Search Results (3)

Peptides are an important class of biomolecules that perform many physiological functions and which occupy a significant and increasing share of the pharmaceutical market. Methods to determine the solid-state structures of peptides in different environments are important to help understand their biological functions and to aid the development of drug formulations. Here, a new magic-angle spinning (MAS) solid-state nuclear magnetic resonance (SSNMR) approach is described for the structural analysis of uniformly ¹³C-labeled solid peptides. Double-quantum (DQ) coherence between selective pairs of ¹³C nuclei in peptide backbone and side-chain CH₃ groups is excited to provide restraints on (i) ¹³C–¹³C internuclear distances and (ii) the relative orientations of C–H bonds. DQ coherence is selected by adjusting the MAS frequency to the difference in the resonance frequencies of selected nuclear pairs (the rotational resonance condition), which reintroduces the dipolar coupling between the nuclei. Interatomic distances are then measured using a constant time SSNMR experiment to eliminate uncertainties arising from relaxation effects. Further, the relative orientations of C–H bond vectors are determined using a DQ heteronuclear local field SSNMR experiment, employing ¹³C–¹H coupling amplification to increase sensitivity. These methods are applied to determine the molecular conformation of a uniformly ¹³C-labeled peptide, N-formyl-l-methionyl-l-leucyl-l-phenylalanine (fMLF). From just six distance and six angular restraints, two possible molecular conformations are determined, one of which is in excellent agreement with the crystal structure of a closely related peptide. The method is envisaged to a useful addition to the SSNMR repertoire for the solid-state structure determination of peptides in a variety of forms, including amyloid fibrils and pharmaceutical formulations. Full article

Solid-state NMR (ss-NMR) is a powerful tool to investigate noncrystallizable, poorly soluble molecular systems, such as membrane proteins, amyloids, and cell walls, in environments that closely resemble their physical sites of action. Rotational-echo double resonance (REDOR) is an ss-NMR methodology, which by reintroducing heteronuclear dipolar coupling under magic angle spinning conditions provides intramolecular and intermolecular distance restraints at the atomic level. In addition, REDOR can be exploited as a selection tool to filter spectra based on dipolar couplings. Used extensively as a spectroscopic ruler between isolated spins in site-specifically labeled systems and more recently as a building block in multidimensional ss-NMR pulse sequences allowing the simultaneous measurement of multiple distances, REDOR yields atomic-scale information on the structure and interaction of proteins. By extending REDOR to the determination of ¹H–X dipolar couplings in recent years, the limit of measurable distances has reached ~15–20 Å, making it an attractive method of choice for the study of complex biomolecular assemblies. Following a methodological introduction including the most recent implementations, examples are discussed to illustrate the versatility of REDOR in the study of biological systems. Full article

In this paper, we define D-magic labelings for oriented graphs where D is a distance set. In particular, we label the vertices of the graph with distinct integers $\{1,2,\dots ,|V\left(G\right)\left|\right\}$ in such a way that the sum of all the vertex labels that are a distance in D away from a given vertex is the same across all vertices. We give some results related to the magic constant, construct a few infinite families of D-magic graphs, and examine trees, cycles, and multipartite graphs. This definition grew out of the definition of D-magic (undirected) graphs. This paper explores some of the symmetries we see between the undirected and directed version of D-magic labelings. Full article