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  • 1
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 245-266 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: The conformation of the ligand in complex with a macromolecular target can be studied by nuclear magnetic resonance (NMR) in solution for both tightly and weakly forming complexes. In the weak binding regime (koff 〉 104 Hz), the structure of the bound ligand is accessible also for very large complexes (〉100 kDa), which are not amenable to NMR studies in the tight binding regime. Here I review the state-of-the-art NMR methodology used for screening ligands and for the structural investigation of bound ligand conformations, in both tight and weak binding regimes. The advantages and disadvantages of each approach are critically described. The NMR methodology used to investigate transiently forming complexes has expanded considerably in the past few years, opening new possibilities for a detailed description of ligand-target interactions. Novel methods for the determination of the bound ligand conformation, in particular transferred cross-correlated relaxation, are thoroughly reviewed, and their advantages with respect to established methodology are discussed, using the epothilone-tubulin complex as a primary example.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1573-5001
    Keywords: dipolar couplings ; methylene groups ; spin state selective transfer ; structure determination ; SPITZE-HSQC ; ubiquitin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Heteronuclear dipolar couplings of the protein backbone have proven to have a big impact on the accuracy of protein NMR structures. H,H dipolar couplings might have the same impact on side chains. Here we present a method that combines both heteronuclear and homonuclear dipolar couplings to investigate the local conformation of methylene groups. A new pulse sequence (SPITZE-HSQC) is presented, that allows to measure the two C,H and the H,H dipolar couplings at the same time, using spin state selective transfers. The new method has been applied to the methylene groups of glycines in the protein ubiquitin. The C,H and the H,H dipolar couplings might have a key role in fast stereospecific assignment of protons in CH2 groups.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1573-5001
    Keywords: Secondary structure ; Uteroglobin ; h-cc10kDa
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Human uteroglobin (h-UG) or Clara cell 10kDa (cc10kDa) is a steroid-dependent, 17 kDahomodimeric, secretory protein with potent anti-inflammatory/immunomodulatory properties.However, the exact physiological role still remains to be determined. It has been hypothesisedthat its activity is exerted through the binding of a specific target represented by a smallmolecule (still unknown), and that the binding is regulated by the formation/disruption of twocysteine bonds. The binding properties of the reduced UG have been proved in vitro forseveral different molecules, but no in vivo data are available to date. However, binding hasbeen observed between reduced rabbit UG and a protein of an apparent molecular mass of90 kDa and, more recently, we found an h-UG-binding protein (putative receptor), of anapparent molecular mass of 190 kDa, on the surface of several cell types. The recognitioninvolves oxidised h-UG. These findings pose the problem of the relevance of the oxidationstate in the recognition process. To determine the solution structure of the oxidised h-UG, weproduced wild-type as well as uniformly 15N- and 15N/13C-labelled samples of therecombinant protein. The assignments of the 1H, 15N and 13C resonances are presented,based on a series of homonuclear 2D and 3D and heteronuclear 2D and 3D double and tripleresonance NMR experiments. Our results indicate that h-UG is an extremely stable proteinunder a wide range of temperatures and pH conditions. The secondary structure in solutionis in general agreement with previously reported crystal structures of rabbit UG, suggestingthat cc10kDa and h-UG are indeed the same protein. Small local differences found in the N-and C-terminal helices seem to support the hypothesis that flexibility involves these residues;moreover, it possibly accounts for the residual binding properties observed when the proteinis in the oxidised state.
    Type of Medium: Electronic Resource
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