Complete assignments of magnetic resonances of ribonuclease H from Escherichia coli by double- and triple-resonance 2D and 3D NMR spectroscopies

Biochemistry ◽  
1993 ◽  
Vol 32 (21) ◽  
pp. 5656-5669 ◽  
Author(s):  
Toshio Yamazaki ◽  
Mayumi Yoshida ◽  
Kuniaki Nagayama
Biochemistry ◽  
1993 ◽  
Vol 32 (48) ◽  
pp. 13109-13122 ◽  
Author(s):  
Steven R. Van Doren ◽  
Alexander V. Kurochkin ◽  
Qi Zhuang Ye ◽  
Linda L. Johnson ◽  
Donald J. Hupe ◽  
...  

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3567
Author(s):  
Mathias Percipalle ◽  
Yamanappa Hunashal ◽  
Jan Steyaert ◽  
Federico Fogolari ◽  
Gennaro Esposito

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.


1990 ◽  
Vol 265 (23) ◽  
pp. 13553-13559 ◽  
Author(s):  
W. Yang ◽  
W.A. Hendrickson ◽  
E.T. Kalman ◽  
R.J. Crouch

1989 ◽  
Vol 85 (2) ◽  
pp. 337-358 ◽  
Author(s):  
S Boentges ◽  
B.U Meier ◽  
C Griesinger ◽  
R.R Ernst
Keyword(s):  
3D Nmr ◽  

1990 ◽  
Vol 112 (13) ◽  
pp. 5024-5030 ◽  
Author(s):  
Andre Padilla ◽  
Geerten W. Vuister ◽  
Rolf Boelens ◽  
Gerard J. Kleywegt ◽  
Adrien Cave ◽  
...  

Biochemistry ◽  
1991 ◽  
Vol 30 (41) ◽  
pp. 10043-10057 ◽  
Author(s):  
Jeffrey G. Pelton ◽  
Dennis A. Torchia ◽  
Norman D. Meadow ◽  
Cing Yuen Wong ◽  
Saul Roseman

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1910
Author(s):  
Csilla Sebők ◽  
Patrik Tráj ◽  
Júlia Vörösházi ◽  
Máté Mackei ◽  
Márton Papp ◽  
...  

The liver with resident tissue macrophages is the site of vivid innate immunity, activated also by pathogen-associated molecular patterns (PAMPs) leaking through the intestinal barrier. As gut-derived inflammatory diseases are of outstanding importance in broiler chickens, the present study aimed to establish a proper hepatic inflammatory model by comparing the action of different PAMPs from poultry pathogens on chicken 2D and 3D primary hepatocyte—non-parenchymal cell co-cultures, the latter newly developed with a magnetic bioprinting method. The cultures were challenged by the bacterial endotoxins lipopolysaccharide (LPS) from Escherichia coli, lipoteichoic acid (LTA) from Staphylococcus aureus and by enterotoxin (ETxB) from Escherichia coli, Salmonella Typhimurium derived flagellin, phorbol myristate acetate (PMA) as a model proinflammatory agent and polyinosinic polycytidylic acid (poly I:C) for mimicking viral RNA exposure. Cellular metabolic activity was assessed with the CCK-8 test, membrane damage was monitored with the lactate dehydrogenase (LDH) leakage assay and interleukin-6 and -8 (Il-6 and -8) concentrations were measured in cell culture medium with a chicken specific ELISA. Both LPS and LTA increased the metabolic activity of the 3D cultures, concomitantly decreasing the LDH leakage, while in 2D cultures ETxB stimulated, PMA and poly I:C depressed the metabolic activity. Based on the moderately increased extracellular LDH activity, LTA seemed to diminish cell membrane integrity in 2D and poly I:C in both cell culture models. The applied endotoxins remarkably reduced the IL-8 release of 3D cultured cells, suggesting the effective metabolic adaptation and the presumably initiated anti-inflammatory mechanisms of the 3D spheroids. Notwithstanding that the IL-6 and IL-8 production of 2D cells was mostly not influenced by the endotoxins used, only the higher LTA dose was capable to evoke an IL-8 surge. Flagellin, PMA and poly I:C exerted proinflammatory action in certain concentrations in both 2D and 3D cultures, reflected by the increased cellular IL-6 release. Based on these data, LTA, flagellin, PMA and poly I:C can be considered as potent candidates to induce inflammation in chicken primary hepatic cell cultures, while LPS failed to trigger proinflammatory cytokine production, suggesting the relatively high tolerance of avian liver cells to certain bacterial endotoxins. These results substantiate that the established 3D co-cultures seemed to be proper tools for testing potential proinflammatory molecules; however, the remarkable differences between 2D and 3D models should be addressed and further studied.


2015 ◽  
Vol 191 (3) ◽  
pp. 376-380 ◽  
Author(s):  
David Kalbermatter ◽  
Jean-Marc Jeckelmann ◽  
Po-Lin Chiu ◽  
Zöhre Ucurum ◽  
Thomas Walz ◽  
...  
Keyword(s):  

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