High-Sensitivity Rheo-NMR Spectroscopy for Protein Studies

Shear stress as a driver of degradation for protein-based therapeutics: More accomplice than culprit

Protein degradation is a major concern for protein-based therapeutics. It may alter the biological activity of the product and raise the potential for undesirable effects on the patients. Among the numerous drivers of protein degradation, shear stress has been the focus around which much work has revolved since the 1970s. In the pharmaceutical realm, the product is often processed through several unit operations, which include mixing, pumping, filtration, filling, and atomization. Nonetheless, the drug might be exposed to significant shear stresses, which might cooperatively contribute to product degradation, together with interfacial stress. This review presents fundamentals of shear stress about protein structure, followed by an overview of the drivers of product degradation. The impact of shear stress on protein stability in different unit operations is then presented, and recommendations for limiting the adverse effects on the biopharmaceutical formulations are outlined. Finally, several devices used to explore the effects of shear stress are discussed.

Solution structure of the HOIL-1L NZF domain reveals a conformational switch regulating linear ubiquitin affinity

Attachment of polyubiquitin (poly-Ub) chains to proteins is a major posttranslational modification in eukaryotes. Linear ubiquitin chain assembly complex, consisting of HOIP (HOIL-1-interacting protein), HOIL-1L (heme-oxidized IRP2 Ub ligase 1), and SHARPIN (Shank-associated RH domain-interacting protein), specifically synthesizes "head-to-tail" poly-Ub chains, which are linked via the N-terminal methionine α-amino and C-terminal carboxylate of adjacent Ub units and are thus commonly called "linear" poly-Ub chains. Linear ubiquitin chain assembly complex-assembled linear poly-Ub chains play key roles in immune signaling and suppression of cell death and have been associated with immune diseases and cancer; HOIL-1L is one of the proteins known to selectively bind linear poly-Ub via its Npl4 zinc finger (NZF) domain. Although the structure of the bound form of the HOIL-1L NZF domain with linear di-Ub is known, several aspects of the recognition specificity remain unexplained. Here, we show using NMR and orthogonal biophysical methods, how the NZF domain evolves from a free to the specific linear di-Ub-bound state while rejecting other potential Ub species after weak initial binding. The solution structure of the free NZF domain revealed changes in conformational stability upon linear Ub binding, and interactions between the NZF core and tail revealed conserved electrostatic contacts, which were sensitive to charge modulation at a reported phosphorylation site: threonine-207. Phosphomimetic mutations reduced linear Ub affinity by weakening the integrity of the linear di-Ub-bound conformation. The described molecular determinants of linear di-Ub binding provide insight into the dynamic aspects of the Ub code and the NZF domain's role in full-length HOIL-1L.

Conformational Fluctuations and Induced Orientation of a Protein, Its Solvation Shell, and Bulk Water in Weak Non-Unfolding External Electric Fields

Extreme external electric fields have been reported to disrupt the tertiary structure of stably folded proteins; however, the effects of weaker electric fields on many biomolecules, especially net-uncharged proteins, and on the surrounding aqueous environment have been rarely discussed. To explore these effects at the atomic level, here, we have used molecular dynamics simulations to estimate rotational motion and induced structural fluctuations in the model protein ubiquitin and its hydration layer due to applied non-unfolding electrostatic fields. When exposed to weak electric fields of up to 0.2 V nm-1, ubiquitin displayed competition between internal structure-maintaining molecular interactions and the external orienting force, which disrupted the local structure in certain regions of the protein. Moreover, relative to hydration water, bulk water showed a greater tendency to align with the electric field, indicating that the presence of protein caused hydration water to acquire rotational mobility different from that in a pure-water system. The differential influence of the applied electric field on the hydration and bulk water surrounding ubiquitin will be common to almost all (nonmembrane) biomacromolecules. Our findings highlight the importance of local dipoles and their electric polarizability even in net-uncharged biomolecules.

A molecular-mechanical link in shear-induced self-assembly of a functionalized biopolymeric fluid

23Na multiple quantum filtered (MQF) rheo-NMR methods were applied to probe the molecular foundation for flow induced self-assembly in 0.5% κ-carrageenan fluid. This method is sensitive enough to utilize an endogenous sodium ion concentration of approximately 0.02%. Rheo-NMR experiments were conducted at different temperatures and shear rates to explore varying molecular dynamics of the biopolymer in the fluid under shear. The temperature in the rheo-NMR experiments was changes from 288 K to 313 K to capture transition of κ-carrageenan molecules from helices to coils. At each temperature, the fluid was also tested for flow and oscillatory shear behaviour using bulk rheometry methods. It was found that the 23Na MQF signals were observed for the 0.5% κ-carrageenan solution only under shear and when the fluid demonstrated yielding and/or shear-thinning behaviour. At temperatures of 303 K and above, no 23Na MQF signals were observed independent of the presence or absence of shear as the molecular phase transition to random coils occurs and the fluid becomes Newtonian.

Rheo-NMR Spectroscopy for Cryogenic-Probe-Equipped NMR Instruments to Monitor Protein Aggregation

Cryogenic-probe-based Rheo-NMR spectroscopy is a recently developed methodology to obtain solution NMR spectra of protein samples in situ under external shear. It is applicable to atomic-resolution monitoring of protein aggregation in situ, thereby aiding understanding of the transient structural changes and state conversion of amyloidogenic proteins, which are strongly associated with the both the onset and the progression of neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. Here, we present detailed experimental procedures for the instrumental setup and practical tips for preparation of NMR measurement to analyze protein aggregation by this technique. This protocol will thus aid future Rheo-NMR spectroscopic studies not only of protein aggregation but also of other phenomena related to shear stress, such as shear-induced viscosity increase and shear-enhanced crystallization. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Setup of a Rheo-NMR Instrument Basic Protocol 2: Adjustment of the Vertical and Horizontal Positions of the Glass Stick Basic Protocol 3: Monitoring Protein Aggregation by Rheo-NMR Spectroscopy.

Contact-mediated nucleation in melt emulsions investigated by rheo-nuclear magnetic resonance

Increasing the efficiency of disperse phase crystallization is of great interest for melt emulsion production as the fraction of solidified droplets determines product quality and stability. Nucleation events must appear within every single one of the μm-sized droplets for solidification. Therefore, primary crystallization requires high subcooling and is, thus, time and energy consuming. Contact-mediated nucleation is a mechanism for intensifying the crystallization process. It is defined as the successful nucleation of a subcooled liquid droplet induced by contact with an already crystallized droplet. We investigated contact-mediated nucleation under shear flow conditions up to shear rates of 457 s^-1 for a quantitative assessment of this mechanism. Rheo-nuclear magnetic resonance was successfully used for the time-resolved determination of the solids fraction of the dispersed phase of melt emulsions upon contact-mediated nucleation events. The measurements were carried out in a dedicated Taylor-Couette cell. The efficiency of contact-mediated nucleation λsec decreased with increasing shear rate, whereas the effective second order kinetic constant kcoll,eff increased approximately linearly at small shear rates and showed a linear decrease for shear rates higher than about 200 s^-1 . These findings are in accordance with coalescence theory. Thus, the nucleation rate is optimal at specific flow conditions. There are limitations for successful inoculation at a low shear rate because of rare contact events and at a high shear rate due to too short contact time.

Multiple-State Monitoring of SOD1 Amyloid Formation at Single-Residue Resolution by Rheo-NMR Spectroscopy

Formation of protein aggregates or fibrils entails the conversion of soluble native protein monomers via multiple molecular states. No spectroscopic techniques have succeeded in capturing the transient molecular-scale events of fibrillation in situ. Here we report residue- and state-specific real-time monitoring of the fibrillation of amyotrophic lateral sclerosis-related SOD1 by rheology NMR (Rheo-NMR) spectroscopy. Under moderately denaturing conditions, where NMR signals of folded and unfolded monomeric SOD1 are simultaneously observable, the cross-peak intensities of folded monomeric SOD1 decreased faster than those of the unfolded species, and a 3₁₀-helix in folded SOD1 was deformed prior to global unfolding. Furthermore, real-time protein dynamics analysis identified residues involved in the core structure formation of SOD1 oligomers. Our findings provide insight into local and global unfolding events in SOD1 and fibril formation. This Rheo-NMR analysis will be applicable not only to atomic-level monitoring of other amyloidogenic proteins but also to quantification of shear-induced structural changes of non-amyloidogenic proteins and elucidation of shear-enhanced chemical phenomena such as viscosity increase and crystallization of various solution-state compounds.

Polymer Chain Mobility under Shear-A Rheo-NMR Investigation

The local dynamics in polymer melts and the impact of external shear in a Couette geometry have been investigated using rheological nuclear magnetic resonance (NMR). The spin-spin relaxation time, T₂, which is sensitive to chain-segment motion, has been measured as a function of shear rate for two samples of poly(dimethylsiloxane). For the low-molecular-weight sample, a mono-exponential decay is observed, which becomes slightly faster with shear, indicating restrictions of the polymer chain motion. For the high-weight sample, a much faster bi-exponential decay is observed, indicative of entanglements. Both components in this decay become longer with shear. This implies that the free polymer segments between entanglements become effectively longer as a result of shear.

Real-time monitoring of the aggregation of Alzheimer's amyloid-β via1H magic angle spinning NMR spectroscopy

Proton magic-angle-spinning NMR used for real-time analysis of amyloid aggregation reveals that mechanical rotation of Aβ_1-40 monomers increases the rate of formation of aggregates, and that the increasing lag-time with peptide concentration suggests the formation of growth-incompetent species. EGCG's ability to shift off-pathway aggregation is also demonstrated.

Hydrogen-Deuterium Exchange Profiles of Polyubiquitin Fibrils

Ubiquitin and its polymeric forms are conjugated to intracellular proteins to regulate diverse intracellular processes. Intriguingly, polyubiquitin has also been identified as a component of pathological protein aggregates associated with Alzheimer's disease and other neurodegenerative disorders. We recently found that polyubiquitin can form amyloid-like fibrils, and that these fibrillar aggregates can be degraded by macroautophagy. Although the structural properties appear to function in recognition of the fibrils, no structural information on polyubiquitin fibrils has been reported so far. Here, we identify the core of M1-linked diubiquitin fibrils from hydrogen-deuterium exchange experiments using solution nuclear magnetic resonance (NMR) spectroscopy. Intriguingly, intrinsically flexible regions became highly solvent-protected in the fibril structure. These results indicate that polyubiquitin fibrils are formed by inter-molecular interactions between relatively flexible structural components, including the loops and edges of secondary structure elements.

Real-Time Observation of the Interaction between Thioflavin T and an Amyloid Protein by Using High-Sensitivity Rheo-NMR

Amyloid fibril formation is associated with numerous neurodegenerative diseases. To elucidate the mechanism of fibril formation, the thioflavin T (ThT) fluorescence assay is widely used. ThT is a fluorescent dye that selectively binds to amyloid fibrils and exhibits fluorescence enhancement, which enables quantitative analysis of the fibril formation process. However, the detailed binding mechanism has remained unclear. Here we acquire real-time profiles of fibril formation of superoxide dismutase 1 (SOD1) using high-sensitivity Rheo-NMR spectroscopy and detect weak and strong interactions between ThT and SOD1 fibrils in a time-dependent manner. Real-time information on the interaction between ThT and fibrils will contribute to the understanding of the binding mechanism of ThT to fibrils. In addition, our method provides an alternative way to analyze fibril formation.