The 15N nuclear magnetic resonance of Friend leukemic cell (gly-15N) hemoblogin. The resolution of noncovalent bonding interactions

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.

In-cell NMR: from metabolites to macromolecules

In-cell NMR of macromolecules has gained momentum over the last ten years as an approach that might bridge the branches of cell biology and structural biology. In this review, we put it in the context of earlier efforts that aimed to characterize by NMR the cellular environment of live cells and their intracellular metabolites. Although technical aspects distinguish these earlier in vivo NMR studies and the more recent in cell NMR efforts to characterize macromolecules in a cellular environment, we believe that both share major concerns ranging from sensitivity and line broadening to cell viability. Approaches to overcome the limitations in one subfield thereby can serve the other one and vice versa. The relevance in biomedical sciences might stretch from the direct following of drug metabolism in the cell to the observation of target binding, and thereby encompasses in-cell NMR both of metabolites and macromolecules. We underline the efforts of the field to move to novel biological insights by some selected examples.

Complexed nitrogen heterosuperbenzene: the coordinating properties of a remarkable ligand

Tetra-peri-(tert-butyl-benzo)-di-peri-(pyrimidino)-coronene 1, the parent compound of the nitrogen heterosuperbenzene family N-HSB, is employed as a novel monotopic ligand in the formation of [Pd(eta3-C3H5)(1)]PF6 2 and [Ru(bpy)2(1)](PF6)2 (where bpy = 2,2'-bipyridine 3a and d8-2,2'-bipyridine 3b). These N-coordinated complexes are fully characterized by 1H NMR and IR spectroscopy and ESI-MS. Metal coordination has a profound effect on both the absorption and the emission properties of 1. Pd(II) coordination causes a red-shift in the low-energy absorptions, a decrease in the intensity of the n-pi absorptions, and a quenching of the emission. Ru(II) coordination causes absorption throughout the visible region and creates two new complexes that join an elite group of compounds known as "black" absorbers. 3a and 3b possess two discernible 1MLCT bands. The one of exceptionally low energy (lambda(max) = 615 nm) has an associated (3)MLCT emission (lambda(max) = 880 nm) due to the unprecedented electron delocalization and acceptor properties of the rigid aromatic N-HSB 1. Both Ru(II) complexes are near-IR emitters with unusually protracted emission lifetimes of 320 ns at 77 K. They are photochemically inert, and their electrochemical properties are consistent with the presence of a low-lying pi orbital on 1. The first two reversible reductions (E(1/2) (CH3CN), -0.54 V, -1.01 V vs SCE) are due to the stepwise reduction of 1 and are anodically shifted as compared to [Ru(bpy)3]2+. Temperature- and concentration-dependent NMR studies on 2 and 3a suggest extensive aggregation is occurring in solution.

Cross-peptide bond 13C--15N coupling constants by 13C and J cross-polarization 15N NMR

Comparative 13C--15N coupling constants are reported for the linear dipeptide tBoc-L-[U-13C]Ala-[15N]GlyOMe and the corresponding cyclic diketopiperazine, both in dimethylsulfoxide (DMSO) and, upon removal of the tBoc group, in water solutions. Spectra were obtained by 13C NMR and by the first application of J cross-polarization (JCP) 15N NMR, which greatly reduces the time required to accumulate 15N NMR spectra. In DMSO there was evidence for the formation of complexed species which were not present in water. The values obtained for the cross-peptide bond coupling constant 2J13C alpha--15N were consistently less (by 2.2 Hz in DMSO, 4.3 Hz in water) for the cyclic than for the linear peptide, which may be related to the cross-peptide bond conformation. The 15N resonance for the cyclic peptide was shifted only 2 ppm downfield from the linear peptide chemical shift value in both solvents.