Hydrogen/deuterium exchange mass spectrometry identifies two highly protected regions in recombinant full-length prion protein amyloid fibrils

Structure of prion β-oligomers as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations

The conversion of the native monomeric cellular prion protein (PrP^C ) into an aggregated pathological β-oligomeric form (PrP^β ) and an infectious form (PrP^Sc ) is the central element in the development of prion diseases. The structure of the aggregates and the molecular mechanisms of the conformational changes involved in the conversion are still unknown. We applied mass spectrometry combined with chemical crosslinking, hydrogen/deuterium exchange, limited proteolysis, and surface modification for the differential characterization of the native and the urea+acid-converted prion β-oligomer structures to obtain insights into the mechanisms of conversion and aggregation. For the determination of the structure of the monomer and the dimer unit of the β-oligomer, we applied a recently-developed approach for de novo protein structure determination which is based on the incorporation of zero-length and short-distance crosslinking data as intra- and inter-protein constraints in discrete molecular dynamics simulations (CL-DMD). Based on all of the structural-proteomics experimental data and the computationally predicted structures of the monomer units, we propose the potential mode of assembly of the β-oligomer. The proposed β-oligomer assembly provides a clue on the β-sheet nucleation site, and how template-based conversion of the native prion molecule occurs, growth of the prion aggregates, and maturation into fibrils may occur.

Mutation-Dependent Refolding of Prion Protein Unveils Amyloidogenic-Related Structural Ramifications: Insights from Molecular Dynamics Simulations

The main focus of prion structural biology studies is to understand the molecular basis of prion diseases caused by misfolding, and aggregation of the cellular prion protein PrP^C remains elusive. Several genetic mutations are linked with human prion diseases and driven by the conformational conversion of PrP^C to the toxic PrP^Sc. The main goal of this study is to gain a better insight into the molecular effect of disease-associated V210I mutation on this process by molecular dynamics simulations. This inherited mutation elicited copious structural changes in the β1-α1-β2 subdomain, including an unfolding of a helix α1 and the elongation of the β-sheet. These unusual structural changes likely appeared to detach the β1-α1-β2 subdomain from the α2-α3 core, an early misfolding event necessary for the conformational conversion of PrP^C to PrP^Sc. Ultimately, the unfolded α1 and its prior β1-α1 loop further engaged with unrestrained conformational dynamics and were widely considered as amyloidogenic-inducing traits. Furthermore, the resulting folding intermediate possesses a highly unstable β1-α1-β2 subdomain, thereby enhancing the aggregation of misfolded PrP^C through intermolecular interactions between frequently refolding regions. Briefly, these remarkable changes as seen in the mutant β1-α1-β2 subdomain are consistent with previous experimental results and thus provide a molecular basis of PrP^C misfolding associated with the conformational conversion of PrP^C to PrP^Sc.

Condition-dependent structural collapse in the intrinsically disordered N-terminal domain of prion protein

Prion protein is composed of a structure-unsolved N-terminal domain and a globular C-terminal domain. Under limited trypsin digestion, mouse recombinant prion protein can be cleaved into two parts at residue Lys105. Here, we termed these two fragments as the N-domain (sequence 23-105) and the C-domain (sequence 106-230). In this study, the structural properties of the N-domain, the C-domain, and the full-length protein were explored using small-angle X-ray scattering, analytical ultracentrifugation, circular dichroism spectroscopy, and the 8-anilino-1-naphthalenesulfonic acid binding assay. The conformation and size of the prion protein were found to change sensitively under the solvent conditions. The positive residues in the sequence 23-99 of the N-domain were found to be responsible for the enhanced flexibility with the salt concentration reduced below 5 mM. The C-domain containing a hydrophobic patch tends to unfold and aggregate during a salt-induced structural collapse. The N-domain collapsed together with the C-domain at pH 5.2, whereas it collapsed independently at pH 4.2. The positively charged cluster (sequence 100-105) in the N-domain contributed to protecting the exposed hydrophobic surface of the C-domain.

Development of a new largely scalable in vitro prion propagation method for the production of infectious recombinant prions for high resolution structural studies

The resolution of the three-dimensional structure of infectious prions at the atomic level is pivotal to understand the pathobiology of Transmissible Spongiform Encephalopathies (TSE), but has been long hindered due to certain particularities of these proteinaceous pathogens. Difficulties related to their purification from brain homogenates of disease-affected animals were resolved almost a decade ago by the development of in vitro recombinant prion propagation systems giving rise to highly infectious recombinant prions. However, lack of knowledge about the molecular mechanisms of the misfolding event and the complexity of systems such as the Protein Misfolding Cyclic Amplification (PMCA), have limited generating the large amounts of homogeneous recombinant prion preparations required for high-resolution techniques such as solid state Nuclear Magnetic Resonance (ssNMR) imaging. Herein, we present a novel recombinant prion propagation system based on PMCA that substitutes sonication with shaking thereby allowing the production of unprecedented amounts of multi-labeled, infectious recombinant prions. The use of specific cofactors, such as dextran sulfate, limit the structural heterogeneity of the in vitro propagated prions and makes possible, for the first time, the generation of infectious and likely homogeneous samples in sufficient quantities for studies with high-resolution structural techniques as demonstrated by the preliminary ssNMR spectrum presented here. Overall, we consider that this new method named Protein Misfolding Shaking Amplification (PMSA), opens new avenues to finally elucidate the three-dimensional structure of infectious prions.

Segments in the Amyloid Core that Distinguish Hamster from Mouse Prion Fibrils

Prion diseases are transmissible fatal neurodegenerative disorders affecting humans and other mammals. The disease transmission can occur between different species but is limited by the sequence homology between host and inoculum. The crucial molecular event in the progression of this disease is prion formation, starting from the conformational conversion of the normal, membrane-anchored prion protein (PrP^C) into the misfolded, β-sheet-rich and aggregation-prone isoform (PrP^Sc), which then self-associates into the infectious amyloid form called prion. Amyloid is the aggregate formed from one-dimensional protein association. As amyloid formation is a key hallmark in prion pathogenesis, studying which segments in prion protein are involved in the amyloid formation can provide molecular details in the cross-species transmission barrier of prion diseases. However, due to the difficulties of studying protein aggregates, very limited knowledge about prion structure or prion formation was disclosed by now. In this study, cross-seeding assay was used to identify the segments involved in the amyloid fibril formation of full-length hamster prion protein, SHaPrP(23-231). Our results showed that the residues in the segments 108-127, 172-194 (helix 2 in PrP^C) and 200-227 (helix 3 in PrP^C) are in the amyloid core of hamster prion fibrils. The segment 127-143, but not 107-126 (which corresponds to hamster sequence 108-127), was previously reported to be involved in the amyloid core of full-length mouse prion fibrils. Our results indicate that hamster prion protein and mouse prion protein use different segments to form the amyloid core in amyloidogenesis. The sequence-dependent core formation can be used to explain the seeding barrier between mouse and hamster.

Structural Determinants of the Prion Protein N-Terminus and Its Adducts with Copper Ions

The N-terminus of the prion protein is a large intrinsically disordered region encompassing approximately 125 amino acids. In this paper, we review its structural and functional properties, with a particular emphasis on its binding to copper ions. The latter is exploited by the region’s conformational flexibility to yield a variety of biological functions. Disease-linked mutations and proteolytic processing of the protein can impact its copper-binding properties, with important structural and functional implications, both in health and disease progression.

Techniques to elucidate the conformation of prions

Proteinaceous infectious particles (prions) are unique pathogens as they are devoid of any coding nucleic acid. Whilst it is assumed that prion disease is transmitted by a misfolded isoform of the cellular prion protein, the structural insight of prions is still vague and research for high resolution structural information of prions is still ongoing. In this review, techniques that may contribute to the clarification of the conformation of prions are presented and discussed.

A Structural and Functional Comparison Between Infectious and Non-Infectious Autocatalytic Recombinant PrP Conformers

Infectious prions contain a self-propagating, misfolded conformer of the prion protein termed PrP^Sc. A critical prediction of the protein-only hypothesis is that autocatalytic PrP^Sc molecules should be infectious. However, some autocatalytic recombinant PrP^Sc molecules have low or undetectable levels of specific infectivity in bioassays, and the essential determinants of recombinant prion infectivity remain obscure. To identify structural and functional features specifically associated with infectivity, we compared the properties of two autocatalytic recombinant PrP conformers derived from the same original template, which differ by >10⁵-fold in specific infectivity for wild-type mice. Structurally, hydrogen/deuterium exchange mass spectrometry (DXMS) studies revealed that solvent accessibility profiles of infectious and non-infectious autocatalytic recombinant PrP conformers are remarkably similar throughout their protease-resistant cores, except for two domains encompassing residues 91-115 and 144-163. Raman spectroscopy and immunoprecipitation studies confirm that these domains adopt distinct conformations within infectious versus non-infectious autocatalytic recombinant PrP conformers. Functionally, in vitro prion propagation experiments show that the non-infectious conformer is unable to seed mouse PrP^C substrates containing a glycosylphosphatidylinositol (GPI) anchor, including native PrP^C. Taken together, these results indicate that having a conformation that can be specifically adopted by post-translationally modified PrP^C molecules is an essential determinant of biological infectivity for recombinant prions, and suggest that this ability is associated with discrete features of PrP^Sc structure.

A key prediction of the prion hypothesis is that autocatalytic, misfolded PrP^Sc molecules should be highly infectious. Various recombinant PrP^Sc conformers are able to self-propagate in vitro, yet paradoxically only some of these conformers possess significant levels of specific infectivity in bioassays. Here we use two closely-matched autocatalytic recombinant PrP conformers that share the same origin but differ by >10⁵-fold in specific infectivity to study the molecular basis of prion infectivity. We show that infectious and non-infectious autocatalytic recombinant PrP conformers have subtle structural differences, and that GPI-anchored PrP substrate molecules can only adopt the infectious PrP^Sc conformation. We conclude that post-translational modifications of host PrP^C molecules play a critical role in restricting the range of recombinant PrP^Sc conformers that are biologically infectious.

Fibril Core of Transforming Growth Factor Beta-Induced Protein (TGFBIp) Facilitates Aggregation of Corneal TGFBIp

Mutations in the transforming growth factor beta-induced (TGFBI) gene result in a group of hereditary diseases of the cornea that are collectively known as TGFBI corneal dystrophies. These mutations translate into amino acid substitutions mainly within the fourth fasciclin 1 domain (FAS1-4) of the transforming growth factor beta-induced protein (TGFBIp) and cause either amyloid or nonamyloid protein aggregates in the anterior and central parts of the cornea, depending on the mutation. The A546T substitution in TGFBIp causes lattice corneal dystrophy (LCD), which manifests as amyloid-type aggregates in the corneal stroma. We previously showed that the A546T substitution renders TGFBIp and the FAS1-4 domain thermodynamically less stable compared with the wild-type (WT) protein, and the mutant FAS1-4 is prone to amyloid formation in vitro. In the present study, we identified the core of A546T FAS1-4 amyloid fibrils. Significantly, we identified the Y571-R588 region of TGFBIp, which we previously found to be enriched in amyloid deposits in LCD patients. We further found that the Y571-R588 peptide seeded fibrillation of A546T FAS1-4, and, more importantly, we demonstrated that native TGFBIp aggregates in the presence of fibrils formed by the core peptide. Collectively, these data suggest an involvement of the Y571-R588 peptide in LCD pathophysiology.

Revealing structural changes of prion protein during conversion from α-helical monomer to β-oligomers by means of ESR and nanochannel encapsulation

Under nondenaturing neutral pH conditions, full-length mouse recombinant prion protein lacking the only disulfide bridge can spontaneously convert from an α-helical-dominant conformer (α-state) to a β-sheet-rich conformer (β-state), which then associates into β-oligomers, and the kinetics of this spontaneous conversion depends on the properties of the buffer used. The molecular details of this structural conversion have not been reported due to the difficulty of exploring big protein aggregates. We introduced spin probes into different structural segments (three helices and the loop between strand 1 and helix 1), and employed a combined approach of ESR spectroscopy and protein encapsulation in nanochannels to reveal local structural changes during the α-to-β transition. Nanochannels provide an environment in which prion protein molecules are isolated from each other, but the α-to-β transition can still occur. By measuring dipolar interactions between spin probes during the transition, we showed that helix 1 and helix 3 retained their helicity, while helix 2 unfolded to form an extended structure. Moreover, our pulsed ESR results allowed clear discrimination between the intra- and intermolecular distances between spin labeled residues in helix 2 in the β-oligomers, making it possible to demonstrate that the unfolded helix 2 segment lies at the association interface of the β-oligomers to form cross-β structure.

Cofactor molecules induce structural transformation during infectious prion formation

The spread of misfolded proteins may occur in many neurodegenerative diseases. Mammalian prions are currently the only misfolded proteins in which high specific biological infectivity can be produced in vitro. Using a system that generates infectious prions de novo from purified recombinant PrP and conversion cofactors palmitoyl-oleoyl-phosphatidylglycerol (POPG) and RNA, we examined by deuterium exchange mass spectrometry (DXMS) the stepwise protein conformational changes that occur during prion formation. We found that initial incubation with POPG causes major structural changes in PrP involving all three α helices and one β strand, with subsequent addition of RNA rendering the N terminus highly exposed. Final conversion into the infectious PrP(Sc) form was accompanied by globally decreased solvent exposure, with persistence of the major cofactor-induced conformational features. Thus, we report that cofactor molecules appear to induce major structural rearrangements during prion formation, initiating a dynamic sequence of conformational changes resulting in biologically active prions.

Water signal attenuation by D2O infusion as a novel contrast mechanism for 1H perfusion MRI

Deuterium oxide (D2 O), which is commercially available and nonradioactive, was proposed as a perfusion tracer before the clinical usage of conventional gadolinium-based MRI contrast agents. However, the sensitivity of direct deuterium detection is the major challenge for its application. In this study, we propose a contrast-enhanced strategy to indirectly trace administered D2 O by monitoring the signal attenuation of (1) H MRI. Experiments on D2 O concentration phantoms and in vivo rat brains were conducted to prove the concept of the proposed contrast mechanism. An average maximum signal drop ratio of 5.25 ± 0.91% was detected on (1) H MR images of rat brains with 2 mL of D2 O administered per 100 g of body weight. As a diffusible tracer for perfusion, D2 O infusion is a practicable method for the assessment of tissue perfusion and has the potential to provide different information from gadolinium-based contrast agents, which have limited permeability for blood vessels. Furthermore, the observed negative relaxivities of D2 O reveal the (1) H-D exchange effect. Therefore, applications of perfusion MRI with D2 O as a contrast agent are worthy of further investigation.

Burial of the polymorphic residue 129 in amyloid fibrils of prion stop mutants

Misfolding of the natively α-helical prion protein into a β-sheet rich isoform is related to various human diseases such as Creutzfeldt-Jakob disease and Gerstmann-Sträussler-Scheinker syndrome. In humans, the disease phenotype is modified by a methionine/valine polymorphism at codon 129 of the prion protein gene. Using a combination of hydrogen/deuterium exchange coupled to NMR spectroscopy, hydroxyl radical probing detected by mass spectrometry, and site-directed mutagenesis, we demonstrate that stop mutants of the human prion protein have a conserved amyloid core. The 129 residue is deeply buried in the amyloid core structure, and its mutation strongly impacts aggregation. Taken together the data support a critical role of the polymorphic residue 129 of the human prion protein in aggregation and disease.

Determination of amyloid core structure using chemical shifts

Amyloid fibrils are the pathological hallmark of a large variety of neurodegenerative disorders. The structural characterization of amyloid fibrils, however, is challenging due to their non-crystalline, heterogeneous, and often dynamic nature. Thus, the structure of amyloid fibrils of many proteins is still unknown. We here show that the structure calculation program CS-Rosetta can be used to obtain insight into the core structure of amyloid fibrils. Driven by experimental solid-state NMR chemical shifts and taking into account the polymeric nature of fibrils CS-Rosetta allows modeling of the core of amyloid fibrils. Application to the Y145X stop mutant of the human prion protein reveals a left-handed β-helix.

Using multiple structural proteomics approaches for the characterization of prion proteins

Structural proteomics approaches are valuable tools, particularly in cases where the exact mechanisms of protein conformational changes or the structures of proteins and protein complexes cannot be elucidated by traditional structural biology techniques like X-ray crystallography or NMR methods. Each structural proteomics method can provide a different set of data, all of which can be used as structural constraints for modeling the protein. We have applied a combination of limited proteolysis, surface modification, chemical crosslinking, and hydrogen/deuterium exchange for the characterization of structural differences in prion proteins in native monomeric and in the aggregated β-oligomeric states. Data from these multiple proteomics approaches are in remarkable agreement in pointing to the rearrangement of the beta sheet 1-helix1-beta sheet 2-helix 2 (β1-H1-β2-H2) region as a major conformational change between the native and oligomeric prion protein forms. This data is also consistent with the β1-H1-β2 loop moving away from the H2-H3 core during the prion protein conversion. This is an example of how complementary data from multiple structural proteomics approaches can provide novel insights into the three-dimensional structures of proteins and protein complexes. This article is part of a Special Issue entitled: From protein structures to clinical applications.

Non-reducing alkaline solubilization and rapid on-column refolding of recombinant prion protein

Mature prion protein (PrP) is a 208-residue polypeptide that contains a single disulfide bond. We report an alternative method to purify recombinant mouse PrP produced in Escherichia coli. Bacterial inclusion bodies were solubilized in a buffer containing 2 M urea at pH 12.5. The solubilized protein was rapidly purified on a nickel affinity column without a chaotrope gradient, followed by ion-exchange chromatography. The yield and purity of PrP produced by this alternative approach was similar to that obtained using a conventional solubilization and on-column refolding protocol. Recombinant PrP produced using the non-reducing purification protocol is properly folded, as determined by circular dichroism, and a competent substrate for amyloid fibril formation, as determined by Thoflavin-T dye binding assays. In summary, this report describes a rapid method for producing properly folded recombinant PrP without reducing agents or a chaotrope gradient.

MALDI-ToF mass spectrometry for studying noncovalent complexes of biomolecules

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been demonstrated to be a valuable tool to investigate noncovalent interactions of biomolecules. The direct detection of noncovalent assemblies is often more troublesome than with electrospray ionization. Using dedicated sample preparation techniques and carefully optimized instrumental parameters, a number of biomolecule assemblies were successfully analyzed. For complexes dissociating under MALDI conditions, covalent stabilization with chemical cross-linking is a suitable alternative. Indirect methods allow the detection of noncovalent assemblies by monitoring the fading of binding partners or altered H/D exchange patterns.

Hydrogen exchange mass spectrometry as an analytical tool for the analysis of amyloid fibrillogenesis

In this study, we have used glucagon as a model system for analyzing amyloid fibrillogenesis by hydrogen exchange MALDI mass spectrometry (HXMS). The hydrogen exchange mass spectrometry data correlated well with the traditional method based on Thioflavin T fluorescence and provided quantitative information by measuring the fibrillating molecules directly. The hydrogen exchange mass spectrometry data collected during fibrillogenesis revealed that glucagon fibrillation was a two component system showing an on/off type of interaction where only monomeric and fibrils were present without any substantial amount of intermediate species. This was evident by the extensive deuteration of the monomer and protection of the entire 29 residue glucagon peptide upon fibrillation.. The method complements the traditional procedures and has the potential to provide new information with respect to the nature of transient species, the structure of the growing fibrils and the mechanism of formation.

Globular domain of the prion protein needs to be unlocked by domain swapping to support prion protein conversion

Prion diseases are fatal transmissible neurodegenerative diseases affecting many mammalian species. The normal prion protein (PrP) converts into a pathological aggregated form, PrPSc, which is enriched in the β-sheet structure. Although the high resolution structure of the normal PrP was determined, the structure of the converted form of PrP remains inaccessible to high resolution techniques. To map the PrP conversion process we introduced disulfide bridges into different positions within the globular domain of PrP, tethering selected secondary structure elements. The majority of tethered PrP mutants exhibited increased thermodynamic stability, nevertheless, they converted efficiently. Only the disulfides that tether subdomain B1-H1-B2 to subdomain H2-H3 prevented PrP conversion in vitro and in prion-infected cell cultures. Reduction of disulfides recovered the ability of these mutants to convert, demonstrating that the separation of subdomains is an essential step in conversion. Formation of disulfide-linked proteinase K-resistant dimers in fibrils composed of a pair of single cysteine mutants supports the model based on domain-swapped dimers as the building blocks of prion fibrils. In contrast to previously proposed structural models of PrPSc suggesting conversion of large secondary structural segments, we provide evidence for the conservation of secondary structural elements of the globular domain upon PrP conversion. Previous studies already showed that dimerization is the rate-limiting step in PrP conversion. We show that separation and swapping of subdomains of the globular domain is necessary for conversion. Therefore, we propose that the domain-swapped dimer of PrP precedes amyloid formation and represents a potential target for therapeutic intervention.

Experimental approaches to the interaction of the prion protein with nucleic acids and glycosaminoglycans: Modulators of the pathogenic conversion

The concept that transmissible spongiform encephalopathies (TSEs) are caused only by proteins has changed the traditional paradigm that disease transmission is due solely to an agent that carries genetic information. The central hypothesis for prion diseases proposes that the conversion of a cellular prion protein (PrP(C)) into a misfolded, β-sheet-rich isoform (PrP(Sc)) accounts for the development of (TSE). There is substantial evidence that the infectious material consists chiefly of a protein, PrP(Sc), with no genomic coding material, unlike a virus particle, which has both. However, prions seem to have other partners that chaperone their activities in converting the PrP(C) into the disease-causing isoform. Nucleic acids (NAs) and glycosaminoglycans (GAGs) are the most probable accomplices of prion conversion. Here, we review the recent experimental approaches that have been employed to characterize the interaction of prion proteins with nucleic acids and glycosaminoglycans. A PrP recognizes many nucleic acids and GAGs with high affinities, and this seems to be related to a pathophysiological role for this interaction. A PrP binds nucleic acids and GAGs with structural selectivity, and some PrP:NA complexes can become proteinase K-resistant, undergoing amyloid oligomerization and conversion to a β-sheet-rich structure. These results are consistent with the hypothesis that endogenous polyanions (such as NAs and GAGs) may accelerate the rate of prion disease progression by acting as scaffolds or lattices that mediate the interaction between PrP(C) and PrP(Sc) molecules. In addition to a still-possible hypothesis that nucleic acids and GAGs, especially those from the host, may modulate the conversion, the recent structural characterization of the complexes has raised the possibility of developing new diagnostic and therapeutic strategies.

Prion fibrillization is mediated by a native structural element that comprises helices H2 and H3

Aggregation and misfolding of the prion protein (PrP) are thought to be the cause of a family of lethal neurodegenerative diseases affecting humans and other animals. Although the structures of PrP from several species have been solved, still little is known about the mechanisms that lead to the misfolded species. Here, we show that the region of PrP comprising the hairpin formed by the helices H2 and H3 is a stable independently folded unit able to retain its secondary and tertiary structure also in the absence of the rest of the sequence. We also prove that the isolated H2H3 is highly fibrillogenic and forms amyloid fibers morphologically similar to those obtained for the full-length protein. Fibrillization of H2H3 but not of full-length PrP is concomitant with formation of aggregates. These observations suggest a "banana-peeling" mechanism for misfolding of PrP in which H2H3 is the aggregation seed that needs to be first exposed to promote conversion from a helical to a beta-rich structure.

Tetracysteine-tagged prion protein allows discrimination between the native and converted forms

The conformational conversion of prion protein (PrP) from a native conformation to the amyloid form is a hallmark of transmissible spongiform encephalopathies. Conversion is usually monitored by fluorescent dyes, which bind generic amyloids and are less suited for living cell imaging. We report a new method for the synthesis of membrane-permeable and membrane-impermeable biarsenical reagents, which are then used to monitor murine PrP (mPrP) misfolding. We introduced tetracysteine (TC) tags into three different positions of mPrP, which folded into a native-like structure. Whereas mPrPs with a TC tag inserted at the N-terminus or C-terminus supported fibril formation, insertion into the helix 2-helix 3 loop inhibited conversion. We devised a quantitative protease-free method to determine the fraction of converted PrP, based on the ability of the fluorescein arsenical helix binder reagent to differentiate between the monomeric and fibrilized form of TC-tagged PrP, and showed that TC-tagged mPrP could be detected on transfected cells, thereby expanding the potential use of this method for the detection and study of conformational diseases.