Optical trapping with high forces reveals unexpected behaviors of prion fibrils

Full-colour Jabuticaba-like nanostructures via the multiplex and orthogonal self-assembly of protein-conjugated quantum dots with engineered biofilms

The integration of inorganic components with bacterial biofilms is of great significance for expanding the functionality of artificial biological materials. However, so far, the complexities and functionalities of biofilm-based scaffolds assembled via metal-peptide coordination chemistries remain limited. Here, we present a platform for the multiplexed and specific coupling of recombinant protein-functionalized fluorescent red-green-blue (RGB) quantum dots (QDs) with engineered biofilms to form Jabuticaba-like nanostructures. Full-color living Jabuticaba-like nanostructures have been achieved through the interaction of extracellular peptides that are fabricated by biofilms with the proteins that modify the surface of the RGB QDs through orthogonal SpyTag/SpyCatcher, IsopeptagN/PilinN, and IsopeptagC/PilinC pairs. We envision that living cell populations will enable the multiplexable, scalable and bottom-up assembly of versatile materials that integrate both abiotic and biotic components into multifunctional systems.

Understanding the mechanism of amylin aggregation: From identifying crucial segments to tracing dominant sequential events to modeling potential aggregation suppressors

One of the most abundant, prevailing, and life-threatening human diseases that are currently baffling the scientific community is type 2 diabetes (T2D). The self-association of human amylin has been implicated in the pathogenesis of T2D, though with an inconclusive understanding of the mechanism. Hence, we focused on the characterization of the conformational ensembles of all the species that are believed to define the structural polymorphism of the aggregation process - the functional monomeric, the initially self-associated oligomeric, and the structured protofibril - by employing near-equilibrium, non-equilibrium, and equilibrium atomistic simulations on the sporadic, two familial variants (S20G and G33R), and their proline-substituted forms (S20P and G33P). The dynamic near-equilibrium assays hint toward - the abundance of helical conformation in the monomeric state, the retainment of the helicity in the initial self-associated oligomeric phase pointing toward the existence of the helix-helix association mechanism, the difference in preference of specific segments to have definite secondary structural features, the phase-dependent variability in the dominance of specific segments and mutation sites, and the simultaneous presence of generic and unique features among various sequences. Furthermore, the non-equilibrium pulling assays exemplify a generic sequential unzipping mechanism of the protofibrils, however, the sequence-dependent uniqueness comes from the difference in location and magnitude of the control of a specific terminus. Importantly, the equilibrium thermodynamic assays efficiently rank order the potential of aggregability among sequences and consequently suggests the probability of designing effective aggregation suppressors against sporadic and familial amylin variants incorporating proline as the mutation.

Myosin II Adjusts Motility Properties and Regulates Force Production Based on Motor Environment

Introduction

Myosin II has been investigated with optical trapping, but single motor-filament assay arrangements are not reflective of the complex cellular environment. To understand how myosin interactions propagate up in scale to accomplish system force generation, we devised a novel actomyosin ensemble optical trapping assay that reflects the hierarchy and compliancy of a physiological environment and is modular for interrogating force effectors.

Methods

Hierarchical actomyosin bundles were formed in vitro. Fluorescent template and cargo actin filaments (AF) were assembled in a flow cell and bundled by myosin. Beads were added in the presence of ATP to bind the cargo AF and activate myosin force generation to be measured by optical tweezers.

Results

Three force profiles resulted across a range of myosin concentrations: high force with a ramp-plateau, moderate force with sawtooth movement, and baseline. The three force profiles, as well as high force output, were recovered even at low solution concentration, suggesting that myosins self-optimize within AFs. Individual myosin steps were detected in the ensemble traces, indicating motors are taking one step at a time while others remain engaged in order to sustain productive force generation.

Conclusions

Motor communication and system compliancy are significant contributors to force output. Environmental conditions, motors taking individual steps to sustain force, the ability to backslip, and non-linear concentration dependence of force indicate that the actomyosin system contains a force-feedback mechanism that senses the local cytoskeletal environment and communicates to the individual motors whether to be in a high or low duty ratio mode.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12195-022-00731-1.

Stability matters, too - the thermodynamics of amyloid fibril formation

Amyloid fibrils are supramolecular homopolymers of proteins that play important roles in biological functions and disease. These objects have received an exponential increase in attention during the last few decades, due to their role in the aetiology of a range of severe disorders, most notably some of a neurodegenerative nature. While an overwhelming number of experimental studies exist that investigate how, and how fast, amyloid fibrils form and how their formation can be inhibited, a much more limited body of experimental work attempts to answer the question as to why these types of structures form (i.e. the thermodynamic driving force) and how stable they actually are. In this review, I attempt to give an overview of the types of experiments that have been performed to-date to answer these questions, and to summarise our current understanding of amyloid thermodynamics.

Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives

In neurodegenerative diseases, a wide range of amyloid proteins or peptides such as amyloid-beta and α-synuclein fail to keep native functional conformations, followed by misfolding and self-assembling into a diverse array of aggregates. The aggregates further exert toxicity leading to the dysfunction, degeneration and loss of cells in the affected organs. Due to the disordered structure of the amyloid proteins, endogenous molecules, such as lipids, are prone to interact with amyloid proteins at a low concentration and influence amyloid cytotoxicity. The heterogeneity of amyloid proteinscomplicates the understanding of the amyloid cytotoxicity when relying only on conventional bulk and ensemble techniques. As complementary tools, single-molecule techniques (SMTs) provide novel insights into the different subpopulations of a heterogeneous amyloid mixture as well as the cytotoxicity, in particular as involved in lipid membranes. This review focuses on the recent advances of a series of SMTs, including single-molecule fluorescence imaging, single-molecule force spectroscopy and single-nanopore electrical recording, for the understanding of the amyloid molecular mechanism. The working principles, benefits and limitations of each technique are discussed and compared in amyloid protein related studies.. We also discuss why SMTs show great potential and are worthy of further investigation with feasibility studies as diagnostic tools of neurodegenerative diseases and which limitations are to be addressed.

Extracellular protein isolation from the matrix of anammox biofilm using ionic liquid extraction

Anaerobic ammonium oxidation (anammox)-performing bacteria self-assemble into compact biofilms by expressing extracellular polymeric substances (EPS). Anammox EPS are poorly characterized, largely due to their low solubility in typical aqueous solvents. Pronase digestion achieved 19.5 ± 0.9 and 41.4 ± 1.4% (w/w) more solubilization of laboratory enriched Candidatus Brocadia sinica anammox granules than DNase and amylase, respectively. Nuclear magnetic resonance profiling of the granules confirmed proteins as dominant biopolymer within the EPS. Ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate and N,N-dimethylacetamide (EMIM-Ac/DMAc) mixture was applied to extract the major structural proteins. Further treatment by anion exchange chromatography isolated homologous serine (S)- and threonine (T)-rich proteins BROSI_A1236 and UZ01_01563, which were major components of the extracted proteins, and sequentially highly similar to putative anammox extracellular proteins KUSTD1514 and WP_070066018.1 of Ca. Kuenenia stuttgartiensis and Ca. Brocadia sapporoensis, respectively. Six monosaccharides (i.e., arabinose, xylose, rhamnose, fucose, galactose, and mannose) were enriched for BROSI_A1236 against all other major proteins. The sugars, however, contributed < 0.5% (w/w) of total granular biomass and were likely co-enriched as glycoprotein appendages. This study demonstrates that BROSI_A1236 is a major extracellular component of Ca. B. sinica anammox biofilms that is likely a common anammox extracellular polymer, and can be isolated from the matrix following ionic liquid extraction.

Elucidating optical field directed hierarchical self-assembly of homogenous versus heterogeneous nanoclusters with femtosecond optical tweezers

Insights into the morphology of nanoclusters would facilitate the design of nano-devices with improved optical, electrical, and magnetic responses. We have utilized optical gradient forces for the directed self-assembly of colloidal clusters using high-repetition-rate femtosecond laser pulses to delineate their structure and dynamics. We have ratified our experiments with theoretical models derived from the Langevin equation and defined the valid ranges of applicability. Our femtosecond optical tweezer-based technique characterizes the in-situ formation of hierarchical self-assembled clusters of homomers as well as heteromers by analyzing the back focal plane displacement signal. This technique is able to efficiently distinguish between nano-particles in heterogeneous clusters and is in accordance with our theory. Herein, we report results from our technique, and also develop a model to describe the mechanism of such processes where corner frequency changes. We show how the corner frequency changes enables us to recognize the structure and dynamics of the coagulation of colloidal homogeneous and heterogeneous clusters in condensed media over a broad range of nanoparticle sizes. The methods described here are advantageous, as the backscatter position-sensitive detection probes the in-situ self-assembly process while other light scattering approaches are leveraged for the characterization of isolated clusters.

Amyloid fibrils embodying distinctive yeast prion phenotypes exhibit diverse morphologies

Yeast prions are self-templating protein-based mechanisms of inheritance whose conformational changes lead to the acquisition of diverse new phenotypes. The best studied of these is the prion domain (NM) of Sup35, which forms an amyloid that can adopt several distinct conformations (strains) that confer distinct phenotypes when introduced into cells that do not carry the prion. Here, we investigate the structure of NM fibrils templated into the prion conformation with cellular lysates. Our electron microscopy studies reveal that NM fibrils that confer either a strong or a weak prion phenotype are both mixtures of thin and thick fibrils that result from differences in packing of the M domain. Strong NM fibrils have more thin fibrils and weak NM fibrils have more thick fibrils. Interestingly, both mass per length and solid state NMR reveal that the thin and thick fibrils have different underlying molecular structures in the prion strain variants that do not interconvert.

Correlation between the hierarchical structures and nanomechanical properties of amyloid fibrils

Amyloid fibrils have recently been highlighted due to their excellent mechanical properties, which not only play a role in their biological functions but also imply their applications in biomimetic material design. Despite recent efforts to unveil how the excellent mechanical properties of amyloid fibrils originate, it has remained elusive how the anisotropic nanomechanical properties of hierarchically structured amyloid fibrils are determined. Here, we characterize the anisotropic nanomechanical properties of hierarchically structured amyloid fibrils using atomic force microscopy experiments and atomistic simulations. It is shown that the hierarchical structure of amyloid fibrils plays a crucial role in determining their radial elastic property but does not make any effect on their bending elastic property. This is attributed to the role of intermolecular force acting between the filaments (constituting the fibril) on the radial elastic modulus of amyloid fibrils. Our finding illustrates how the hierarchical structure of amyloid fibrils encodes their anisotropic nanomechanical properties. Our study provides key design principles of amyloid fibrils, which endow valuable insight into the underlying mechanisms of amyloid mechanics.

Specification of Physiologic and Disease States by Distinct Proteins and Protein Conformations

Protein conformational states-from intrinsically disordered ensembles to amyloids that underlie the self-templating, infectious properties of prion-like proteins-have attracted much attention. Here, we highlight the diversity, including differences in biophysical properties, that drive distinct biological functions and pathologies among self-templating proteins. Advances in chemical genomics, gene editing, and model systems now permit deconstruction of the complex interplay between these protein states and the host factors that react to them. These methods reveal that conformational switches modulate normal and abnormal information transfer and that intimate relationships exist between the intrinsic function of proteins and the deleterious consequences of their misfolding.

Mechanical Deformation Mechanisms and Properties of Prion Fibrils Probed by Atomistic Simulations

Prion fibrils, which are a hallmark for neurodegenerative diseases, have recently been found to exhibit the structural diversity that governs disease pathology. Despite our recent finding concerning the role of the disease-specific structure of prion fibrils in determining their elastic properties, the mechanical deformation mechanisms and fracture properties of prion fibrils depending on their structures have not been fully characterized. In this work, we have studied the tensile deformation mechanisms of prion and non-prion amyloid fibrils by using steered molecular dynamics simulations. Our simulation results show that the elastic modulus of prion fibril, which is formed based on left-handed β-helical structure, is larger than that of non-prion fibril constructed based on right-handed β-helix. However, the mechanical toughness of prion fibril is found to be less than that of non-prion fibril, which indicates that infectious prion fibril is more fragile than non-infectious (non-prion) fibril. Our study sheds light on the role of the helical structure of amyloid fibrils, which is related to prion infectivity, in determining their mechanical deformation mechanisms and properties.

Trapping and manipulation of nanoparticles using multifocal optical vortex metalens

Optical trapping and manipulation have emerged as a powerful tool in the biological and physical sciences. In this work, we present a miniature optical tweezers device based on multifocal optical vortex metalens (MOVM). The MOVM is capable of generating multiple focal fields with specific orbital angular momentum at arbitrary position. The optical force of the vortex field exerted on both high-refractive-index particle and low-refractive-index particle are analyzed. The simulation results show that the two kinds of dielectric particles can be trapped simultaneously. Besides, it is also feasible to manipulate plasmonic nanoparticles even under the resonant condition, which is realized by constructing a 4Pi focusing system with metalenses. Moreover, the metalens can be made into an array format that is suitable for trapping and manipulating various nanoparticles with diverse motion behaviors. The work illustrates the potential of such optical tweezers for further development in lab-on-a-chip devices, and may open up new avenues for optical manipulation and their applications in extensive scientific fields.

A dominant-negative mutant inhibits multiple prion variants through a common mechanism

Prions adopt alternative, self-replicating protein conformations and thereby determine novel phenotypes that are often irreversible. Nevertheless, dominant-negative prion mutants can revert phenotypes associated with some conformations. These observations suggest that, while intervention is possible, distinct inhibitors must be developed to overcome the conformational plasticity of prions. To understand the basis of this specificity, we determined the impact of the G58D mutant of the Sup35 prion on three of its conformational variants, which form amyloids in S. cerevisiae. G58D had been previously proposed to have unique effects on these variants, but our studies suggest a common mechanism. All variants, including those reported to be resistant, are inhibited by G58D but at distinct doses. G58D lowers the kinetic stability of the associated amyloid, enhancing its fragmentation by molecular chaperones, promoting Sup35 resolubilization, and leading to amyloid clearance particularly in daughter cells. Reducing the availability or activity of the chaperone Hsp104, even transiently, reverses curing. Thus, the specificity of inhibition is determined by the sensitivity of variants to the mutant dosage rather than mode of action, challenging the view that a unique inhibitor must be developed to combat each variant.

Heparin acts as a structural component of β-endorphin amyloid fibrils rather than a simple aggregation promoter

The aggregation promoter heparin is commonly used to study the aggregation kinetics and biophysical properties of protein amyloids. However, the underlying mechanism for amyloid promotion by heparin remains poorly understood. In the case of the neuropeptide β-endorphin that can reversibly adopt a functional amyloid form in nature, aggregation in the presence of heparin leads to a loss of function. Applying correlative optical super-resolution microscopy methods, we show that heparin incorporates into emerging β-endorphin fibrils forming an integral component and is essential for amyloid templating. This will have direct implications on β-endorphin's normal physiological function and raises concerns on the biological relevance of heparin-promoted amyloid models.

Distinct Prion Domain Sequences Ensure Efficient Amyloid Propagation by Promoting Chaperone Binding or Processing In Vivo

Prions are a group of proteins that can adopt a spectrum of metastable conformations in vivo. These alternative states change protein function and are self-replicating and transmissible, creating protein-based elements of inheritance and infectivity. Prion conformational flexibility is encoded in the amino acid composition and sequence of the protein, which dictate its ability not only to form an ordered aggregate known as amyloid but also to maintain and transmit this structure in vivo. But, while we can effectively predict amyloid propensity in vitro, the mechanism by which sequence elements promote prion propagation in vivo remains unclear. In yeast, propagation of the [PSI⁺] prion, the amyloid form of the Sup35 protein, has been linked to an oligopeptide repeat region of the protein. Here, we demonstrate that this region is composed of separable functional elements, the repeats themselves and a repeat proximal region, which are both required for efficient prion propagation. Changes in the numbers of these elements do not alter the physical properties of Sup35 amyloid, but their presence promotes amyloid fragmentation, and therefore maintenance, by molecular chaperones. Rather than acting redundantly, our observations suggest that these sequence elements make complementary contributions to prion propagation, with the repeat proximal region promoting chaperone binding to and the repeats promoting chaperone processing of Sup35 amyloid.

Protein misfolding and assembly into ordered aggregates known as amyloid has emerged as a novel mechanism for regulation of protein function. In the case of prion proteins, the resulting amyloid is transmissible, creating protein-based elements of infectivity and inheritance. These unusual properties are linked to the amino acid composition and sequence of the protein, which confer both conformational flexibility and persistence in vivo, the latter of which occurs through mechanisms that are currently poorly understood. Here, we address this open question by studying a region of the yeast prion Sup35 that has been genetically linked to persistence. We find that this region is composed of two separable elements that are both required for efficient persistence of the amyloid. These elements do not contribute to amyloid stability. Rather, they promote distinct aspects of its functional interactions with molecular chaperones, which are required for efficient conformational self-replication and transmission.

Enhanced and selective optical trapping in a slot-graphite photonic crystal

Applicability of optical trapping tools for nanomanipulation is limited by the available laser power and trap efficiency. We utilized the strong confinement of light in a slot-graphite photonic crystal to develop high-efficiency parallel trapping over a large area. The stiffness is 35 times higher than our previously demonstrated on-chip, near field traps. We demonstrate the ability to trap both dielectric and metallic particles of sub-micron size. We find that the growth kinetics of nanoparticle arrays on the slot-graphite template depends on particle size. This difference is exploited to selectively trap one type of particle out of a binary colloidal mixture, creating an efficient optical sieve. This technique has rich potential for analysis, diagnostics, and enrichment and sorting of microscopic entities.

A Decentralized Approach to the Formulation of Hypotheses: A Hierarchical Structural Model for a Prion Self-Assembled System

Innovation in hypotheses is a key transformative driver for scientific development. The conventional centralized hypothesis formulation approach, where a dominant hypothesis is typically derived from a primary phenomenon, can, inevitably, impose restriction on the range of conceivable experiments and legitimate hypotheses, and ultimately impede understanding of the system of interest. We report herein the proposal of a decentralized approach for the formulation of hypotheses, through initial preconception-free phenomenon accumulation and subsequent reticular logical reasoning processes. The two-step approach can provide an unbiased, panoramic view of the system and as such should enable the generation of a set of more coherent and therefore plausible hypotheses. As a proof-of-concept demonstration of the utility of this open-ended approach, a hierarchical model has been developed for a prion self-assembled system, allowing insight into hitherto elusive static and dynamic features associated with this intriguing structure.

Pharmacological chaperone reshapes the energy landscape for folding and aggregation of the prion protein

The development of small-molecule pharmacological chaperones as therapeutics for protein misfolding diseases has proven challenging, partly because their mechanism of action remains unclear. Here we study Fe-TMPyP, a tetrapyrrole that binds to the prion protein PrP and inhibits misfolding, examining its effects on PrP folding at the single-molecule level with force spectroscopy. Single PrP molecules are unfolded with and without Fe-TMPyP present using optical tweezers. Ligand binding to the native structure increases the unfolding force significantly and alters the transition state for unfolding, making it more brittle and raising the barrier height. Fe-TMPyP also binds the unfolded state, delaying native refolding. Furthermore, Fe-TMPyP binding blocks the formation of a stable misfolded dimer by interfering with intermolecular interactions, acting in a similar manner to some molecular chaperones. The ligand thus promotes native folding by stabilizing the native state while also suppressing interactions driving aggregation.

Investigation of the early stages of human γD-crystallin aggregation process

Cataract, a major cause of visual impairment worldwide, is a common disease of the eye lens related to protein aggregation. Several factors including the exposure of ultraviolet irradiation and possibly acidic condition may induce the unfolding and subsequent aggregation of the crystallin proteins leading to crystalline lens opacification. Human γD-crystallin (HγDC), a 173 residue monomeric protein, abundant in the nucleus of the human eye lens, has been shown to aggregate and form amyloid fibrils under acidic conditions and that this aggregation route is thought to be a potential initiation pathway for the onset of age-related nuclear cataract. However, the underlying mechanism of fibril formation remains elusive. This report is aimed at examining the structural changes and possible amyloid fibril formation pathway of HγDC using molecular dynamics and molecular docking simulations. Our findings demonstrated that incubation of HγDC under the acidic condition redistributes the protein surface charges and affects the protein interaction with its surrounding solvent environment. This brings about a twist motion in the overall tertiary structure that gives rise to newly formed anti-parallel β-strands in the C-terminal flexible loop regions. The change in protein structural conformation also involves an alteration in specific salt-bridge interactions. Altogether, these findings revealed a plausible mechanism for amyloid fibril formation of HγDC that is important to the early stages of HγDC aggregation involved in cataractogenesis.

Mechanistic and Structural Insights into the Prion-Disaggregase Activity of Hsp104

Hsp104 is a dynamic ring translocase and hexameric AAA+ protein found in yeast, which couples ATP hydrolysis to disassembly and reactivation of proteins trapped in soluble preamyloid oligomers, disordered protein aggregates, and stable amyloid or prion conformers. Here, we highlight advances in our structural understanding of Hsp104 and how Hsp104 deconstructs Sup35 prions. Although the atomic structure of Hsp104 hexamers remains uncertain, volumetric reconstruction of Hsp104 hexamers in ATPγS, ADP-AlFx (ATP hydrolysis transition-state mimic), and ADP via small-angle x-ray scattering has revealed a peristaltic pumping motion upon ATP hydrolysis. This pumping motion likely drives directional substrate translocation across the central Hsp104 channel. Hsp104 initially engages Sup35 prions immediately C-terminal to their cross-β structure. Directional pulling by Hsp104 then resolves N-terminal cross-β structure in a stepwise manner. First, Hsp104 fragments the prion. Second, Hsp104 unfolds cross-β structure. Third, Hsp104 releases soluble Sup35. Deletion of the Hsp104 N-terminal domain yields a hypomorphic disaggregase, Hsp104(∆N), with an altered pumping mechanism. Hsp104(∆N) fragments Sup35 prions without unfolding cross-β structure or releasing soluble Sup35. Moreover, Hsp104(∆N) activity cannot be enhanced by mutations in the middle domain that potentiate disaggregase activity. Thus, the N-terminal domain is critical for the full repertoire of Hsp104 activities.

Proteins with Intrinsically Disordered Domains Are Preferentially Recruited to Polyglutamine Aggregates

Intracellular protein aggregation is the hallmark of several neurodegenerative diseases. Aggregates formed by polyglutamine (polyQ)-expanded proteins, such as Huntingtin, adopt amyloid-like structures that are resistant to denaturation. We used a novel purification strategy to isolate aggregates formed by human Huntingtin N-terminal fragments with expanded polyQ tracts from both yeast and mammalian (PC-12) cells. Using mass spectrometry we identified the protein species that are trapped within these polyQ aggregates. We found that proteins with very long intrinsically-disordered (ID) domains (≥100 amino acids) and RNA-binding proteins were disproportionately recruited into aggregates. The removal of the ID domains from selected proteins was sufficient to eliminate their recruitment into polyQ aggregates. We also observed that several neurodegenerative disease-linked proteins were reproducibly trapped within the polyQ aggregates purified from mammalian cells. Many of these proteins have large ID domains and are found in neuronal inclusions in their respective diseases. Our study indicates that neurodegenerative disease-associated proteins are particularly vulnerable to recruitment into polyQ aggregates via their ID domains. Also, the high frequency of ID domains in RNA-binding proteins may explain why RNA-binding proteins are frequently found in pathological inclusions in various neurodegenerative diseases.

A Single-Strand Annealing Protein Clamps DNA to Detect and Secure Homology

Repair of DNA breaks by single-strand annealing (SSA) is a major mechanism for the maintenance of genomic integrity. SSA is promoted by proteins (single-strand-annealing proteins [SSAPs]), such as eukaryotic RAD52 and λ phage Redβ. These proteins use a short single-stranded region to find sequence identity and initiate homologous recombination. However, it is unclear how SSAPs detect homology and catalyze annealing. Using single-molecule experiments, we provide evidence that homology is recognized by Redβ monomers that weakly hold single DNA strands together. Once annealing begins, dimerization of Redβ clamps the double-stranded region and nucleates nucleoprotein filament growth. In this manner, DNA clamping ensures and secures a successful detection for DNA sequence homology. The clamp is characterized by a structural change of Redβ and a remarkable stability against force up to 200 pN. Our findings not only present a detailed explanation for SSAP action but also identify the DNA clamp as a very stable, noncovalent, DNA-protein interaction.

Sensitive detection of aggregated prion protein via proximity ligation

The DNA assisted solid-phase proximity ligation assay (SP-PLA) provides a unique opportunity to specifically detect prion protein (PrP) aggregates by investigating the collocation of 3 or more copies of the specific protein. We have developed an SP-PLA that can detect PrP aggregates in brain homogenates from infected hamsters even after a 10(7)-fold dilution. In contrast, brain homogenate from uninfected animals did not generate a detectable signal at 100-fold higher concentration. Using either of the 2 monoclonal anti-PrP antibodies, 3F4 and 6H4, we successfully detected low concentrations of aggregated PrP. The presented results provide a proof of concept that this method might be an interesting tool in the development of diagnostic approaches of prion diseases.

Force generation by the growth of amyloid aggregates

The generation of mechanical forces are central to a wide range of vital biological processes, including the function of the cytoskeleton. Although the forces emerging from the polymerization of native proteins have been studied in detail, the potential for force generation by aberrant protein polymerization has not yet been explored. Here, we show that the growth of amyloid fibrils, archetypical aberrant protein polymers, is capable of unleashing mechanical forces on the piconewton scale for individual filaments. We apply microfluidic techniques to measure the forces released by amyloid growth for two systems: insulin and lysozyme. The level of force measured for amyloid growth in both systems is comparable to that observed for actin and tubulin, systems that have evolved to generate force during their native functions and, unlike amyloid growth, rely on the input of external energy in the form of nucleotide hydrolysis for maximum force generation. Furthermore, we find that the power density released from growing amyloid fibrils is comparable to that of high-performance synthetic polymer actuators. These findings highlight the potential of amyloid structures as active materials and shed light on the criteria for regulation and reversibility that guide molecular evolution of functional polymers.

Extraction of accurate biomolecular parameters from single-molecule force spectroscopy experiments

The atomic force microscope (AFM) is able to manipulate biomolecules and their complexes with exquisite force sensitivity and distance resolution. This capability, complemented by theoretical models, has greatly improved our understanding of the determinants of mechanical strength in proteins and revealed the diverse effects of directional forces on the energy landscape of biomolecules. In unbinding experiments, the interacting partners are usually immobilized on their respective substrates via extensible linkers. These linkers affect both the force and contour length (Lc) of the complex at rupture. Surprisingly, while the former effect is well understood, the latter is largely neglected, leading to incorrect estimations of Lc, a parameter that is often used as evidence for the detection of specific interactions and remodeling events and for the inference of interaction regions. To address this problem, a model that predicts contour length measurements from single-molecule forced-dissociation experiments is presented that considers attachment position on the AFM tip, geometric effects, and polymer dynamics of the linkers. Modeled data are compared with measured contour length distributions from several different experimental systems, revealing that current methods underestimate contour lengths. The model enables nonspecific interactions to be identified unequivocally, allows accurate determination of Lc, and, by comparing experimental and modeled distributions, enables partial unfolding events before rupture to be identified unequivocally.

Reconstructing folding energy landscape profiles from nonequilibrium pulling curves with an inverse Weierstrass integral transform

The energy landscapes that drive structure formation in biopolymers are difficult to measure. Here we validate experimentally a novel method to reconstruct landscape profiles from single-molecule pulling curves using an inverse Weierstrass transform (IWT) of the Jarzysnki free-energy integral. The method was applied to unfolding measurements of a DNA hairpin, replicating the results found by the more-established weighted histogram (WHAM) and inverse Boltzmann methods. Applying both WHAM and IWT methods to reconstruct the folding landscape for a RNA pseudoknot having a stiff energy barrier, we found that landscape features with sharper curvature than the force probe stiffness could not be recovered with the IWT method. The IWT method is thus best for analyzing data from stiff force probes such as atomic force microscopes.

Locating folds of the in-register parallel β-sheet of the Sup35p prion domain infectious amyloid

The [PSI+] prion is a self-propagating amyloid of the translation termination factor, Sup35p, of Saccharomyces cerevisiae. The N-terminal 253 residues (NM) of this 685-residue protein normally function in regulating mRNA turnover but spontaneously form infectious amyloid in vitro. We converted the three Ile residues in Sup35NM to Leu and then replaced 16 single residues with Ile, one by one, and prepared Ile-1-(13)C amyloid of each mutant, seeding with amyloid formed by the reference sequence Sup35NM. Using solid-state NMR, we showed that 10 of the residues examined, including six between residues 30 and 90, showed the ∼0.5-nm distance between labels diagnostic of the in-register parallel amyloid architecture. The five scattered N domain residues with wider spacing may be in turns or loops; one is a control at the C terminus of M. All mutants, except Q56I, showed little or no [PSI+] transmission barrier from the reference sequence, suggesting that they could assume a similar amyloid architecture in vitro when seeded with filaments of reference sequence Sup35NM. Infection of yeast cells expressing the reference SUP35 gene sequence with amyloid of several mutants produced [PSI+] transfectants with similar efficiency as did reference sequence Sup35NM amyloid. Our work provides a stringent demonstration that the Sup35 prion domain has the folded in-register parallel β-sheet architecture and suggests common locations of the folds. This architecture naturally suggests a mechanism of inheritance of conformation, the central mystery of prions.

Mechanisms of cellular proteostasis: insights from single-molecule approaches

Cells employ a variety of strategies to maintain proteome homeostasis. Beginning during protein biogenesis, the translation machinery and a number of molecular chaperones promote correct de novo folding of nascent proteins even before synthesis is complete. Another set of molecular chaperones helps to maintain proteins in their functional, native state. Polypeptides that are no longer needed or pose a threat to the cell, such as misfolded proteins and aggregates, are removed in an efficient and timely fashion by ATP-dependent proteases. In this review, we describe how applications of single-molecule manipulation methods, in particular optical tweezers, are shedding new light on the molecular mechanisms of quality control during the life cycles of proteins.

Diverse metastable structures formed by small oligomers of α-synuclein probed by force spectroscopy

Oligomeric aggregates are widely suspected as toxic agents in diseases caused by protein aggregation, yet they remain poorly characterized, partly because they are challenging to isolate from a heterogeneous mixture of species. We developed an assay for characterizing structure, stability, and kinetics of individual oligomers at high resolution and sensitivity using single-molecule force spectroscopy, and applied it to observe the formation of transient structured aggregates within single oligomers of α-synuclein, an intrinsically-disordered protein linked to Parkinson's disease. Measurements of the molecular extension as the proteins unfolded under tension in optical tweezers revealed that even small oligomers could form numerous metastable structures, with a surprisingly broad range of sizes. Comparing the structures formed in monomers, dimers and tetramers, we found that the average mechanical stability increased with oligomer size. Most structures formed within a minute, with size-dependent rates. These results provide a new window onto the complex α-synuclein aggregation landscape, characterizing the microscopic structural heterogeneity and kinetics of different pathways.

Optimal control of particle separation in inertial microfluidics

Recently, inertial mircofluidics has emerged as a promising tool to manipulate complex liquids with possible biomedical applications, for example, to particle separation. Indeed, in experiments different particle types were separated based on their sizes (A.J. Mach, D. Di Carlo, Biotechnol. Bioeng. 107, 302 (2010)). In this article we use a theoretical study to demonstrate how concepts from optimal control theory help to design optimized profiles of control forces that allow to steer particles to almost any position at the outlet of a microfluidic channel. We also show that one specific control force profile is sufficient to guide two types of particles to different locations at the channel outlet, where they can be separated from each other. The particles just differ by their size which determines the strength of the inertial lift forces they experience. Our approach greatly enhances the efficiency of particle separation in the inertial regime.

Non-targeted identification of prions and amyloid-forming proteins from yeast and mammalian cells

The formation of amyloid aggregates is implicated both as a primary cause of cellular degeneration in multiple human diseases and as a functional mechanism for providing extraordinary strength to large protein assemblies. The recent identification and characterization of several amyloid proteins from diverse organisms argues that the amyloid phenomenon is widespread in nature. Yet identifying new amyloid-forming proteins usually requires a priori knowledge of specific candidates. Amyloid fibers can resist heat, pressure, proteolysis, and denaturation by reagents such as urea or sodium dodecyl sulfate. Here we show that these properties can be exploited to identify naturally occurring amyloid-forming proteins directly from cell lysates. This proteomic-based approach utilizes a novel purification of amyloid aggregates followed by identification by mass spectrometry without the requirement for special genetic tools. We have validated this technique by blind identification of three amyloid-based yeast prions from laboratory and wild strains and disease-related polyglutamine proteins expressed in both yeast and mammalian cells. Furthermore, we found that polyglutamine aggregates specifically recruit some stress granule components, revealing a possible mechanism of toxicity. Therefore, core amyloid-forming proteins as well as strongly associated proteins can be identified directly from cells of diverse origin.

Hsp104 drives "protein-only" positive selection of Sup35 prion strains encoding strong [PSI(+)]

Structurally distinct, self-templating prion "strains" can encode distinct phenotypes and amplify at different rates depending upon the environment. Indeed, prion strain ensembles can evolve in response to environmental challenges, which makes them highly challenging drug targets. It is not understood how the proteostasis network amplifies one prion strain at the expense of another. Here, we demonstrate that Hsp104 remodels the distinct intermolecular contacts of different synthetic Sup35 prion strains in a way that selectively amplifies prions encoding strong [PSI(+)] and simultaneously eliminates prions encoding weak [PSI(+)]. Hsp104 has reduced ability to fragment prions encoding weak [PSI(+)], but readily converts them to nontemplating forms. By contrast, Hsp104 readily fragments prions encoding strong [PSI(+)], but has reduced ability to eliminate their infectivity. Thus, we illuminate direct mechanisms underpinning how the proteostasis network can drive prion strain selection.

Single-molecule assays for investigating protein misfolding and aggregation

Protein misfolding and aggregation are relevant to many fields. Recently, their investigation has experienced a revival as a central topic in the research of numerous human diseases, including Parkinson's and Alzheimer's. Much has been learned from ensemble biochemical approaches, but the inherently heterogeneous nature of the underlying processes has obscured many important details. Single-molecule techniques offer unique capabilities to study heterogeneous systems, while providing high temporal and structural resolution to characterize them. In this Perspective, we give an overview of the single-molecule assays that have been applied to protein misfolding and aggregation, which are mainly based on fluorescence and force spectroscopy. We describe some of the technical challenges involved in studying aggregation at the single-molecule level and discuss what has been learned about aggregation mechanisms from the different approaches.

Single-molecule approaches to prion protein misfolding

The structural conversion of the prion protein PrP into a transmissible, misfolded form is the central element of prion disease, yet there is little consensus as to how it occurs. Key aspects of conversion into the diseased state remain unsettled, from details about the earliest stages of misfolding such as the involvement of partially- or fully-unfolded intermediates to the structure of the infectious state. Part of the difficulty in understanding the structural conversion arises from the complexity of the underlying energy landscapes. Single molecule methods provide a powerful tool for probing complex folding pathways as in prion misfolding, because they allow rare and transient events to be observed directly. We discuss recent work applying single-molecule probes to study misfolding in prion proteins, and what it has revealed about the folding dynamics of PrP that may underlie its unique behavior. We also discuss single-molecule studies probing the interactions that stabilize non-native structures within aggregates, pointing the way to future work that may help identify the microscopic events triggering pathogenic conversion. Although single-molecule approaches to misfolding are relatively young, they have a promising future in prion science.

Back-focal-plane position detection with extended linear range for photonic force microscopy

In photonic force microscopes, the position detection with high temporal and spatial resolution is usually implemented by a quadrant position detector placed in the back focal plane of a condenser. An objective with high numerical aperture (NA) for the optical trap has also been used to focus a detection beam. In that case the displacement of the probe at a fixed position of the detector produces a unique and linear response only in a restricted region of the probe displacement, usually several hundred nanometers. There are specific experiments where the absolute position of the probe is a relevant measure together with the probe position relative the optical trap focus. In our scheme we introduce the detection beam into the condenser with low NA through a pinhole with tunable size. This combination permits us to create a wide detection spot and to achieve the linear range of several micrometers by the probe position detection without reducing the trapping force.

Small heat shock proteins potentiate amyloid dissolution by protein disaggregases from yeast and humans

The authors define how small heat-shock proteins synergize to regulate the assembly and disassembly of a beneficial prion, and then they exploit this knowledge to identify the human amyloid depolymerase.

How small heat shock proteins (sHsps) might empower proteostasis networks to control beneficial prions or disassemble pathological amyloid is unknown. Here, we establish that yeast sHsps, Hsp26 and Hsp42, inhibit prionogenesis by the [PSI⁺] prion protein, Sup35, via distinct and synergistic mechanisms. Hsp42 prevents conformational rearrangements within molten oligomers that enable de novo prionogenesis and collaborates with Hsp70 to attenuate self-templating. By contrast, Hsp26 inhibits self-templating upon binding assembled prions. sHsp binding destabilizes Sup35 prions and promotes their disaggregation by Hsp104, Hsp70, and Hsp40. In yeast, Hsp26 or Hsp42 overexpression prevents [PSI⁺] induction, cures [PSI⁺], and potentiates [PSI⁺]-curing by Hsp104 overexpression. In vitro, sHsps enhance Hsp104-catalyzed disaggregation of pathological amyloid forms of α-synuclein and polyglutamine. Unexpectedly, in the absence of Hsp104, sHsps promote an unprecedented, gradual depolymerization of Sup35 prions by Hsp110, Hsp70, and Hsp40. This unanticipated amyloid-depolymerase activity is conserved from yeast to humans, which lack Hsp104 orthologues. A human sHsp, HspB5, stimulates depolymerization of α-synuclein amyloid by human Hsp110, Hsp70, and Hsp40. Thus, we elucidate a heretofore-unrecognized human amyloid-depolymerase system that could have applications in various neurodegenerative disorders.

Amyloid fibers are protein aggregates that are associated with numerous neurodegenerative diseases, including Parkinson's disease, for which there are no effective treatments. They can also play beneficial roles; in yeast, for example, they are associated with increased survival and the evolution of new traits. Amyloid fibers are also central to many revolutionary concepts and important questions in biology and nanotechnology, including long-term memory formation and versatile self-organizing nanostructures. Thus, there is an urgent need to understand how we can promote beneficial amyloid assembly, or reverse pathogenic assembly, at will. In this study, we define the mechanisms by which small heat-shock proteins synergize to regulate the assembly and disassembly of a beneficial yeast prion. We then exploit this knowledge to discover an amyloid depolymerase machinery that is conserved from yeast to humans. Remarkably, the human small heat shock protein, HspB5, stimulates Hsp110, Hsp70, and Hsp40 chaperones to gradually depolymerize amyloid fibers formed by α-synuclein (which are implicated in Parkinson's disease) from their ends on a biologically relevant timescale. This newly identified and highly conserved amyloid-depolymerase system could have important therapeutic applications for various neurodegenerative disorders.

Optimized back-focal-plane interferometry directly measures forces of optically trapped particles

Back-focal-plane interferometry is used to measure displacements of optically trapped samples with very high spatial and temporal resolution. However, the technique is closely related to a method that measures the rate of change in light momentum. It has long been known that displacements of the interference pattern at the back focal plane may be used to track the optical force directly, provided that a considerable fraction of the light is effectively monitored. Nonetheless, the practical application of this idea has been limited to counter-propagating, low-aperture beams where the accurate momentum measurements are possible. Here, we experimentally show that the connection can be extended to single-beam optical traps. In particular, we show that, in a gradient trap, the calibration product κ · β (where κ is the trap stiffness and 1/β is the position sensitivity) corresponds to the factor that converts detector signals into momentum changes; this factor is uniquely determined by three construction features of the detection instrument and does not depend, therefore, on the specific conditions of the experiment. Then, we find that force measurements obtained from back-focal-plane displacements are in practice not restricted to a linear relationship with position and hence they can be extended outside that regime. Finally, and more importantly, we show that these properties are still recognizable even when the system is not fully optimized for light collection. These results should enable a more general use of back-focal-plane interferometry whenever the ultimate goal is the measurement of the forces exerted by an optical trap.

Single-molecule observation of helix staggering, sliding, and coiled coil misfolding

The biological functions of coiled coils generally depend on efficient folding and perfect pairing of their α-helices. Dynamic changes in the helical registry that lead to staggered helices have only been proposed for a few special systems and not found in generic coiled coils. Here, we report our observations of multiple staggered helical structures of two canonical coiled coils. The partially folded structures are formed predominantly by coiled coil misfolding and occasionally by helix sliding. Using high-resolution optical tweezers, we characterized their energies and transition kinetics at a single-molecule level. The staggered states occur less than 2% of the time and about 0.1% of the time at zero force. We conclude that dynamic changes in helical registry may be a general property of coiled coils. Our findings should have broad and unique implications in functions and dysfunctions of proteins containing coiled coils.

Direct observation of multiple misfolding pathways in a single prion protein molecule

Protein misfolding is a ubiquitous phenomenon associated with a wide range of diseases. Single-molecule approaches offer a powerful tool for deciphering the mechanisms of misfolding by measuring the conformational fluctuations of a protein with high sensitivity. We applied single-molecule force spectroscopy to observe directly the misfolding of the prion protein PrP, a protein notable for having an infectious misfolded state that is able to propagate by recruiting natively folded PrP. By measuring folding trajectories of single PrP molecules held under tension in a high-resolution optical trap, we found that the native folding pathway involves only two states, without evidence for partially folded intermediates that have been proposed to mediate misfolding. Instead, frequent but fleeting transitions were observed into off-pathway intermediates. Three different misfolding pathways were detected, all starting from the unfolded state. Remarkably, the misfolding rate was even higher than the rate for native folding. A mutant PrP with higher aggregation propensity showed increased occupancy of some of the misfolded states, suggesting these states may act as intermediates during aggregation. These measurements of individual misfolding trajectories demonstrate the power of single-molecule approaches for characterizing misfolding directly by mapping out nonnative folding pathways.

Fibrillogenesis of huntingtin and other glutamine containing proteins

This chapter focuses on the aggregation of glutamine containing peptides and proteins with an emphasis on huntingtin protein, whose aggregation leads to the development of Huntington's disease. The kinetics that leads to the formation of amyloids, the structure of aggregates of various types and the morphological mechanical properties of amyloid fibrils are described. The kinetics of amyloid fibril formation has been proposed to follow a nucleation dependent polymerization model, dependent upon the size of the nucleus. This model and the effect of the polyglutamine length on the nucleus size are reviewed. Aggregate structure is characterized at two different levels. The atomic-scale resolution structure of fibrillar and crystalline aggregates of polyglutamine containing proteins and peptides was determined by X-ray crystallography and solid-state nuclear magnetic resonance (NMR). The chapter outlines the results obtained by both these techniques. Atomic force microscopy (AFM) was instrumental in elucidating the morphology of fibrils, their organization and assembly. The chapter also discusses the high stability of amyloid fibrils, including their mechanical properties as revealed by AFM.

Physical properties of polymorphic yeast prion amyloid fibers

Amyloid fibers play important roles in many human diseases and natural biological processes and have immense potential as novel nanomaterials. We explore the physical properties of polymorphic amyloid fibers formed by yeast prion protein Sup35. Amyloid fibers that conferred distinct prion phenotypes ([PSI(+)]), strong (S) versus weak (W) nonsense suppression, displayed different physical properties. Both S[PSI(+)] and W[PSI(+)] fibers contained structural inhomogeneities, specifically local regions of static curvature in S[PSI(+)] fibers and kinks and self-cross-linking in W[PSI(+)] fibers. Force-extension experiments with optical tweezers revealed persistence lengths of 1.5 μm and 3.3 μm and axial stiffness of 5600 pN and 9100 pN for S[PSI(+)] and W[PSI(+)] fibers, respectively. Thermal fluctuation analysis confirmed the twofold difference in persistence length between S[PSI(+)] and W[PSI(+)] fibers and revealed a torsional stiffness of kinks and cross-links of ~100-200 pN·nm/rad.

Opposing effects of glutamine and asparagine govern prion formation by intrinsically disordered proteins

Sequences rich in glutamine (Q) and asparagine (N) residues often fail to fold at the monomer level. This, coupled to their unusual hydrogen-bonding abilities, provides the driving force to switch between disordered monomers and amyloids. Such transitions govern processes as diverse as human protein-folding diseases, bacterial biofilm assembly, and the inheritance of yeast prions (protein-based genetic elements). A systematic survey of prion-forming domains suggested that Q and N residues have distinct effects on amyloid formation. Here, we use cell biological, biochemical, and computational techniques to compare Q/N-rich protein variants, replacing Ns with Qs and Qs with Ns. We find that the two residues have strong and opposing effects: N richness promotes assembly of benign self-templating amyloids; Q richness promotes formation of toxic nonamyloid conformers. Molecular simulations focusing on intrinsic folding differences between Qs and Ns suggest that their different behaviors are due to the enhanced turn-forming propensity of Ns over Qs.

Chemical biology of prion protein: tools to bridge the in vitro/vivo interface

Research on prion protein (PrP) and pathogenic prion has been very intensive because of its importance as model system for neurodegenerative diseases. One important aspect of this research has been the application of chemical biology tools. In this review we describe new developments like native chemical ligation (NCL) and expressed protein ligation (EPL) for the synthesis and semisynthesis of proteins in general and PrP in particular. These techniques allow the synthesis of designed tailor made analogs which can be used in conjunction with modern biophysical methods like fluorescence spectroscopy, solid state Nuclear Magnetic Resonance (ssNMR), and Electron Paramagnetic Resonance (EPR). Another aspect of prion research is concerned with the interaction of PrP with small organic molecules and metals. The results are critically reviewed and put into perspective of their implication for PrP function.