It is proposed to convert nuclear Overhauser effects (NOEs) into relatively precise distances for detailed structural studies of proteins. To this purpose, it is demonstrated that the measurement of NOE buildups between amide protons in perdeuterated human ubiquitin using a designed (15)N-resolved HMQC-NOESY experiment enables the determination of (1)H(N)-(1)H(N) distances up to 5 A with high accuracy and precision. These NOE-derived distances have an experimental random error of approximately 0.07 A, which is smaller than the pairwise rmsd (root-mean-square deviation) of 0.24 A obtained with corresponding distances extracted from either an NMR or an X-ray structure (pdb codes: 1D3Z and 1UBQ), and also smaller than the pairwise rmsd between distances from X-ray and NMR structures (0.15 A). Because the NOE contains both structural and dynamical information, a comparison between the 3D structures and NOE-derived distances may also give insights into through-space dynamics. It appears that the extraction of motional information from NOEs by comparison to the X-ray structure or the NMR structure is challenging because the motion may be masked by the quality of the structures. Nonetheless, a detailed analysis thereof suggests motions between beta-strands and large complex motions in the alpha-helix of ubiquitin. The NOE-derived motions are, however, of smaller amplitude and possibly of a different character than those present in a 20 ns molecular dynamic simulation of ubiquitin in water using the GROMOS force field. Furthermore, a recently published set of structures representing the conformational distribution over time scales up to milliseconds (pdb: 2K39) does not satisfy the NOEs better than the single X-ray structure. Hence, the measurement of possibly thousands of exact NOEs throughout the protein may serve as an excellent probe toward a correct representation of both structure and dynamics of proteins.

SUMMARY HET-S (97% identical to HET-s) has an N-terminal globular domain that exerts a prion-inhibitory effect in cis on its own prion-forming domain (PFD) and in trans on HET-s prion propagation. We show that HET-S fails to form fibrils in vitro and that it inhibits HET-s PFD fibrillization in trans. In vivo analyses indicate that β-structuring of the HET-S PFD is required for HET-S activity. The crystal structures of the globular domains of HET-s and HET-S are highly similar, comprising a helical fold, while NMR-based characterizations revealed no differences in the conformations of the PFDs. We conclude that prion inhibition is not encoded by structure but rather in stability and oligomerization properties: when HET-S forms a prion seed or is incorporated into a HET-s fibril via its PFD, the β-structuring in this domain induces a change in its globular domain, generating a molecular species that is incompetent for fibril growth.

No abstract

Although NMR relaxation phenomena provide a great deal of insight into local molecular dynamics, the dynamic picture of biomacromolecules is still largely incomplete, as no method is available to detect motions between atoms that are far apart in the sequence. Our recent investigations (Vögeli et al. J. Am. Chem. Soc. 2009, 131 (47), 17215−17225) indicate that extraction of exact effective distances from NOE rates might allow the determination of such motions. Using this approach, we measured exact effective distances between amide protons in (15)N,(13)C,(2)H-labeled ubiquitin at three temperatures (284, 307, and 326 K). Comparisons among the three data sets reveal that, whereas the correlation-time-corrected cross-relaxation rates increase by 18% from 284 to 307 K, those at 326 K increase by 32% as compared to those at 284 K. Because theoretical considerations indicate that the NOE is largely insensitive to fast motion, as long as the local order parameter (e.g., S(NH)(2)) is larger than 0.5, the effective distance can be calculated from the NOE using its [linear span]r(-6)[linear span] dependency. Doing so, the average NOE increases translate into effective distance changes of 2.4% and 4.0% in the temperature ranges measured. The data presented demonstrate that the determination of quantitative NOEs is a powerful tool for extracting small structural and dynamical changes in a biomolecule.

The arsenic(III) and antimony(III) cyanides M(CN)3 (M=As, Sb) have been prepared in quantitative yields from the corresponding trifluorides through fluoride-cyanide exchange with Me3 SiCN in acetonitrile. When the reaction was carried out in the presence of one equivalent of 2,2'-bipyridine, the adducts [M(CN)3 ⋅(2,2'-bipy)] were obtained. The crystal structures of As(CN)3 , [As(CN)3 ⋅(2,2'-bipy)] and [Sb(CN)3 ⋅(2,2'-bipy)] were determined and are surprisingly different. As(CN)3 possesses a polymeric three-dimensional structure, [As(CN)3 ⋅(2,2'-bipy)] exhibits a two-dimensional sheet structure, and [Sb(CN)3 ⋅(2,2'-bipy)] has a chain structure, and none of the structures resembles those found for the corresponding arsenic and antimony triazides.