Direct observation of the molecular mechanism underlying protein polymerization

Charge Detection Mass Spectrometry Reveals Conformational Heterogeneity in Megadalton-Sized Monoclonal Antibody Aggregates

Aggregation of protein-based therapeutics can occur during development, production, or storage and can lead to loss of efficacy and potential toxicity. Native mass spectrometry of a covalently linked pentameric monoclonal antibody complex with a mass of ∼800 kDa reveals several distinct conformations, smaller complexes, and abundant higher-order aggregates of the pentameric species. Charge detection mass spectrometry (CDMS) reveals individual oligomers up to the pentamer mAb trimer (15 individual mAb molecules; ∼2.4 MDa) whereas intermediate aggregates composed of 6-9 mAb molecules and aggregates larger than the pentameric dimer (1.6 MDa) were not detected/resolved by standard mass spectrometry, size exclusion chromatography (SEC), capillary electrophoresis (CE-SDS), or by mass photometry. Conventional quadrupole time-of-flight mass spectrometry (QTOF MS), mass photometry, SEC, and CE-SDS did not resolve partially or more fully unfolded conformations of each oligomer that were readily identified using CDMS by their significantly higher extents of charging. Trends in the charge-state distributions of individual oligomers provides detailed insight into how the structures of compact and elongated mAb aggregates change as a function of aggregate size. These results demonstrate the advantages of CDMS for obtaining accurate masses and information about the conformations of large antibody aggregates despite extensive overlapping m/z values. These results open up the ability to investigate structural changes that occur in small, soluble oligomers during the earliest stages of aggregation for antibodies or other proteins.

Assessing nanobody interaction with SARS-CoV-2 Nsp9

The interaction between SARS-CoV-2 non-structural protein Nsp9 and the nanobody 2NSP90 was investigated by NMR spectroscopy using the paramagnetic perturbation methodology PENELOP (Paramagnetic Equilibrium vs Nonequilibrium magnetization Enhancement or LOss Perturbation). The Nsp9 monomer is an essential component of the replication and transcription complex (RTC) that reproduces the viral gRNA for subsequent propagation. Therefore preventing Nsp9 recruitment in RTC would represent an efficient antiviral strategy that could be applied to different coronaviruses, given the Nsp9 relative invariance. The NMR results were consistent with a previous characterization suggesting a 4:4 Nsp9-to-nanobody stoichiometry with the occurrence of two epitope pairs on each of the Nsp9 units that establish the inter-dimer contacts of Nsp9 tetramer. The oligomerization state of Nsp9 was also analyzed by molecular dynamics simulations and both dimers and tetramers resulted plausible. A different distribution of the mapped epitopes on the tetramer surface with respect to the former 4:4 complex could also be possible, as well as different stoichiometries of the Nsp9-nanobody assemblies such as the 2:2 stoichiometry suggested by the recent crystal structure of the Nsp9 complex with 2NSP23 (PDB ID: 8dqu), a nanobody exhibiting essentially the same affinity as 2NSP90. The experimental NMR evidence, however, ruled out the occurrence in liquid state of the relevant Nsp9 conformational change observed in the same crystal structure.

Electrophoretic Deposition Interferometric Scattering Mass Photometry

Interferometric scattering microscopy (iSCAT) has rapidly developed as a quantitative tool for the label-free detection of single macromolecules and nanoparticles. In practice, this measurement records the interferometric scattering signal of individual nanoparticles in solution as they land and stick on a coverslip, exhibiting an intensity that varies linearly with particle volume and an adsorption rate that reflects the solution-phase transport kinetics of the system. Together, such measurements provide a multidimensional gauge of the particle size and concentration in solution over time. However, the landing kinetics of particles in solution also manifest a measurement frequency limitation imposed by the slow long-range mobility of particle diffusion to the measurement interface. Here we introduce an effective means to overcome the inherent diffusion-controlled sampling limitation of spontaneous mass photometry. We term this methodology electrophoretic deposition interferometric scattering microscopy (EPD-iSCAT). This approach uses a coverslip supporting a conductive thin film of indium tin oxide (ITO). Charging this ITO film to a potential of around +1 V electrophoretically draws charged nanoparticles from solution and binds them in the focal plane of the microscope. Regulating this potential offers a direct means of controlling particle deposition. Thus, we find for a 0.1 nM solution of 50 nm polystyrene nanoparticles that the application of +1 V to an EPD-iSCAT coverslip assembly drives an electrophoretic deposition rate constant of 1.7 s-1 μm-2 nM-1. Removal of the potential causes deposition to cease. This user control of EPD-iSCAT affords a means to apply single-molecule mass photometry to monitor long-term changes in solution, owing to slow kinetic processes. In contrast with conventional coverslips chemically derivatized with charged thin films, EPD-iSCAT maintains a deposition rate that varies linearly with the bulk concentration.

Cascaded momentum-space polarization filters enabled label-free black-field microscopy for single nanoparticles analysis

Label-free optical imaging of single-nanometer-scale matter is extremely important for a variety of biomedical, physical, and chemical investigations. One central challenge is that the background intensity is much stronger than the intensity of the scattering light from single nano-objects. Here, we propose an optical module comprising cascaded momentum-space polarization filters that can perform vector field modulation to block most of the background field and result in an almost black background; in contrast, only a small proportion of the scattering field is blocked, leading to obvious imaging contrast enhancement. This module can be installed in various optical microscopies to realize a black-field microscopy. Various single nano-objects with dimensions smaller than 20 nm appear distinctly in the black-field images. The chemical reactions occurring on single nanocrystals with edge lengths of approximately 10 nm are in situ real-time monitored by using the black-field microscopy. This label-free black-field microscopy is highly promising for a wide range of future multidisciplinary science applications.

Label-Free Imaging of DNA Interactions with 2D Materials

Two-dimensional (2D) materials offer potential as substrates for biosensing devices, as their properties can be engineered to tune interactions between the surface and biomolecules. Yet, not many methods can measure these interactions in a liquid environment without introducing labeling agents such as fluorophores. In this work, we harness interferometric scattering (iSCAT) microscopy, a label-free imaging technique, to investigate the interactions of single molecules of long dsDNA with 2D materials. The millisecond temporal resolution of iSCAT allows us to capture the transient interactions and to observe the dynamics of unlabeled DNA binding to a hexagonal boron nitride (hBN) surface in solution for extended periods (including a fraction of 10%, of trajectories lasting longer than 110 ms). Using a focused ion beam technique to engineer defects, we find that DNA binding affinity is enhanced at defects; when exposed to long lanes, DNA binds preferentially at the lane edges. Overall, we demonstrate that iSCAT imaging is a useful tool to study how biomolecules interact with 2D materials, a key component in engineering future biosensors.

Comparing brute force to transition path sampling for gas hydrate nucleation with a flat interface: comments on time reversal symmetry

Fluid to solid nucleation is often investigated with the rare event method transition path sampling (TPS). I claim that the inherent irreversibility of solid nucleation, even at stationary conditions, calls into question TPS's applicability for determining solid nucleation mechanisms, especially for pre-critical behavior. Even when applied to a phenomenon which displays time reversal asymmetry like solid nucleation, TPS is a good means of exploring phase space and giving trends in post-critical structure, and its ability to facilitate nucleation rate and free energy calculations remains outstanding. Forward-only splitting and ratcheting methods such as forward flux sampling are more attractive for understanding nucleation mechanisms as they do not require time reversal symmetry, but at low driving forces may suffer from the same limitations as brute force: they may never make it to the first ratchet. Here I briefly summarize the TPS method and gas hydrate nucleation simulation literature, focusing on topics within both to facilitate a comparison of brute force hydrate nucleation to transition path sampling of hydrate nucleation. Perhaps anecdotally, the brute force technique results in more crystalline trajectories despite having higher driving forces than TPS. I maintain this difference is because of the inherent irreversibility of hydrate nucleation, meaning its pre-critical behavior cannot accurately be determined by the melting trajectories that comprise approximately half of the configurations in TPS's path ensemble.

Mass photometric detection and quantification of nanoscale α-synuclein phase separation

Protein liquid-liquid phase separation can lead to disease-related amyloid fibril formation. The mechanisms of conversion of monomeric protein into condensate droplets and of the latter into fibrils remain elusive. Here, using mass photometry, we demonstrate that the Parkinson's disease-related protein, α-synuclein, can form dynamic nanoscale clusters at physiologically relevant, sub-saturated concentrations. Nanoclusters nucleate in bulk solution and promote amyloid fibril formation of the dilute-phase monomers upon ageing. Their formation is instantaneous, even under conditions where macroscopic assemblies appear only after several days. The slow growth of the nanoclusters can be attributed to a kinetic barrier, probably due to an interfacial penalty from the charged C terminus of α-synuclein. Our findings reveal that α-synuclein phase separation occurs at much wider ranges of solution conditions than reported so far. Importantly, we establish mass photometry as a promising methodology to detect and quantify nanoscale precursors of phase separation. We also demonstrate its general applicability by probing the existence of nanoclusters of a non-amyloidogenic protein, Ddx4n1.

Effect of temperature and nucleotide on the binding of BiP chaperone to a protein substrate

BiP (immunoglobulin heavy-chain binding protein) is a Hsp70 monomeric ATPase motor that plays broad and crucial roles in maintaining proteostasis inside the cell. Structurally, BiP is formed by two domains, a nucleotide-binding domain (NBD) with ATPase activity connected by a flexible hydrophobic linker to the substrate-binding domain. While the ATPase and substrate binding activities of BiP are allosterically coupled, the latter is also dependent on nucleotide binding. Recent structural studies have provided new insights into BiP's allostery; however, the influence of temperature on the coupling between substrate and nucleotide binding to BiP remains unexplored. Here, we study BiP's binding to its substrate at the single molecule level using thermo-regulated optical tweezers which allows us to mechanically unfold the client protein and explore the effect of temperature and different nucleotides on BiP binding. Our results confirm that the affinity of BiP for its protein substrate relies on nucleotide binding, by mainly regulating the binding kinetics between BiP and its substrate. Interestingly, our findings also showed that the apparent affinity of BiP for its protein substrate in the presence of nucleotides remains invariable over a wide range of temperatures, suggesting that BiP may interact with its client proteins with similar affinities even when the temperature is not optimal. Thus, BiP could play a role as a "thermal buffer" in proteostasis.