Hydration shell differentiates folded and disordered states of a Trp-cage miniprotein, allowing characterization of structural heterogeneity by wide-line NMR measurements

Water molecule ordering on the surface of an intrinsically disordered protein

The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the hydration of intrinsically disordered proteins (IDPs) is more limited. Here, we compare the local structure of water molecules hydrating a globular protein, lysozyme, and the intrinsically disordered N-terminal of c-Src kinase (SH4UD) using molecular dynamics simulation. The radial distributions from the protein surface of the first and the second hydration shells are similar for the folded protein and the IDP. However, water molecules in the first hydration shell of both the folded protein and the IDP are perturbed from the bulk. This perturbation involves a loss of tetrahedrality, which is, however, significantly more marked for the folded protein than the IDP. This difference arises from an increase in the first hydration shell of the IDP of the fraction of hydration water molecules interacting with oxygen. The water ordering is independent of the compactness of the IDP. In contrast, the lifetimes of water molecules in the first hydration shell increase with IDP compactness, indicating a significant impact of IDP configuration on water surface pocket kinetics, which here is linked to differential pocket volumes and polarities.

Raman study of water deposited in solid argon matrix

New Raman data are presented concerning H₂O and D₂O water aggregation in argon matrix having the ratio of number of argon atoms to water molecules close to 40:1. Experiments were conducted at temperatures from 8 K to 34 K allowing observation of OH and OD stretching vibrations of water monomers, dimers, trimers and higher multimers, as well as broad bands corresponding to solid amorphous water. Molecular dynamics simulations were performed for thirteen or sometimes fourteen water molecules dispersed among 500 argon atoms. Resulting final configurations included dimers, trimers, tetramers and pentamers, all in open chain configurations which upon optimization resulted in mostly cyclic conformations. Observed OH stretching vibrations were assigned by comparing calculated normal modes in harmonic approximation at the B3LYP/aug-cc-pVDZ and PBEPBE1/aug-cc-pVDZ level of theory with our data and previously observed bands from infrared matrix isolation studies and Raman jet cooled experiments. Raman bands assigned to water multimers in argon matrix are shifted 20 to 25 cm^-1 towards lower wavenumbers with respect to the positions of OH stretching vibrations of almost free water clusters.

Antibodies Processed Using High Dilution Technology Distantly Change Structural Properties of IFNγ Aqueous Solution

Terahertz spectroscopy allows for the analysis of vibrations corresponding to the large-scale structural movements and collective dynamics of hydrogen-bonded water molecules. Previously, differences had been detected in the emission spectra of interferon-gamma (IFNγ) solutions surrounded by extremely diluted solutions of either IFNγ or antibodies to IFNγ without direct contact compared to a control. Here we aimed to analyse the structural properties of water in a sample of an aqueous solution of IFNγ via terahertz time-domain spectroscopy (THz-TDS). Tubes with the IFNγ solution were immersed in fluidised lactose saturated with test samples (dilutions of antibodies to IFNγ or control) and incubated at 37 °C for 1, 1.5-2, 2.5-3, or 3.5-4 h. Fluidised lactose was chosen since it is an excipient in the manufacture of drugs based on diluted antibodies to IFNγ. After incubation, spectra were recorded within a wavenumber range of 10 to 110 cm-1 with a resolution of 4 cm-1. Lactose saturated with dilutions of antibodies to IFNγ (incubated for more than 2.5 h) changed the structural properties of an IFNγ aqueous solution without direct contact compared to the control. Terahertz spectra revealed stronger intermolecular hydrogen bonds and an increase in the relaxation time of free and weakly bound water molecules. The methodology developed on the basis of THz-TDS could potentially be applied to quality control of pharmaceuticals based on extremely diluted antibodies.

Bacterial fermentation and isotope labelling optimized for amyloidogenic proteins

We developed a cost sensitive isotope labelling procedure using a fed-batch fermentation method and tested its efficiency producing the 15 N-, 13 C- and 15 N/13 C-labelled variants of an amyloidogenic miniprotein (E5: EEEAVRLYIQWLKEGGPSSGRPPPS). E5 is a surface active protein, which forms amyloids in solution. Here, we confirm, using both PM-IRRAS and AFM measurements, that the air-water interface triggers structural rearrangement and promotes the amyloid formation of E5, and thus it is a suitable test protein to work out efficient isotope labelling schemes even for such difficult sequences. E. coli cells expressing the recombinant, ubiquitin-fused miniprotein were grown in minimal media containing either unlabelled nutrients, or 15 N-NH4 Cl and/or 13 C-D-Glc. The consumption rates of NH4 Cl and D-Glc were quantitatively monitored during fermentation and their ratio was established to be 1:5 (for NH4 Cl: D-Glc). One- and two-step feeding schemes were custom-optimized to enhance isotope incorporation expressing five different E5 miniprotein variants. With the currently optimized protocols we could achieve a 1.5- to 5-fold increase of yields of several miniproteins coupled to a similar magnitude of cost reduction as compared to flask labelling protocols.

Ionic Mobility in Ion-Exchange Membranes

Membrane technologies are widely demanded in a number of modern industries. Ion-exchange membranes are one of the most widespread and demanded types of membranes. Their main task is the selective transfer of certain ions and prevention of transfer of other ions or molecules, and the most important characteristics are ionic conductivity and selectivity of transfer processes. Both parameters are determined by ionic and molecular mobility in membranes. To study this mobility, the main techniques used are nuclear magnetic resonance and impedance spectroscopy. In this comprehensive review, mechanisms of transfer processes in various ion-exchange membranes, including homogeneous, heterogeneous, and hybrid ones, are discussed. Correlations of structures of ion-exchange membranes and their hydration with ion transport mechanisms are also reviewed. The features of proton transfer, which plays a decisive role in the membrane used in fuel cells and electrolyzers, are highlighted. These devices largely determine development of hydrogen energy in the modern world. The features of ion transfer in heterogeneous and hybrid membranes with inorganic nanoparticles are also discussed.

Similarities and Differences among Protein Dynamics Studied by Variable Temperature Nuclear Magnetic Resonance Relaxation

Understanding and describing the dynamics of proteins is one of the major challenges in biology. Here, we use multifield variable-temperature NMR longitudinal relaxation (R₁) measurements to determine the hierarchical activation energies of motions of four different proteins: two small globular proteins (GB1 and the SH3 domain of α-spectrin), an intrinsically disordered protein (the C-terminus of the nucleoprotein of the Sendai virus, Sendai Ntail), and an outer membrane protein (OmpG). The activation energies map the motions occurring in the side chains, in the backbone, and in the hydration shells of the proteins. We were able to identify similarities and differences in the average motions of the proteins. We find that the NMR relaxation properties of the four proteins do share similar features. The data characterizing average backbone motions are found to be very similar, the same for methyl group rotations, and similar activation energies are measured. The main observed difference occurs for the intrinsically disordered Sendai Ntail, where we observe much lower energy of activation for motions of protons associated with the protein-solvent interface as compared to the others. We also observe variability between the proteins regarding side chain ¹⁵N relaxation of lysine residues, with a higher activation energy observed in OmpG. This hints at strong interactions with negatively charged lipids in the bilayer and provides a possible mechanistic clue for the "positive-inside" rule for helical membrane proteins. Overall, these observations refine the understanding of the similarities and differences between hierarchical dynamics in proteins.

Unperturbed Detection of the Dynamic Structure in the Hydrophobic Core of Trp-Cage via Two-Dimensional Infrared Spectroscopy

The tyrosine ring mode is an intrinsic non-perturbing site-specific infrared reporter for conformational dynamics within protein systems. This transition is influenced by direct and indirect interactions associated with the electron-donating ability and the hydrophobicity of the surrounding molecules. Utilizing an intrinsic tyrosine moiety, two-dimensional infrared spectra of Trp-cage, often called the "hydrogen atom" of protein folding, were measured in the folded and denatured states to uncover the dynamics of the hydrophobic core. The vibrational lifetimes and the correlation decays of the tyrosine ring mode showed significant changes upon both temperature and chemical denaturation of the Trp-cage miniprotein, indicating important structural features of the hydrophobic core and its dynamics. The observed Trp6-Tyr3 interactions are in good agreement with the prior studies of the folded state, but they reach beyond the static structure. These stacking interactions and orientations fluctuate on the picosecond time scale as measured through the spectral dephasing within a dehydrated environment.