Characterization of a Disulfide-Crosslinked αIIbβ3 Cytoplasmic Domain Heterodimer by NMR.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 415-415
Author(s):  
Douglas G. Metcalf ◽  
Joseph M. Kielec ◽  
Kathleen G. Valentine ◽  
A. Joshua ◽  
William F. DeGrado ◽  
...  

Abstract The platelet integrin αIIbβ3 is the prototypic example of regulated integrin function. Thus, αIIbβ3 is inactive on unstimulated platelets, but switches to an active conformation following platelet stimulation. Recent experiments suggest that disruption of the heteromeric association of the αIIb and β3 transmembrane (TM) and/or cytoplasmic domains shifts αIIbβ3 from an inactive to an active conformation. However, structural information about these heteromeric associations is sparse. Thus far, the structure of the TM heterodimer has only been studied by molecular modeling. Although interactions between soluble cytosolic tail peptides have been studied by NMR spectroscopy, these studies may not reflect native contacts because they fail to account for constraining TM domain interactions. To obtain an NMR structure for the αIIbβ3 cytosolic tail heterodimer that reflects its native structure, we expressed 13C- and 15N-labeled peptides corresponding to αIIb residues 988-1008 and β3 residues 713-762 in E. coli. Residues 987 in αIIb and 712 in β3 were replaced with cysteines, based on modeling that predicted that a disulfide bond between these residues will fix the peptides in their native orientation. The peptides were disulfide-crosslinked using 2,2′-dithiobis(5-nitropyridine) chemistry, dissolved in dodecylphosphocholine micelles at pH 6.5, and NMR data were collected at 37 °C on a 750 MHz spectrometer. Currently, >98% of the complex’s peptide backbone and >90% of its side chains have been assigned. When compared to published chemical shift data for the monomeric β3 cytoplasmic tail, there were no differences for residues 725–741 and 747–762. However, there were chemical shift differences between the αIIb/β3 heterodimer and the β3 monomer for the membrane-embedded region of the β3 peptide, residues 713–724, suggesting that this region interacts with αIIb. Similarly, chemical shifts for the monomer and heterodimer were different for β3 residues 742–746. This region of β3 contains an NPXY motif and is a site at which the β3 cytoplasmic tail interacts with signaling and structural proteins. This result implies that the shift from heterodimer to monomer causes a structural change in this region, perhaps enabling it to interact with other proteins. Finally, we observed arginine side chain protons on the αIIb subunit. Arginine protons are usually not observable by NMR and their detection may reflect the existence of a salt bridge involving arginine. The αIIb cytoplasmic tail contains two arginine residues, one of which, Arg995, is predicted to form a salt bridge with β3 Asp723. Although the detected arginine protons could belong to Arg995 and/or Arg997, they displayed an NOE with the β3 Asp723 amide, a finding consistent with the predicted αIIb Arg995-β3 Asp723 salt bridge. In conclusion, we have characterized the structure of a disulfide-crosslinked αIIb/β3 cytoplasmic tail heterodimer using NMR spectroscopy and compared our results to prior work on the β3 cytoplasmic tail monomer. Our analysis indicates that when constrained by a proximal disulfide bond, the αIIb and β3 cytoplasmic tails interact, providing one mechanism for maintaining αIIbβ3 in an inactive state.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 2866-2866
Author(s):  
Douglas G. Metcalf ◽  
Joseph M. Kielec ◽  
Kathleen G. Valentine ◽  
A. Joshua Wand ◽  
William F. DeGrado ◽  
...  

Abstract The platelet integrin αIIbβ3 is the prototypic example of regulated integrin function. Thus, αIIbβ3 is present in a resting conformation on unstimulated platelets, but switches to an active conformation following platelet stimulation. Recent experiments suggest that disrupting a heteromeric interaction between the αIIb and β3 transmembrane (TM) and cytoplasmic domains shifts αIIbβ3 from its resting to its active conformation. However, structural information about the heteromeric interaction is sparse. Thus far, the structure of the TM heterodimer has only been studied by molecular modeling. Interactions between soluble cytosolic tail peptides have been studied by NMR spectroscopy, but these studies may not reflect native contacts because they fail to account for constraining TM domain interactions. To obtain an NMR structure for the αIIbβ3 cytosolic tail heterodimer that reflects its native structure, we expressed 13C- and 15N-labeled peptides corresponding to αIIb residues 988–1008 and β3 residues 713–762 in E. coli. Residues 987 in αIIb and 712 in β3 were replaced with cysteines, based on modeling that predicts the resultant disulfide bond will fix the peptides in their native orientation. Crosslinked heterodimers were dissolved in dodecylphosphocholine micelles at pH 6.5 and analyzed at 37°C on a 750 MHz NMR spectrometer. Previously, we presented a preliminary analysis of this construct indicating that when constrained by the proximal disulfide bond, the αIIb and β3 cytoplasmic tails interact and the cytosolic tail of β3 consists of three helices. We have now solved the final structure which defines the β3 interface that interacts with the αIIb cytoplasmic tail. The αIIb-β3 heterodimer interface is dynamic, but can be localized to β3 residues 716 and 719 because they have different chemical shifts in the crosslinked heterodimer than they do in the component monomers. This positions β3 residue 723 at the αIIb-β3 interface, consistent with the putative Arg995-Asp723 salt bridge. Interestingly, the αIIb tail is natively unstructured so a static interface for αIIb could not be identified. Additionally, the completed structure defines the relative orientations of the three β3 helices. The β3 cytoplasmic tail contains a sharp kink at residue 724 that fixes the membrane embedded helix (residues 713–723) and the first cytoplasmic helix (residues 725–736) at a right angle. The kink was defined by multiple NMR parameters including NOE distance restraints between residues 721 and 727. The distal cytoplasmic helix (residues 746–757) is related to the rest of the molecule by a flexible loop (residues 737– 745). N15 NOESY-HSQC crosspeak intensities provide evidence that the flexible loop and distal helix undergo increased motion relative to the first two helices, and the final structure reflects this motion because there is no preferred orientation for the distal helix relative to the first two helices. Lastly, the distal helix and flexible loop are joined by β3’s canonical NPXY motif which forms an N-terminal cap for the distal helix. In conclusion, we have solved the NMR structure of a disulfide-crosslinked αIIb/β3 cytoplasmic tail heterodimer. Our analysis indicates that, when constrained by a disulfide bond, the αIIb and β3 cytoplasmic tails interact, providing one mechanism for maintaining αIIbβ3 in a resting state.


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.


1999 ◽  
Vol 77 (11) ◽  
pp. 1994-2000 ◽  
Author(s):  
Judith A MacInnis ◽  
R Palepu ◽  
D Gerrard Marangoni

The micellar properties of a family of surfactants, the sodium cyclohexylalkanoates, have been investigated in aqueous solution using multinuclear NMR spectroscopy. C-13 chemical shift measurements have been used to determine both the cmc values and the micellar aggregation numbers (Ns values) of these surfactants. The cmc values and the degrees of counterion binding were estimated from 23Na chemical shift measurements. The critical micelle concentrations (cmc's) and the aggregation numbers determined from the NMR experiments indicate that these amphiphiles have high cmc's and low aggregation numbers when compared to other single-headed surfactants (most notably the sodium alkanoates). The conformational changes incurred by the carbon atoms upon micelle formation have been deduced from the 13C chemical shift differences (δsurf,mic - δsurf,aq). These results are used to discuss the formation of the aggregates of the sodium cyclohexylalkanoate surfactants as a function of the length of the alkanoate side chain.Key words: micelles, surfactants, NMR spectroscopy, chemical shifts, aggregation numbers, degree of counterion binding, conformational changes.


1980 ◽  
Vol 58 (18) ◽  
pp. 1947-1956 ◽  
Author(s):  
Alex D. Bain ◽  
Russell A. Bell ◽  
Jeremy R. Everett ◽  
Donald W. Hughes

An alternative two-dimensional nmr pulse sequence, (90°–t1/2–90°–t1/2–FID),correlates the chemical shifts of coupled nuclei. The application of this technique to the solution of the complicated proton nmr spectra of oligoribonucleotides is discussed.


2020 ◽  
Vol 75 (5) ◽  
pp. 459-472 ◽  
Author(s):  
Jenna K. Buchanan ◽  
Paul G. Plieger

Abstract9Be solution NMR spectroscopy is a useful tool for the characterisation of beryllium complexes. An updated comprehensive table of the 9Be NMR chemical shifts of beryllium complexes in solution is presented. The recent additions span a greater range of chemical shifts than those previously reported, and more overlap is observed between the chemical shift regions of four-coordinate complexes and those with lower coordination numbers. Four-coordinate beryllium species have smaller ω1/2 values than the two- and three-coordinate species due to their higher order symmetry. In contrast to previous studies, no clear relationship is observed between chemical shift and the size and number of chelate rings.


Author(s):  
M. Cohn

It was a mere ten years after the discovery of NMR that Oleg Jardetzky under the mentorship of the physical chemist John Wertz (Wertz and Jardetzky, 1956) began using 23Na NMR with the aim of studying Na+ transport in biological systems as suggested by William Lipscomb. Jardetzky found that Na+ NMR provided a unique method for following the binding of Na+ in weak complexes. Advantage was taken of the sensitivity of quadrupolar nuclei to their chemical environment as reflected in their relaxation rates which could be readily observed at a field of 7,030 gauss available at the time (Jardetzky and Wertz, 1956). From the very first, Jardetzky limited his choice to those problems that could be investigated uniquely or most effectively by NMR Spectroscopy. One of Jardetzky’s principal goals was to elucidate, at least in part, the threedimensional structures of biological macromolecules in aqueous solution, a distant goal in the late 1950’s. He realized that before attempting to tackle the structure of these complex molecules, proteins and nucleic acids, by NMR it was essential to initially characterize the spectra of their components, amino acids andnucleosides. In 1957, he published a note in the Journal of Chemical Physics (Takedaand Jardetzky, 1957) on a few amino acids, not only reporting the chemical shifts of all the protons but also showing that in a dipeptide, for example, glycylglycine, the two CH2 groups are non-equivalent. In 1958, he published an NMR paper, a systematic study of the proton NMR spectra of amino acids, in the Journal of Biological Chemistry (Jardetzky and Jardetzky, 1958), thus introducing many facets of NMR Spectroscopy to the biochemical community. This seminal paper included: l) the chemical shifts of the protons of 22 amino acids and their dependence on pH, concentration and ionic strength and 2) the effect of rate processes on the NMR spectrum as exemplified by the exchange of the guanidino protons of arginine with water. Increased structural information from peptide NMR spectroscopy attracted many investigators to this area of research.


1976 ◽  
Vol 31 (5) ◽  
pp. 454-456 ◽  
Author(s):  
O. Lutz ◽  
A. Nolle ◽  
P. Kroneck

Abstract Fourier Transform NMR measurements of 95Mo and 97Mo are reported for several molybdenum compounds in different oxidation states. Using the molybdate ion as a reference, chemical shifts from about +500 ppm to about -1900 ppm have been observed. Experimental parameters and a chemical shift scale are given.


1994 ◽  
Vol 72 (7) ◽  
pp. 1753-1757 ◽  
Author(s):  
Zhigang Chen ◽  
Nicole Morel-Desrosiers ◽  
Jean-Pierre Morel ◽  
Christian Detellier

The interactions of the La(III) cation with D-ribose and with D-arabinose in aqueous solution were investigated by 139La NMR spectroscopy. In the case of D-ribose, the formation of a La(III)-sugar complex was indicated by variations of the 139La chemical shift and linewidth with an increase of the sugar concentration in solution. In contrast, the complexation of La(III) by arabinose is very weak and almost undetectable by 139La NMR. On the basis of a 1:1 stoichiometry, the stability constant for the complex of La(III) with D-ribose was calculated from the observed 139La chemical shift values. A similar treatment was done for the viscosity corrected 139La linewidths using arabinose as an uninteractive reference. The stability constants, K, obtained independently from 139La chemical shifts and linewidths are in good agreement, 2.8 ± 0.5 and 2.2 ± 0.6 M−1 respectively at 299.0 ± 0.5 K. The thermodynamic parameters for the complexation of La(III) by D-ribose could also be obtained: ΔH0 = −12 ± 2 kJ mol−1, and ΔS0 = −31 ± 5 J K−1 mol−1. These values are in very good agreement with those obtained by calorimetric measurements.


2017 ◽  
Vol 46 (41) ◽  
pp. 14094-14097 ◽  
Author(s):  
M. Benedetti ◽  
F. De Castro ◽  
A. Ciccarese ◽  
F. P. Fanizzi

In the [ABrnIm] (A = C, Si, Ge, Sn; n + m = 4) compounds, with the heavier halido ligands bonded to the central IV group elements, the 13C, 29Si, 73Ge and 119Sn NMR chemical shifts were found to be linearly related to the bonded halides ionic radii overall sum, ∑(rh). The 207Pb NMR chemical shift of the unstable [PbH4] hydride could be calculated.


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