anisotropy ◽  
3D Nmr ◽  
Biological Solids

scholarly journals NMR Spectroscopic Determination of the Solution Structure of a Branched Nucleic Acid from Residual Dipolar Couplings by Using Isotopically Labeled Nucleotides

2004 ◽  
Vol 43 (2) ◽  
pp. 187-192 ◽  
Author(s):  
Bernd N. M. van Buuren ◽  
Jürgen Schleucher ◽  
Valentin Wittmann ◽  
Christian Griesinger ◽  
Harald Schwalbe ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Solution Structure ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Spectroscopic Determination

Determination of the solution structure of apo calbindin D9k by NMR spectroscopy

1995 ◽  
Vol 249 (2) ◽  
pp. 441-462 ◽  
Author(s):  
Nicholas J. Skelton ◽  
Johan Kördel ◽  
Walter J. Chazin
Keyword(s):  
Nmr Spectroscopy ◽  
Solution Structure ◽  
Calbindin D9k

Determination of Multiple Torsion-Angle Constraints in U−13C,15N-Labeled Peptides:  3D1H−15N−13C−1H Dipolar Chemical Shift NMR Spectroscopy in Rotating Solids

2002 ◽  
Vol 124 (40) ◽  
pp. 11908-11922 ◽  
Author(s):  
Chad M. Rienstra ◽  
Morten Hohwy ◽  
Leonard J. Mueller ◽  
Christopher P. Jaroniec ◽  
Bernd Reif ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Torsion Angle
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