Self-assembly of toroidal proteins explored using native mass spectrometry

Precision nanoengineering for functional self-assemblies across length scales

As nanotechnology continues to push the boundaries across disciplines, there is an increasing need for engineering nanomaterials with atomic-level precision for self-assembly across length scales, i.e., from the nanoscale to the macroscale. Although molecular self-assembly allows atomic precision, extending it beyond certain length scales presents a challenge. Therefore, the attention has turned to size and shape-controlled metal nanoparticles as building blocks for multifunctional colloidal self-assemblies. However, traditionally, metal nanoparticles suffer from polydispersity, uncontrolled aggregation, and inhomogeneous ligand distribution, resulting in heterogeneous end products. In this feature article, I will discuss how virus capsids provide clues for designing subunit-based, precise, efficient, and error-free self-assembly of colloidal molecules. The atomically precise nanoscale proteinic subunits of capsids display rigidity (conformational and structural) and patchy distribution of interacting sites. Recent experimental evidence suggests that atomically precise noble metal nanoclusters display an anisotropic distribution of ligands and patchy ligand bundles. This enables symmetry breaking, consequently offering a facile route for two-dimensional colloidal crystals, bilayers, and elastic monolayer membranes. Furthermore, inter-nanocluster interactions mediated via the ligand functional groups are versatile, offering routes for discrete supracolloidal capsids, composite cages, toroids, and macroscopic hierarchically porous frameworks. Therefore, engineered nanoparticles with atomically precise structures have the potential to overcome the limitations of molecular self-assembly and large colloidal particles. Self-assembly allows the emergence of new optical properties, mechanical strength, photothermal stability, catalytic efficiency, quantum yield, and biological properties. The self-assembled structures allow reproducible optoelectronic properties, mechanical performance, and accurate sensing. More importantly, the intrinsic properties of individual nanoclusters are retained across length scales. The atomically precise nanoparticles offer enormous potential for next-generation functional materials, optoelectronics, precision sensors, and photonic devices.

Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes

Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.

In situ generation and evolution of polymer toroids by liquid crystallization-assisted seeded dispersion polymerization

An effective method is presented for preparing high solid content azobenzene-containing triblock copolymer toroidal assemblies by liquid crystallization-assisted seeded dispersion polymerization. Vesicles are prepared via polymerization-induced self-assembly (PISA), and used as seeds for further chain extension. By introducing smectic liquid crystalline (LC) ordering into the core-forming block, toroids are formed in situ during the polymerization. The morphological transformation from toroids to barrels is observed under ultraviolet irradiation due to the photo-isomerization of the azobenzene mesogens. This strategy expands the scope of tunable anisotropic morphologies for potential functional nanomaterials based on a LC copolymer by seeded dispersion polymerization.

Probing the mechanism of the peroxiredoxin decamer interaction with its reductase sulfiredoxin from the single molecule to the solution scale

Peroxiredoxins from the Prx1 subfamily (Prx) are highly regulated multifunctional proteins involved in oxidative stress response, redox signaling and cell protection. Prx is a homodimer that associates into a decamer. The monomer C-terminus plays intricate roles in Prx catalytic functions, decamer stability and interaction with its redox partner, the small reductase sulfiredoxin (Srx), that regulates the switching between Prx cellular functions. As only static structures of covalent Prx-Srx complexes have been reported, whether Srx binding dissociates the decameric assembly and how Prx subunit flexibility impacts complex formation are unknown. Here, we assessed the non-covalent interaction mechanism and dynamics in the solution of Saccharomyces cerevisiae Srx with the ten subunits of Prx Tsa1 at the decamer level via a combination of multiscale biophysical approaches including native mass spectrometry. We show that the ten subunits of the decamer can be saturated by ten Srx molecules and that the Tsa1 decamer in complex with Srx does not dissociate in solution. Furthermore, the binding events of atomic force microscopy (AFM) tip-grafted Srx molecules to Tsa1 individual subunits were relevant to the interactions between free molecules in solution. Combined with protein engineering and rapid kinetics, the observation of peculiar AFM force-distance signatures revealed that Tsa1 C-terminus flexibility controls Tsa1/Srx two-step binding and dynamics and determines the force-induced dissociation of Srx from each subunit of the decameric complex in a sequential or concerted mode. This combined approach from the solution to the single-molecule level offers promising prospects for understanding oligomeric protein interactions with their partners.

Fluorescent homopolypeptide toroids

Toroids are important ring-like nanostructures in living systems; intrinsically luminogenic toroids are promising in bioimaging but it is challenging to synthesize such nanoparticles. Herein, we report a fluorescent toroid that...

Ion-dependent slow protein release from in vivo disintegrating micro-granules

Through the controlled addition of divalent cations, polyhistidine-tagged proteins can be clustered in form of chemically pure and mechanically stable micron-scale particles. Under physiological conditions, these materials act as self-disintegrating protein depots for the progressive release of the forming polypeptide, with potential applications in protein drug delivery, diagnosis, or theragnosis. Here we have explored the in vivo disintegration pattern of a set of such depots, upon subcutaneous administration in mice. These microparticles were fabricated with cationic forms of either Zn, Ca, Mg, or Mn, which abound in the mammalian body. By using a CXCR4-targeted fluorescent protein as a reporter building block we categorized those cations regarding their ability to persist in the administration site and to sustain a slow release of functional protein. Ca²⁺ and specially Zn²⁺ have been observed as particularly good promoters of time-prolonged protein leakage. The released polypeptides result is available for selective molecular interactions, such as specific fluorescent labeling of tumor tissues, in which the protein reaches nearly steady levels.

Current status and future prospects for ion-mobility mass spectrometry in the biopharmaceutical industry

Detailed characterization of protein reagents and biopharmaceuticals is key in defining successful drug discovery campaigns, aimed at bringing molecules through different discovery stages up to development and commercialization. There are many challenges in this process, with complex and detailed analyses playing paramount roles in modern industry. Mass spectrometry (MS) has become an essential tool for characterization of proteins ever since the onset of soft ionization techniques and has taken the lead in quality assessment of biopharmaceutical molecules, and protein reagents, used in the drug discovery pipeline. MS use spans from identification of correct sequences, to intact molecule analyses, protein complexes and more recently epitope and paratope identification. MS toolkits could be incredibly diverse and with ever evolving instrumentation, increasingly novel MS-based techniques are becoming indispensable tools in the biopharmaceutical industry. Here we discuss application of Ion Mobility MS (IMMS) in an industrial setting, and what the current applications and outlook are for making IMMS more mainstream.

THE IMS PARADOX: A PERSPECTIVE ON STRUCTURAL ION MOBILITY-MASS SPECTROMETRY

Studies of large proteins, protein complexes, and membrane protein complexes pose new challenges, most notably the need for increased ion mobility (IM) and mass spectrometry (MS) resolution. This review covers evolutionary developments in IM-MS in the authors' and key collaborators' laboratories with specific focus on developments that enhance the utility of IM-MS for structural analysis. IM-MS measurements are performed on gas phase ions, thus "structural IM-MS" appears paradoxical-do gas phase ions retain their solution phase structure? There is growing evidence to support the notion that solution phase structure(s) can be retained by the gas phase ions. It should not go unnoticed that we use "structures" in this statement because an important feature of IM-MS is the ability to deal with conformationally heterogeneous systems, thus providing a direct measure of conformational entropy. The extension of this work to large proteins and protein complexes has motivated our development of Fourier-transform IM-MS instruments, a strategy first described by Hill and coworkers in 1985 (Anal Chem, 1985, 57, pp. 402-406) that has proved to be a game-changer in our quest to merge drift tube (DT) and ion mobility and the high mass resolution orbitrap MS instruments. DT-IMS is the only method that allows first-principles determinations of rotationally averaged collision cross sections (CSS), which is essential for studies of biomolecules where the conformational diversities of the molecule precludes the use of CCS calibration approaches. The Fourier transform-IM-orbitrap instrument described here also incorporates the full suite of native MS/IM-MS capabilities that are currently employed in the most advanced native MS/IM-MS instruments. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Peroxiredoxins wear many hats: Factors that fashion their peroxide sensing personalities

Peroxiredoxins (Prdxs) sense and assess peroxide levels, and signal through protein interactions. Understanding the role of the multiple structural and post-translational modification (PTM) layers that tunes the peroxiredoxin specificities is still a challenge. In this review, we give a tabulated overview on what is known about human and bacterial peroxiredoxins with a focus on structure, PTMs, and protein-protein interactions. Armed with numerous cellular and atomic level experimental techniques, we look at the future and ask ourselves what is still needed to give us a clearer view on the cellular operating power of Prdxs in both stress and non-stress conditions.

Taking Advantage of the Morpheein Behavior of Peroxiredoxin in Bionanotechnology

Morpheeins are proteins that reversibly assemble into different oligomers, whose architectures are governed by conformational changes of the subunits. This property could be utilized in bionanotechnology where the building of nanometric and new high-ordered structures is required. By capitalizing on the adaptability of morpheeins to create patterned structures and exploiting their inborn affinity toward inorganic and living matter, “bottom-up” creation of nanostructures could be achieved using a single protein building block, which may be useful as such or as scaffolds for more complex materials. Peroxiredoxins represent the paradigm of a morpheein that can be applied to bionanotechnology. This review describes the structural and functional transitions that peroxiredoxins undergo to form high-order oligomers, e.g., rings, tubes, particles, and catenanes, and reports on the chemical and genetic engineering approaches to employ them in the generation of responsive nanostructures and nanodevices. The usefulness of the morpheeins’ behavior is emphasized, supporting their use in future applications.

Rapid 3-dimensional shape determination of globular proteins by mobility capillary electrophoresis and native mass spectrometry

Established high-throughput proteomics methods provide limited information on the stereostructures of proteins. Traditional technologies for protein structure determination typically require laborious steps and cannot be performed in a high-throughput fashion. Here, we report a new medium throughput method by combining mobility capillary electrophoresis (MCE) and native mass spectrometry (MS) for the 3-dimensional (3D) shape determination of globular proteins in the liquid phase, which provides both the geometric structure and molecular mass information of proteins. A theory was established to correlate the ion hydrodynamic radius and charge state distribution in the native mass spectrum with protein geometrical parameters, through which a low-resolution structure (shape) of the protein could be determined. Our test data of 11 different globular proteins showed that this approach allows us to determine the shapes of individual proteins, protein complexes and proteins in a mixture, and to monitor protein conformational changes. Besides providing complementary protein structure information and having mixture analysis capability, this MCE and native MS based method is fast in speed and low in sample consumption, making it potentially applicable in top–down proteomics and structural biology for intact globular protein or protein complex analysis.

Using native mass spectrometry and mobility capillary electrophoresis, the ellipsoid dimensions of globular proteins or protein complexes could be measured efficiently.

Switching between Stacked Toroids and Helical Supramolecular Polymers in Aqueous Nanotubules

Although significant advances have been made in supramolecular tubules, reversible polymerization in the tubular walls while maintaining their intact structure remains a great challenge. Here, reversible helical supramolecular polymerization of stacked toroids is reported, while maintaining tubular structures in aqueous solution. At room temperature, the tubules consist of discrete toroid stackings with hydrophobic interior. Upon heating, the tubules based on toroid stackings undergo a reversible helical supramolecular polymerization to transform into helical tubules by interconnecting between spirally open toroids. The helical polymerization arises from a tilting transition of the closed toroids that transform into spirally open toroids driven by the thermal dehydration of a hydrophilic oligoether dendron surrounding the toroid frameworks.

Structural Analysis of the Effect of a Dual-FLAG Tag on Transthyretin

Recombinant proteins have increased our knowledge regarding the physiological role of proteins; however, affinity purification tags are often not cleaved prior to analysis, and their effects on protein structure, stability and assembly are often overlooked. In this study, the stabilizing effects of an N-terminus dual-FLAG (FT2) tag fusion to transthyretin (TTR), a construct used in previous studies, are investigated using native ion mobility-mass spectrometry (IM-MS). A combination of collision-induced unfolding and variable-temperature electrospray ionization is used to compare gas- and solution-phase stabilities of FT2-TTR to wild-type and C-terminal tagged TTR. Despite an increased stability of both gas- and solution-phase FT2-TTR, thermal degradation of FT2-TTR was observed at elevated temperatures, viz., backbone cleavage occurring between Lys9 and Cys10. This cleavage reaction is consistent with previously reported metalloprotease activity of TTR [Liz et al. 2009] and is suppressed by either metal chelation or excess zinc. This study brings to the fore the effect of affinity tag stabilization of TTR and emphasizes unprecedented detail afforded by native IM-MS to assess structural discrepancies of recombinant proteins from their wild-type counterparts.

Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding

Toroidal proteins serve as molecular machines and play crucial roles in biological processes such as DNA replication and RNA transcription. Despite progress in the structural characterization of several toroidal proteins, we still lack a mechanistic understanding of the significance of their architecture, oligomerization states, and intermolecular interactions in defining their biological function. In this work, we analyze the collective dynamics of toroidal proteins with different oligomerization states, namely, dimeric and trimeric DNA sliding clamps, nucleocapsid proteins (4-, 5-, and 6-mers) and Trp RNA-binding attenuation proteins (11- and 12-mers). We observe common global modes, among which cooperative rolling stands out as a mechanism enabling DNA processivity, and clamshell motions as those underlying the opening/closure of the sliding clamps. Alterations in global dynamics due to complexation with DNA or the clamp loader are shown to assist in enhancing motions to enable robust function. The analysis provides new insights into the differentiation and enhancement of functional motions upon intersubunit and intermolecular interactions.

Facile Improvement of Negative Ion Mode Electrospray Ionization Using Capillary Vibrating Sharp-Edge Spray Ionization

Electrospray ionization (ESI) is often affected by corona discharge when spraying 100% aqueous solutions as the voltage that induces discharge can be well below the onset voltage of ESI. As a result, it is especially challenging to perform native mass spectrometry in negative ion mode where 100% aqueous solution is preferred. Here we report a simple instrumentation method to improve the performance of ESI in negative ion mode based on capillary vibrating sharp-edge spray ionization. By attaching a fused silica capillary emitter to a vibrating glass slide, improved signal quality is achieved for various analytes in aqueous solutions over applying ESI alone. Compared to commercial ESI sources using nebulization gas to reduce discharge, 10-100-fold enhancement in signal intensity and 3-10-fold improvement in S/N are achieved for various kinds of molecules including DNA, peptides, proteins, and oligosaccharides. Finally, the new method demonstrates utility for native mass spectrometry analysis of proteins and G-quadruplex DNA. The present method is expected to have great potential to be adopted by the scientific community because of its improved analytical performance, simplicity, and low cost.

Introduction to Protein Nanotechnology

Protein nanotechnology research is at the intersection of protein biology and nanotechnology. Protein molecules are repurposed as nanostructures and nanoscaffolds, and nanoscale tools are used to investigate protein assembly and function. In this chapter, a select review is given of some of the recent examples of protein nanostructures, covering both those directly borrowed from biology and those designed for use in nanotechnology. It updates the introductory chapter to Edition 2 of this volume to reflect significant progress in this field. Some strategies to incorporate protein structures into devices are also covered, with the successes and challenges of this interdisciplinary field identified. This provides an overarching framework for the rest of the volume, which details the case studies of some of the protein building blocks that have been designed and produced, along with tips and tools for their incorporation into devices and making functional measurements.

Peroxiredoxin Proteins as Building Blocks for Nanotechnology

Peroxiredoxins are ubiquitous antioxidant proteins that exhibit a striking variety of quaternary structures, making them appealing building blocks with which nanoscale architectures are created for applications in nanotechnology. The solution environment of the protein, as well as protein sequence, influences the presentation of a particular structure, thereby enabling mesoscopic manipulations that affect arrangments at the nanoscale. This chapter will equip us with the knowledge necessary to not only produce and manipulate peroxiredoxin proteins into desired structures but also to characterize the different structures using dynamic light scattering, analytical centrifugation, and negative stain transmission electron microscopy, thereby setting the stage for us to use these proteins for applications in nanotechnology.

Structure and effective charge characterization of proteins by a mobility capillary electrophoresis based method

Measuring the conformations and effective charges of proteins in solution is critical for investigating protein bioactivity, but their rapid analysis remains a challenging problem. Here we report a mobility capillary electrophoresis (MCE) based method for the rapid analysis of protein stereo-structures and effective charges in different solution environments. With the capability of mixture separation, MCE measures the hydrodynamic radius of a protein through Taylor dispersion analysis and its effective charge through ion mobility analysis. The experimental results acquired from MCE are then utilized to restrain molecular dynamics simulations, so that the most probable conformation of that protein can be obtained. As proof-of-concept demonstrations, the charge states and structures of five proteins were analyzed under close to native environments. The conformation transitions and charge state variations of bovine serum albumin and lysozyme under different pH conditions were also investigated. This method is promising for high-throughput protein analysis, which could potentially be coupled with mass spectrometry for investigating protein stereo-structures and functions in top-down proteomics.

Integrated Use of Biochemical, Native Mass Spectrometry, Computational, and Genome-Editing Methods to Elucidate the Mechanism of a Salmonella deglycase

Salmonellais a foodborne pathogen that causes annually millions of cases of salmonellosis globally, yet Salmonella-specific antibacterials are not available. During inflammation, Salmonella utilizes the Amadori compound fructose-asparagine (F-Asn) as a nutrient through the successive action of three enzymes, including the terminal FraB deglycase. Salmonella mutants lacking FraB are highly attenuated in mouse models of inflammation due to the toxic build-up of the substrate 6-phosphofructose-aspartate (6-P-F-Asp). This toxicity makes Salmonella FraB an appealing drug target, but there is currently little experimental information about its catalytic mechanism. Therefore, we sought to test our postulated mechanism for the FraB-catalyzed deglycation of 6-P-F-Asp (via an enaminol intermediate) to glucose-6-phosphate and aspartate. A FraB homodimer model generated by RosettaCM was used to build substrate-docked structures that, coupled with sequence alignment of FraB homologs, helped map a putative active site. Five candidate active-site residues-including three expected to participate in substrate binding-were mutated individually and characterized. Native mass spectrometry and ion mobility were used to assess collision cross sections and confirm that the quaternary structure of the mutants mirrored the wild type, and that there are two active sites/homodimer. Our biochemical studies revealed that FraB Glu214Ala, Glu214Asp, and His230Ala were inactive in vitro, consistent with deprotonated-Glu214 and protonated-His230 serving as a general base and a general acid, respectively. Glu214Ala or His230Ala introduced into the Salmonella chromosome by CRISPR/Cas9-mediated genome editing abolished growth on F-Asn. Results from our computational and experimental approaches shed light on the catalytic mechanism of Salmonella FraB and of phosphosugar deglycases in general.

Confinement Assembly of ABC Triblock Terpolymers for the High-Yield Synthesis of Janus Nanorings

Block copolymers are versatile building blocks for the self-assembly of functional nanostructures in bulk and solution. While spheres, cylinders, and bilayer sheets are thermodynamically preferred shapes and frequently observed, ring-shaped nanoparticles are more challenging to realize due to energetic penalties that originate from their anisotropic curvature. Today, a handful of concepts exist that produce core-shell nanorings, while more complex ( e. g., patchy) nanorings are currently out of reach and have only been predicted theoretically. Here, we demonstrate that confinement assembly of properly designed ABC triblock terpolymers is a general route to synthesize Janus nanorings in high purity. The triblock terpolymer self-assembles in the spherical confinement of nanoemulsion droplets into prolate ellipsoidal microparticles with an axially stacked lamellar-ring ( lr)-morphology. We clarified and visualized this complex, yet well-ordered, morphology with transmission electron tomography. Blocks A and C formed stacks of lamellae with the B microdomain sandwiched in-between as nanorings. Cross-linking of the B-rings allowed disassembly of the microparticles into Janus nanorings carrying two strictly separated polymer brushes of A and C on the top and bottom. Decreasing the B volume leads to Janus spheres and rods, while an increase of B results in perforated and filled Janus disks. The confinement assembly of ABC triblock terpolymers is a general process that can be extended to other block chemistries and will allow to synthesize a large variety of complex micro- and nanoparticles that inspire studies in self-assembly, interfacial stabilization, colloidal packing, and nanomedicine.

Engineering peroxiredoxin 3 to facilitate control over self-assembly

Oligomeric proteins are abundant in nature and are useful for a range of nanotechnological applications; however, a key requirement in using these proteins is controlling when and how they form oligomeric assemblies. Often, protein oligomerisation is triggered by various cellular signals, allowing for controllable oligomerisation. An example of this is human peroxiredoxin 3 (Prx), a stable protein that natively forms dimers, dodecameric rings, stacks, and tubes in response to a range of environmental stimuli. Although we know the key environmental stimuli for switching between different oligomeric states of Prx, we still have limited molecular knowledge and control over the formation and size of the protein's stacks and tubes. Here, we have generated a range of Prx mutants with either a decreased or knocked out ability to stack, and used both imaging and solution studies to show that Prx stacks through electrostatic interactions that are stabilised by a hydrogen bonding network. Furthermore, we show that altering the length of the polyhistidine tag will alter the length of the Prx stacks, with longer polyhistidine tags giving longer stacks. Finally, we have analysed the effect a variety of heavy metals have on the oligomeric state of Prx, wherein small transition metals like nickel enhances Prx stacking, while larger positively charged metals like tungstate ions can prevent Prx stacking. This work provides further structural characterisation of Prx, to enhance its use as a platform from which to build protein nanostructures for a variety of applications.