Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD

Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein's hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine ¹H-¹³C/²H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10-20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.

Visualizing Proteins in Mammalian Cells by 19 F NMR Spectroscopy

In-cell NMR spectroscopy is a powerful tool to investigate protein behavior in physiologically relevant environments. Although proven valuable for disordered proteins, we show that in commonly used ¹ H-¹⁵ N HSQC spectra of globular proteins, interactions with cellular components often broaden resonances beyond detection. This contrasts ¹⁹ F spectra in mammalian cells, in which signals are readily observed. Using several proteins, we demonstrate that surface charges and interaction with cellular binding partners modulate linewidths and resonance frequencies. Importantly, we establish that ¹⁹ F paramagnetic relaxation enhancements using stable, rigid Ln(III) chelate pendants, attached via non-reducible thioether bonds, provide an effective means to obtain accurate distances for assessing protein conformations in the cellular milieu.

Bioinspired Ice-Binding Materials for Tissue and Organ Cryopreservation

Cryopreservation of tissues and organs can bring transformative changes to medicine and medical science. In the past decades, limited progress has been achieved, although cryopreservation of tissues and organs has long been intensively pursued. One key reason is that the cryoprotective agents (CPAs) currently used for cell cryopreservation cannot effectively preserve tissues and organs because of their cytotoxicity and tissue destructive effect as well as the low efficiency in controlling ice formation. In stark contrast, nature has its unique ways of controlling ice formation, and many living organisms can effectively prevent freezing damage. Ice-binding proteins (IBPs) are regarded as the essential materials identified in these living organisms for regulating ice nucleation and growth. Note that controversial results have been reported on the utilization of IBPs and their mimics for the cryopreservation of tissues and organs, that is, some groups revealed that IBPs and mimics exhibited unique superiorities in tissues cryopreservation, while other groups showed detrimental effects. In this perspective, we analyze possible reasons for the controversy and predict future research directions in the design and construction of IBP inspired ice-binding materials to be used as new CPAs for tissue cryopreservation after briefly introducing the cryo-injuries and the challenges of conventional CPAs in the cryopreservation of tissues and organs.

Fluorine NMR Spectroscopy Enables to Quantify the Affinity Between DNA and Proteins in Cell Lysate

The determination of the binding affinity quantifying the interaction between proteins and nucleic acids is of crucial interest in biological and chemical research. Here, we have made use of site-specific fluorine labeling of the cold shock protein from Bacillus subtilis, BsCspB, enabling to directly monitor the interaction with single stranded DNA molecules in cell lysate. High-resolution 19 F NMR spectroscopy has been applied to exclusively report on resonance signals arising from the protein under study. We have found that this experimental approach advances the reliable determination of the binding affinity between single stranded DNA molecules and its target protein in this complex biological environment by intertwining analyses based on NMR chemical shifts, signal heights, line shapes and simulations. We propose that the developed experimental platform offers a potent approach for the identification of binding affinities characterizing intermolecular interactions in native surroundings covering the nano-to-micromolar range that can be even expanded to in cell applications in future studies.

Drug Screening in Human Cells by NMR Spectroscopy Allows the Early Assessment of Drug Potency

Structure-based drug development is often hampered by the lack of in vivo activity of promising compounds screened in vitro, due to low membrane permeability or poor intracellular binding selectivity. Herein, we show that ligand screening can be performed in living human cells by "intracellular protein-observed" NMR spectroscopy, without requiring enzymatic activity measurements or other cellular assays. Quantitative binding information is obtained by fast, inexpensive ¹ H NMR experiments, providing intracellular dose- and time-dependent ligand binding curves, from which kinetic and thermodynamic parameters linked to cell permeability and binding affinity and selectivity are obtained. The approach was applied to carbonic anhydrase and, in principle, can be extended to any NMR-observable intracellular target. The results obtained are directly related to the potency of candidate drugs, that is, the required dose. The application of this approach at an early stage of the drug design pipeline could greatly increase the low success rate of modern drug development.

What does fluorine do to a protein? Thermodynamic, and highly-resolved structural insights into fluorine-labelled variants of the cold shock protein

Fluorine labelling represents one promising approach to study proteins in their native environment due to efficient suppressing of background signals. Here, we systematically probe inherent thermodynamic and structural characteristics of the Cold shock protein B from Bacillus subtilis (BsCspB) upon fluorine labelling. A sophisticated combination of fluorescence and NMR experiments has been applied to elucidate potential perturbations due to insertion of fluorine into the protein. We show that single fluorine labelling of phenylalanine or tryptophan residues has neither significant impact on thermodynamic stability nor on folding kinetics compared to wild type BsCspB. Structure determination of fluorinated phenylalanine and tryptophan labelled BsCspB using X-ray crystallography reveals no displacements even for the orientation of fluorinated aromatic side chains in comparison to wild type BsCspB. Hence we propose that single fluorinated phenylalanine and tryptophan residues used for protein labelling may serve as ideal probes to reliably characterize inherent features of proteins that are present in a highly biological context like the cell.