Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing

Abeta(1-40) fibril polymorphism implies diverse interaction patterns in amyloid fibrils

Amyloid fibrils characterize a diverse group of human diseases that includes Alzheimer's disease, Creutzfeldt-Jakob and type II diabetes. Alzheimer's amyloid fibrils consist of amyloid-beta (Abeta) peptide and occur in a range of structurally different fibril morphologies. The structural characteristics of 12 single Abeta(1-40) amyloid fibrils, all formed under the same solution conditions, were determined by electron cryo-microscopy and three-dimensional reconstruction. The majority of analyzed fibrils form a range of morphologies that show almost continuously altering structural properties. The observed fibril polymorphism implies that amyloid formation can lead, for the same polypeptide sequence, to many different patterns of inter- or intra-residue interactions. This property differs significantly from native, monomeric protein folding reactions that produce, for one protein sequence, only one ordered conformation and only one set of inter-residue interactions.

In situ Abeta pores in AD brain are cylindrical assembly of Abeta protofilaments

According to the amyloid pore hypothesis, pores formed by small oligomers of misfolded amyloidogenic proteins cause membrane leakage with the unregulated rapid influx of ions leading to cell death. Ultrastructurally, pores reconstituted in vitro have mainly been characterised so far, and the presence of in situ pores in the amyloid tissues has not yet been demonstrated. In this study, the presence of in situbeta amyloid (Abeta) pores was shown with high resolution transmission electron microscopy, in the neuronal cell membrane as well as in the membrane of mitochondria-like organelles in the brain with Alzheimer's disease. They are 16 nm wide and 11 nm long flat columnar structures made up of a single cylindrical layer (wall) of laterally associated Abeta protofilaments which surrounds a 10 nm wide opening or lumen. Protofilaments are the basic unit of the fibrils of all amyloid-forming proteins and peptides. Individual extracellular Abeta protofilaments were 2-3 nm wide straight tubular structures with helical wall formed by the tight coiling of 1 nm wide Abeta filaments. These in situ Abeta pores are similar but not identical to in vitro reconstituted Abeta pores.

Problems in fitting high resolution structures into electron microscopic reconstructions

Great advances have been made in electron microscopy (EM) over the past decade, with the result that a number of protein complexes have been solved at near-atomic resolution using EM imaging. However, only a limited number of such complexes are expected to have the high degree of internal order needed to achieve this type of resolution. Many other complexes and polymers will be visualized and reconstructed by EM at an intermediate level of resolution, where the polypeptide chain cannot be directly traced. Crystal and nuclear magnetic resonance structures for components or subunits of these higher-order assemblies are frequently available. One of the greatest strengths of EM continues to be the ability to dock high-resolution structures of components into low or intermediate resolution reconstructions of assemblies to build pseudoatomic models for quaternary structure. This review discusses the strengths and limitations of this approach, with particular emphasis on protein polymers. I discuss how limitations in resolution can lead to ambiguities in building models, and these cannot be always be resolved with available data. The use of homology models for quaternary structure are particularly problematic, given accumulating evidence for the divergence of quaternary structures at the same time that tertiary structure can be conserved.

Direct characterization of amyloidogenic oligomers by single-molecule fluorescence

A key issue in understanding the pathogenic conditions associated with the aberrant aggregation of misfolded proteins is the identification and characterization of species formed during the aggregation process. Probing the nature of such species has, however, proved to be extremely challenging to conventional techniques because of their transient and heterogeneous character. We describe here the application of a two-color single-molecule fluorescence technique to examine the assembly of oligomeric species formed during the aggregation of the SH3 domain of PI3 kinase. The single-molecule experiments show that the species formed at the stage of the reaction where aggregates have previously been found to be maximally cytotoxic are a heterogeneous ensemble of oligomers with a median size of 38 +/- 10 molecules. This number is remarkably similar to estimates from bulk measurements of the critical size of species observed to seed ordered fibril formation and of the most infective form of prion particles. Moreover, although the size distribution of the SH3 oligomers remains virtually constant as the time of aggregation increases, their stability increases substantially. These findings together provide direct evidence for a general mechanism of amyloid aggregation in which the stable cross-beta structure emerges via internal reorganization of disordered oligomers formed during the lag phase of the self-assembly reaction.

Characterization of dry globular proteins and protein fibrils by synchrotron radiation vacuum UV circular dichroism

Circular dichroism using synchrotron radiation (SRCD) can extend the spectral range down to approximately 130 nm for dry proteins, potentially providing new structural information. Using a selection of dried model proteins, including alpha-helical, beta-sheet, and mixed-structure proteins, we observe a low-wavelength band in the range 130-160 nm, whose intensity and peak position is sensitive to the secondary structure of the protein and may also reflect changes in super-secondary structure. This band has previously been observed for peptides but not for globular proteins, and is compatible with previously published theoretical calculations related to pi-orbital transitions. We also show that drying does not lead to large changes in the secondary structure and does not induce orientational artifacts. In combination with principal component analysis, our SRCD data allow us to distinguish between two different types of protein fibrils, highlighting that bona fide fibrils formed by lysozyme are structurally more similar to the nonclassical fibrillar aggregates formed by the SerADan peptide than with the amyloid formed by alpha-synuclein. Thus, despite the lack of direct structural conclusions, a comprehensive SRCD-based database of dried protein spectra may provide a useful method to differentiate between various types of supersecondary structure and aggregated protein species.

Fluorescent proteins as biomarkers and biosensors: throwing color lights on molecular and cellular processes

Green fluorescent protein (GFP) from jellyfish Aequorea victoria is the most extensively studied and widely used in cell biology protein. GFP-like proteins constitute a fast growing family as several naturally occurring GFP-like proteins have been discovered and enhanced mutants of Aequorea GFP have been created. These mutants differ from wild-type GFP by conformational stability, quantum yield, spectroscopic properties (positions of absorption and fluorescence spectra) and by photochemical properties. GFP-like proteins are very diverse, as they can be not only green, but also blue, orange-red, far-red, cyan, and yellow. They also can have dual-color fluorescence (e.g., green and red) or be non-fluorescent. Some of them possess kindling property, some are photoactivatable, and some are photoswitchable. This review is an attempt to characterize the main color groups of GFP-like proteins, describe their structure and mechanisms of chromophore formation, systemize data on their conformational stability and summarize the main trends of their utilization as markers and biosensors in cell and molecular biology.

Scrapie prion protein structural constraints obtained by limited proteolysis and mass spectrometry

Elucidation of the structure of scrapie prion protein (PrP(Sc)), essential to understand the molecular mechanism of prion transmission, continues to be one of the major challenges in prion research and is hampered by the insolubility and polymeric character of PrP(Sc). Limited proteolysis is a useful tool to obtain insight on structural features of proteins: proteolytic enzymes cleave proteins more readily at exposed sites, preferentially within loops, and rarely in beta-strands. We treated PrP(Sc) isolated from brains of hamsters infected with 263K and drowsy prions with varying concentrations of proteinase K (PK). After PK deactivation, PrP(Sc) was denatured, reduced, and cleaved at Cys179 with 2-nitro-5-thiocyanatobenzoic acid. Fragments were analyzed by nano-HPLC/mass spectrometry and matrix-assisted laser desorption/ionization. Besides the known cleavages at positions 90, 86, and 92 for 263K prions and at positions 86, 90, 92, 98, and 101 for drowsy prions, our data clearly demonstrate the existence of additional cleavage sites at more internal positions, including 117, 119, 135, 139, 142, and 154 in both strains. PK concentration dependence analysis and limited proteolysis after partial unfolding of PrP(Sc) confirmed that only the mentioned cleavage sites at the N-terminal side of the PrP(Sc) are susceptible to PK. Our results indicate that besides the "classic" amino-terminal PK cleavage points, PrP(Sc) contains, in its middle core, regions that show some degree of susceptibility to proteases and must therefore correspond to subdomains with some degree of structural flexibility, interspersed with stretches of amino acids of high resistance to proteases. These results are compatible with a structure consisting of short beta-sheet stretches connected by loops and turns.

Amyloid fibrils: abnormal protein assembly

Amyloid refers to the abnormal fibrous, extracellular, proteinaceous deposits found in organs and tissues. Amyloid is insoluble and is structurally dominated by beta-sheet structure. Unlike other fibrous proteins it does not commonly have a structural, supportive or motility role but is associated with the pathology seen in a range of diseases known as the amyloidoses. These diseases include Alzheimer's, the spongiform encephalopathies and type II diabetes, all of which are progressive disorders with associated high morbidity and mortality. Not surprisingly, research into the physicochemical properties of amyloid and its formation is currently intensely pursued. In this chapter we will highlight the key scientific findings and discuss how the stability of amyloid fibrils impacts on bionanotechnology.

Structure-function relationships of pre-fibrillar protein assemblies in Alzheimer's disease and related disorders

Several neurodegenerative diseases, including Alzheimer's, Parkinson's, Huntington's and prion diseases, are characterized pathognomonically by the presence of intra- and/or extracellular lesions containing proteinaceous aggregates, and by extensive neuronal loss in selective brain regions. Related non-neuropathic systemic diseases, e.g., light-chain and senile systemic amyloidoses, and other organ-specific diseases, such as dialysis-related amyloidosis and type-2 diabetes mellitus, also are characterized by deposition of aberrantly folded, insoluble proteins. It is debated whether the hallmark pathologic lesions are causative. Substantial evidence suggests that these aggregates are the end state of aberrant protein folding whereas the actual culprits likely are transient, pre-fibrillar assemblies preceding the aggregates. In the context of neurodegenerative amyloidoses, the proteinaceous aggregates may eventuate as potentially neuroprotective sinks for the neurotoxic, oligomeric protein assemblies. The pre-fibrillar, oligomeric assemblies are believed to initiate the pathogenic mechanisms that lead to synaptic dysfunction, neuronal loss, and disease-specific regional brain atrophy. The amyloid beta-protein (Abeta), which is believed to cause Alzheimer's disease (AD), is considered an archetypal amyloidogenic protein. Intense studies have led to nominal, functional, and structural descriptions of oligomeric Abeta assemblies. However, the dynamic and metastable nature of Abeta oligomers renders their study difficult. Different results generated using different methodologies under different experimental settings further complicate this complex area of research and identification of the exact pathogenic assemblies in vivo seems daunting. Here we review structural, functional, and biological experiments used to produce and study pre-fibrillar Abeta assemblies, and highlight similar studies of proteins involved in related diseases. We discuss challenges that contemporary researchers are facing and future research prospects in this demanding yet highly important field.

Coalescence of spherical beads of retro-HSP12.6 into linear and ring-shaped amyloid nanofibers

The sequence-reversed form of a small heat shock protein, HSP12.6 (retro-HSP12.6), has been reported to fold and assemble into structured tetramers in aqueous solution. Upon raising the protein concentration to ~1.0-1.5 mg/ml, tetrameric retro-HSP12.6 is known to display a tendency to associate further into spherical beads of 18-20 nm in diameter containing folded protein subunits. Here we report that storage of this protein at low temperatures leads to further association of the beaded structures into linear and ring-shaped amyloid nanofibers of 18-20 nm in diameter. The electron micrographs presented in this communication provide the best visual evidence yet that amyloids can form through the association of smaller structured bead-like intermediates. The results also suggest that folded beta-sheet-rich subunits can participate in amyloid formation.

Amyloidogenesis of natively unfolded proteins

Aggregation and subsequent development of protein deposition diseases originate from conformational changes in corresponding amyloidogenic proteins. The accumulated data support the model where protein fibrillogenesis proceeds via the formation of a relatively unfolded amyloidogenic conformation, which shares many structural properties with the pre-molten globule state, a partially folded intermediate first found during the equilibrium and kinetic (un)folding studies of several globular proteins and later described as one of the structural forms of natively unfolded proteins. The flexibility of this structural form is essential for the conformational rearrangements driving the formation of the core cross-beta structure of the amyloid fibril. Obviously, molecular mechanisms describing amyloidogenesis of ordered and natively unfolded proteins are different. For ordered protein to fibrillate, its unique and rigid structure has to be destabilized and partially unfolded. On the other hand, fibrillogenesis of a natively unfolded protein involves the formation of partially folded conformation; i.e., partial folding rather than unfolding. In this review recent findings are surveyed to illustrate some unique features of the natively unfolded proteins amyloidogenesis.

Structural basis of infectious and non-infectious amyloids

Amyloid fibrils are elongated protein aggregates well known for their association with many human diseases. However, similar structures have also been found in other organisms and amyloid fibrils can also be formed in vitro by other proteins usually under non-physiological conditions. In all cases, these fibrils assemble in a nucleated polymerization reaction with a pronounced lag phase that can be eliminated by supplying pre-formed fibrils as seeds. Once formed, the fibrils are usually very stable, except for their tendency to break into smaller pieces forming more growing ends in the process. These properties give amyloid fibers a self-replicating character dependent only on a source of soluble protein. For some systems and under certain circumstances this can lead to infectious protein structures, so-called prions, that can be passed from one organism to another as in the transmissible spongiform encephalopathies and in fungal prion systems. Structural details about these processes have emerged only recently, mostly on account of the inability of traditional high-resolution methods to deal with insoluble, filamentous specimens. In consequence, current models for amyloid fibrils are based on fewer constraints than common atomic-resolution structures. This review gives an overview of the constraints used for the development of amyloid models and the methods used to derive them. The principally possible structures will be introduced by discussing current models of amyloid fibrils from Alzheimer's beta-peptide, amylin and several fungal systems. The infectivity of some amyloids under specific conditions might not be due to a principal structural difference between infectious and non-infectious amyloids, but could result from an interplay of the rates for filament nucleation, growth, fragmentation, and clearance.

Self-assembly of the octapeptide lanreotide and lanreotide-based derivatives: the role of the aromatic residues

We investigated the spectroscopic properties of the aromatic residues in a set of octapeptides with various self-assembly properties. These octapeptides are based on lanreotide, a cyclic peptide analogue of somatostatin-14 that spontaneously self-assembles into very long and monodisperse hollow nanotubes. A previous study on these lanreotide-based derivatives has shown that the disulfide bridge, the peptide hairpin conformation and the aromatic residues are involved in the self-assembly process and that modification of these properties either decreases the self-assembly propensity or modifies the molecular packing resulting in different self-assembled architectures. In this study we probed the local environment of the aromatic residues, naphthyl-alanine, tryptophan and tyrosine, by Raman and fluorescence spectroscopy, comparing nonassembled peptides at low concentrations with the self-assembled ones at high concentrations. As expected, the spectroscopic characteristics of the aromatic residues were found to be sensitive to the peptide-peptide interactions. Among the most remarkable features we could record a very unusual Raman spectrum for the tyrosine of lanreotide in relation to its propensity to form H-bonds within the assemblies. In Lanreotide nanotubes, and also in the supramolecular architectures formed by its derivatives, the tryptophan side chain is water-exposed. Finally, the low fluorescence polarization of the peptide aggregates suggests that fluorescence energy transfer occurs within the nanotubes.

Possibilities for 'smart' materials exploiting the self-assembly of polypeptides into fibrils

Programmed assembly and self-assembly of soft materials offers significant promise for the generation of new types of materials with useful properties. Through evolutionary processes occurring over billions of years, nature has produced numerous optimised building blocks for the controlled assembly of a wide range of complex architectures. Our challenge now is to imitate these naturally occurring processes for technological applications, either using biological molecules such as DNA and proteins, or macromolecular mimics that retain many of the important features of biological molecules while introducing new functionalities. We focus on a single example of biomolecular self-assembly-the self-assembly of polypeptides, including polypeptide mimics, into quasi-one-dimensional fibres-to provide a flavour of the utility of soft biological materials for construction purposes.

Molecular origin of the self-assembly of lanreotide into nanotubes: a mutational approach

Lanreotide, a synthetic, therapeutic octapeptide analog of somatostatin, self-assembles in water into perfectly hollow and monodisperse (24-nm wide) nanotubes. Lanreotide is a cyclic octapeptide that contains three aromatic residues. The molecular packing of the peptide in the walls of a nanotube has recently been characterized, indicating four hierarchical levels of organization. This is a fascinating example of spontaneous self-organization, very similar to the formation of the gas vesicle walls of Halobacterium halobium. However, this unique peptide self-assembly raises important questions about its molecular origin. We adopted a directed mutation approach to determine the molecular parameters driving the formation of such a remarkable peptide architecture. We have modified the conformation by opening the cycle and by changing the conformation of a Lys residue, and we have also mutated the aromatic side chains of the peptide. We show that three parameters are essential for the formation of lanreotide nanotubes: i), the specificity of two of the three aromatic side chains, ii), the spatial arrangement of the hydrophilic and hydrophobic residues, and iii), the aromatic side chain in the beta-turn of the molecule. When these molecular characteristics are modified, either the peptides lose their self-assembling capability or they form less-ordered architectures, such as amyloid fibers and curved lamellae. Thus we have determined key elements of the molecular origins of lanreotide nanotube formation.

Peptide fibrillization

The fibrillization of peptides is relevant to many diseases based on the deposition of amyloids. The formation of fibrils is being intensively studied, especially in terms of nanotechnology applications, where fibrillar peptide hydrogels are used for cell scaffolds, as supports for functional and responsive biomaterials, biosensors, and nanowires. This Review is concerned with fundamental aspects of the self-assembly of peptides into fibrils, and discusses both natural amyloid-forming peptides and synthetic materials, including peptide fragments, copolymers, and amphiphiles.

Nanoimaging in protein-misfolding and -conformational diseases

Protein misfolding and the subsequent assembly of protein molecules into aggregates of various morphologies represent common mechanisms that link a number of important human diseases, known as protein-misfolding diseases. The current list of these disorders includes (but is not limited to) numerous neurodegenerative diseases, cataracts, arthritis, medullary carcinoma of the thyroid, late-onset diabetes mellitus, symptomatic (hemodialysis-related) beta(2)-microglobulin amyloidosis, arthritis and many other systemic, localized and familial amyloidoses. Progress in understanding protein-misfolding pathologies and in potential rational drug design aimed at the inhibition or reversal of protein aggregation depends on our ability to study the details of the misfolding process, to follow the aggregation process and to see and analyze the structure and mechanical properties of the aggregated particles. Nanoimaging provides a method to monitor the aggregation process, visualize protein aggregates and analyze their properties and provides fundamental knowledge of key factors that lead to protein misfolding and self-assembly in various protein-misfolding pathologies, therefore advancing medicine dramatically.

Peptide conformation and supramolecular organization in amylin fibrils: constraints from solid-state NMR

The 37-residue amylin peptide, also known as islet amyloid polypeptide, forms fibrils that are the main peptide or protein component of amyloid that develops in the pancreas of type 2 diabetes patients. Amylin also readily forms amyloid fibrils in vitro that are highly polymorphic under typical experimental conditions. We describe a protocol for the preparation of synthetic amylin fibrils that exhibit a single predominant morphology, which we call a striated ribbon, in electron microscopy and atomic force microscopy images. Solid-state nuclear magnetic resonance (NMR) measurements on a series of isotopically labeled samples indicate a single molecular structure within the striated ribbons. We use scanning transmission electron microscopy and several types of one- and two-dimensional solid-state NMR techniques to obtain constraints on the peptide conformation and supramolecular structure in these amylin fibrils and to derive molecular structural models that are consistent with the experimental data. The basic structural unit in amylin striated ribbons, which we call the protofilament, contains four layers of parallel beta-sheets, formed by two symmetric layers of amylin molecules. The molecular structure of amylin protofilaments in striated ribbons closely resembles the protofilament in amyloid fibrils with a similar morphology formed by the 40-residue beta-amyloid peptide that is associated with Alzheimer's disease.

How is protein aggregation in amyloidogenic diseases modulated by biological membranes?

The fate of proteins with amyloidogenic properties depends critically on their immediate biochemical environment. However, the role of biological interfaces such as membrane surfaces, as promoters of pathological aggregation of amyloidogenic proteins, is rarely studied and only established for the amyloid-beta protein (A beta) involved in Alzheimer's disease, and alpha-synuclein in Parkinsonism. The occurrence of binding and misfolding of these proteins on membrane surfaces, is poorly understood, not at least due to the two-dimensional character of this event. Clearly, the nature of the folding pathway for A beta protein adsorbed upon two-dimensional aggregation templates, must be fundamentally different from the three-dimensional situation in solution. Here, we summarize the current research and focus on the function of membrane interfaces as aggregation templates for amyloidogenic proteins (and even prionic ones). One major aspect will be the relationship between membrane properties and protein association and the consequences for amyloidogenic products. The other focus will be on a general understanding of protein folding pathways on two-dimensional templates on a molecular level. Finally, we will demonstrate the potential importance of membrane-mediated aggregation for non-amphiphatic soluble amyloidogenic proteins, by using the SOD1 protein involved in the amyotrophic lateral sclerosis syndrome.

Charge transport and intrinsic fluorescence in amyloid-like fibrils

The self-assembly of polypeptides into stable, conductive, and intrinsically fluorescent biomolecular nanowires is reported. We have studied the morphology and electrical conduction of fibrils made of an elastin-related polypeptide, poly(ValGlyGlyLeuGly). These amyloid-like nanofibrils, with a diameter ranging from 20 to 250 nm, result from self-assembly in aqueous solution at neutral pH. Their morphological properties and conductivity have been investigated by atomic force microscopy, scanning tunneling microscopy, and two-terminal transport experiments at the micro- and nanoscales. We demonstrate that the nanofibrils can sustain significant electrical conduction in the solid state at ambient conditions and have remarkable stability. We also show intrinsic blue-green fluorescence of the nanofibrils by confocal microscopy analyses. These results indicate that direct (label-free) excitation can be used to investigate the aggregation state or the polymorphism of amyloid-like fibrils (and possibly of other proteinaceous material) and open up interesting perspectives for the use of peptide-based nanowire structures, with tunable physical and chemical properties, for a wide range of nanobiotechnological and bioelectronic applications.

CSSP2: An improved method for predicting contact-dependent secondary structure propensity

The calculation of contact-dependent secondary structure propensity (CSSP) has been reported to sensitively detect non-native beta-strand propensities in the core sequences of amyloidogenic proteins. Here we describe a noble energy-based CSSP method implemented on dual artificial neural networks that rapidly and accurately estimate the potential for the non-native secondary structure formation in local regions of protein sequences. In this method, we attempted to quantify long-range interaction patterns in diverse secondary structures by potential energy calculations and decomposition on a pairwise per-residue basis. The calculated energy parameters and seven-residue sequence information were used as inputs for artificial neural networks (ANNs) to predict sequence potential for secondary structure conversion. The trained single ANN using the >(i, i+/-4) interaction energy parameter exhibited 74% accuracy in predicting the secondary structure of test sequences in their native energy state, while the dual ANN-based predictor using (i, i+/-4) and >(i, i+/-4) interaction energies showed 83% prediction accuracy. The present method provides a simple and accurate tool for predicting sequence potential for secondary structure conversions without using 3D structural information.

Evidence of native-like substructure(s) in polypeptide chains of carbonic anhydrase deposited into insoluble aggregates during thermal unfolding

A non-specific protease, subtilisin, was used to probe the existence of folded structure in thermal aggregates of bovine carbonic anhydrase-II (BCA). BCA aggregates and native BCA were subjected to proteolysis and electrophoretic analyses which revealed the accumulation of polypeptide fragments of similar size, indicating survival of similar sections of folded structure burying peptide bonds away from scission in the two samples. N-terminal sequencing revealed that the termini of size-matched fragments from the two samples were either identical, or located very close to each other, and predominantly on the surface of the 3-dimensional structure of native BCA. The susceptibility to proteolysis of very nearly the same sites in the two samples suggests that native-like elements of structure survive within BCA aggregates. The finding that thermal aggregation can involve interactions among molecules retaining elements of native-like structure, suggests that complete chain unfolding may not be a necessary prerequisite for all aggregation.

Elastic fibers and amyloid deposition in vascular tissue

Amyloid fibrils are associated with a large number of diseases, such as Alzheimer’s dementia and others. Evidence links Alzheimer’s dementia with vascular diseases and only few data connect amyloids and atherosclerosis and aging via deposits in the aortic intima. Recent results demonstrate that some elastin polypeptide sequences are also able to produce amyloid fibers. This finding could have useful implications in the study of amyloids in cardiovascular tissue whose main constituent is elastin. In this review, we have also outlined the main characterizing features regarding the structure of amyloid fibrils. Finally, we describe, as a future perspective, the design of proper inhibitors of amyloid deposition in vascular walls as potential therapeutic drugs.

High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus

The treatment of helical objects as a string of single particles has become an established technique to resolve their three-dimensional (3D) structure using electron cryo-microscopy. It can be applied to a wide range of helical particles such as viruses, microtubules and helical filaments. We have made improvements to this approach using Tobacco Mosaic Virus (TMV) as a test specimen and obtained a map from 210,000 asymmetric units at a resolution better than 5 A. This was made possible by performing a full correction of the contrast transfer function of the microscope. Alignment of helical segments was helped by constraints derived from the helical symmetry of the virus. Furthermore, symmetrization was implemented by multiple inclusions of symmetry-related views in the 3D reconstruction. We used the density map to build an atomic model of TMV. The model was refined using a real-space refinement strategy that accommodates multiple conformers. The atomic model shows significant deviations from the deposited model for the helical form of TMV at the lower-radius region (residues 88 to 109). This region appears more ordered with well-defined secondary structure, compared with the earlier helical structure. The RNA phosphate backbone is sandwiched between two arginine side-chains, stabilizing the interaction between RNA and coat protein. A cluster of two or three carboxylates is buried in a hydrophobic environment isolating it from neighboring subunits. These carboxylates may represent the so-called Caspar carboxylates that form a metastable switch for viral disassembly. Overall, the observed differences suggest that the new model represents a different, more stable state of the virus, compared with the earlier published model.

Novel method for quantitative determination of amyloid fibrils of α-synuclein and amyloid β/A4 protein by using resveratrol

Amyloidosis producing insoluble fibrillar protein aggregates is the common pathological feature of various neurodegenerative disorders such as Parkinson's and Alzheimer's diseases in which alpha-synuclein and amyloid beta/A4 protein (Abeta) participate to form Lewy bodies and senile plaques, respectively. To develop a novel analytical tool for amyloidosis, resveratrol, the major phenolic constituent of red wine and isolatable from grapevines, was employed to monitor the amyloids of alpha-synuclein and Abeta. Specific interaction to the amyloids enhanced the intrinsic fluorescence of resveratrol at 395 nm with an advent of new shoulder peak at 440 nm following an excitation at 320 nm. An increase in the resveratrol binding fluorescence was proportional to the quantity of amyloids. Typical sigmoidal kinetics of the amyloidosis of alpha-synuclein assessed with the thioflavin-T binding fluorescence or the beta-sheet content was fully reproduced by the resveratrol binding fluorescence. The resveratrol binding to the amyloids became saturated as the dye concentration increased, whereas the enhanced thioflavin-T binding fluorescence was quenched by the unbound thioflavin-T at the high dye concentration. Because resveratrol does not require any adjustment of the amyloid/dye ratio to obtain optimal amyloid binding fluorescence, and it exerts a higher quantum yield than does thioflavin-T, resveratrol is suggested to be a specific and more reliable fluorescent probe to determine the amyloids quantitatively.

Binding mode of Thioflavin T in insulin amyloid fibrils

Amyloid fibrils share various common structural features and their presence can be detected by Thioflavin T (ThT). In this paper, the binding mode of ThT to insulin amyloid fibrils was examined. Scatchard analysis and isothermal titration calorimetry (ITC) showed at least two binding site populations. The binding site population with the strongest binding was responsible for the characteristic ThT fluorescence. This binding had a capacity of about 0.1 moles of ThT bound per mole of insulin in fibril form. The binding capacity was unaffected by pH, but the affinity was lowest at low pH. Notably, presence of a third binding process prior to the other processes was suggested by ITC. Binding of ThT resulted in only minor changes in the fibril structure according to the X-ray diffraction patterns, where a slightly more dominant equatorial reflection at 16A relative to the intersheet distance of 11A was observed. No change in the interstrand distance of 4.8A was observed. On the basis of our results, we propose that ThT binds in cavities running parallel to the fibril axis, e.g., between the protofilaments forming the fibrils. Such cavities have been proposed previously in insulin fibrils and several other amyloid fibril models.

Kinetics and thermodynamics of amyloid formation from direct measurements of fluctuations in fibril mass

Aggregation of proteins and peptides is a widespread and much-studied problem, with serious implications in contexts ranging from biotechnology to human disease. An understanding of the proliferation of such aggregates under specific conditions requires a quantitative knowledge of the kinetics and thermodynamics of their formation; measurements that to date have remained elusive. Here, we show that precise determination of the growth rates of ordered protein aggregates such as amyloid fibrils can be achieved through real-time monitoring, using a quartz crystal oscillator, of the changes in the numbers of molecules in the fibrils from variations in their masses. We show further that this approach allows the effect of other molecular species on fibril growth to be characterized quantitatively. This method is widely applicable, and we illustrate its power by exploring the free-energy landscape associated with the conversion of the protein insulin to its amyloid form and elucidate the role of a chemical chaperone and a small heat shock protein in inhibiting the aggregation reaction.

Folding versus aggregation: polypeptide conformations on competing pathways

Protein aggregation has now become recognised as an important and generic aspect of protein energy landscapes. Since the discovery that numerous human diseases are caused by protein aggregation, the biophysical characterisation of misfolded states and their aggregation mechanisms has received increased attention. Utilising experimental techniques and computational approaches established for the analysis of protein folding reactions has ensured rapid advances in the study of pathways leading to amyloid fibrils and amyloid-related aggregates. Here we describe recent experimental and theoretical advances in the elucidation of the conformational properties of dynamic, heterogeneous and/or insoluble protein ensembles populated on complex, multidimensional protein energy landscapes. We discuss current understanding of aggregation mechanisms in this context and describe how the synergy between biochemical, biophysical and cell-biological experiments are beginning to provide detailed insights into the partitioning of non-native species between protein folding and aggregation pathways.

Study on the binding of Thioflavin T to β-sheet-rich and non-β-sheet cavities

Amyloid fibril formation plays a role in more than 20 diseases including Alzheimer's disease. In vitro detection of these fibrils is often performed using Thioflavin T (ThT), though the ThT binding mode is largely unknown. In the present study, spectral properties of ThT in binding environments representing beta-sheet-rich and non-beta-sheet cavities were examined. Acetylcholinesterase and gamma-cyclodextrin induced a characteristic ThT fluorescence similar to that with amyloid fibrils, whereas beta-cyclodextrin and the beta-sheet-rich transthyretin did not. The cavities of acetylcholinesterase and gamma-cyclodextrin were of similar diameter and only these cavities could accommodate two ThT ions according to molecular modelling. Binding stoichiometry studies also showed a possible binding of two ThT ions. Thus, the characteristic ThT fluorescence is induced in cavities with a diameter of 8-9A and a length able to accommodate the entire length of the ThT ion. The importance of a cavity diameter capable of binding two ThT ions, among others, indicates that an excimer formation is a plausible mechanism for the characteristic fluorescence. We propose a similar ThT binding mode in amyloid fibrils, where cavities of an appropriate size running parallel to the fibril axis have previously been proposed in several amyloid fibril models.

Fibrillogenic oligomers of human cystatin C are formed by propagated domain swapping

Cystatin C and the prion protein have been shown to form dimers via three-dimensional domain swapping, and this process has also been hypothesized to be involved in amyloidogenesis. Production of oligomers of other amyloidogenic proteins has been reported to precede fibril formation, suggesting oligomers as intermediates in fibrillogenesis. A variant of cystatin C, with a Leu68-->Gln substitution, is highly amyloidogenic, and carriers of this mutation suffer from massive cerebral amyloidosis leading to brain hemorrhage and death in early adulthood. This work describes doughnut-shaped oligomers formed by wild type and L68Q cystatin C upon incubation of the monomeric proteins. Purified oligomers of cystatin C are shown to fibrillize faster and at a lower concentration than the monomeric protein, indicating a role of the oligomers as fibril-assembly intermediates. Moreover, the present work demonstrates that three-dimensional domain swapping is involved in the formation of the oligomers, because variants of monomeric cystatin C, stabilized against three-dimensional domain swapping by engineered disulfide bonds, do not produce oligomers upon incubation under non-reducing conditions. Redox experiments using wild type and stabilized cystatin C strongly suggest that the oligomers, and thus probably the fibrils as well, are formed by propagated domain swapping rather than by assembly of domain-swapped cystatin C dimers.

Insulin amyloid fibrils form an inclusion complex with molecular iodine: a misfolded protein as a nanoscale scaffold

The study describes formation of an intensely violet inclusion complex of insulin amyloid fibrils and molecular iodine. Resonance Raman spectra of complexes formed by staining mature insulin fibrils with iodine and by seeding fibrils in the presence of iodine imply similar topologies of entrapped iodine and oligoiodide species. Iodine captured by growing fibrils remains accessible to a bulk chemical reagent. In light of its small size and the fact that iodine can partition into polar as well as nonpolar media, the data suggest that intrafibrillar structure of insulin amyloid is densely packed with no appreciable void volumes capable of accommodating iodine atoms. The complex is stable: only drastic perturbation of the beta-pleated fibrous scaffold by dimethyl sulfoxide (rather than of the beta-sheet conformation) leads to the release of iodine atoms from surface moieties. While the reaction between iodine and in vivo amyloid deposits was first described by Virchow in the 19th Century [Virchow, R. (1854) Virchows Arch. 6, 268-271], the underlying molecular mechanism has not been thoroughly explored since then. This work shows how the long-forgotten concept can be utilized as a probe of void volumes in protein fibrils, providing a new tool for structural studies on amyloids, and a model for design of protein-based drug delivery media.

AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides

Background

Protein aggregation correlates with the development of several debilitating human disorders of growing incidence, such as Alzheimer's and Parkinson's diseases. On the biotechnological side, protein production is often hampered by the accumulation of recombinant proteins into aggregates. Thus, the development of methods to anticipate the aggregation properties of polypeptides is receiving increasing attention. AGGRESCAN is a web-based software for the prediction of aggregation-prone segments in protein sequences, the analysis of the effect of mutations on protein aggregation propensities and the comparison of the aggregation properties of different proteins or protein sets.

Results

AGGRESCAN is based on an aggregation-propensity scale for natural amino acids derived from in vivo experiments and on the assumption that short and specific sequence stretches modulate protein aggregation. The algorithm is shown to identify a series of protein fragments involved in the aggregation of disease-related proteins and to predict the effect of genetic mutations on their deposition propensities. It also provides new insights into the differential aggregation properties displayed by globular proteins, natively unfolded polypeptides, amyloidogenic proteins and proteins found in bacterial inclusion bodies.

Conclusion

By identifying aggregation-prone segments in proteins, AGGRESCAN shall facilitate (i) the identification of possible therapeutic targets for anti-depositional strategies in conformational diseases and (ii) the anticipation of aggregation phenomena during storage or recombinant production of bioactive polypeptides or polypeptide sets.

A lattice protein with an amyloidogenic latent state: stability and folding kinetics

We have designed a model lattice protein that has two stable folded states, the lower free energy native state and a latent state of somewhat higher energy. The two states have a sizable part of their structures in common (two "alpha-helices") and differ in the content of "alpha-helices" and "beta-strands" in the rest of their structures; i.e. for the native state, this part is alpha-helical, and for the latent state it is composed of beta-strands. Thus, the lattice protein free energy surface mimics that of amyloidogenic proteins that form well organized fibrils under appropriate conditions. A Go-like potential was used and the folding process was simulated with a Monte Carlo method. To gain insight into the equilibrium free energy surface and the folding kinetics, we have combined standard approaches (reduced free energy surfaces, contact maps, time-dependent populations of the characteristic states, and folding time distributions) with a new approach. The latter is based on a principal coordinate analysis of the entire set of contacts, which makes possible the introduction of unbiased reaction coordinates and the construction of a kinetic network for the folding process. The system is found to have four characteristic basins, namely a semicompact globule, an on-pathway intermediate (the bifurcation basin), and the native and latent states. The bifurcation basin is shallow and consists of the structure common to the native and latent states, with the rest disorganized. On the basis of the simulation results, a simple kinetic model describing the transitions between the characteristic states was developed, and the rate constants for the essential transitions were estimated. During the folding process the system dwells in the bifurcation basin for a relatively short time before it proceeds to the native or latent state. We suggest that such a bifurcation may occur generally for proteins in which native and latent states have a sizable part of their structures in common. Moreover, there is the possibility of introducing changes in the system (e.g., mutations), which guide the system toward the native or misfolded state.

Conversion of a monodispersed globular protein into an amyloid-like filament by appending an artificial peptide at the N-terminal

The soluble, globular, alpha-helix-rich peptide SipA(446-684) is a domain of a bacterial protein that binds to mammalian filamentous-actin and re-arranges the host cell's cytoskeleton. We show that adding two copies of NHBP-1, a carbon nanomaterial binding peptide, to its N-terminal can induce SipA(446-684) to polymerize and assume a fibrillar structure under physiological conditions. The fibrils formed showed thioflavine T and Congo red staining profiles that are characteristic of and specific for amyloid-like structures. The alpha-helical structure of the globular protein was retained in the fibrils, suggesting the appended NHBP-1 sequence plays a key role in the formation of cross-beta spines within the fibrils. Consistent with that idea, we observed that a synthetic NHBP-1 peptide can form an amyloid-like structure under appropriate conditions. Thus, our findings add a new subtype of amyloid-like structure formation and suggest this method of assembly could be exploited in nano-biotechnology.

Protein misfolding, functional amyloid, and human disease

Peptides or proteins convert under some conditions from their soluble forms into highly ordered fibrillar aggregates. Such transitions can give rise to pathological conditions ranging from neurodegenerative disorders to systemic amyloidoses. In this review, we identify the diseases known to be associated with formation of fibrillar aggregates and the specific peptides and proteins involved in each case. We describe, in addition, that living organisms can take advantage of the inherent ability of proteins to form such structures to generate novel and diverse biological functions. We review recent advances toward the elucidation of the structures of amyloid fibrils and the mechanisms of their formation at a molecular level. Finally, we discuss the relative importance of the common main-chain and side-chain interactions in determining the propensities of proteins to aggregate and describe some of the evidence that the oligomeric fibril precursors are the primary origins of pathological behavior.

Heme binding inhibits the fibrillization of amyloidogenic apomyoglobin and determines lack of aggregate cytotoxicity

Myoglobin is an alpha-helical globular protein containing two highly conserved tryptophanyl residues at positions 7 and 14 in the N-terminal region. The double W/F replacement renders apomyoglobin highly susceptible to aggregation and amyloid-like fibril formation under physiological conditions. In this work we analyze the early stage of W7FW14F apomyoglobin aggregation following the time dependence of the process by far-UV CD, Fourier-transform infrared (FTIR) spectroscopy, and heme-binding properties. The results show that the aggregation of W7FW14F apomyoglobin starts from a native-like globin state able to bind the prosthetic group with spectroscopic properties similar to those observed for wild-type apoprotein. Nevertheless, it rapidly aggregates, forming amyloid fibrils. However, when the prosthetic group is added before the beginning of aggregation, amyloid fibrillization is inhibited, although the aggregation process is not prevented. Moreover, the apomyoglobin aggregates formed in these conditions are not cytotoxic differently from what is observed for all amyloidogenic proteins. These results open new insights into the relationship between the structure adopted by the protein into the aggregates and their ability to trigger the impairment of cell viability.

Amyloid fibrils formation and amorphous aggregation in concanavalin A

We here report an experimental study on the thermal aggregation process of concanavalin A, a protein belonging to the legume lectins family. The aggregation process and the involved conformational changes of the protein molecules were followed by means of fluorescence techniques, light scattering, circular dichroism, zeta potential measurements and atomic force microscopy. Our results show that the aggregation process of concanavalin A may evolve through two distinct pathways leading, respectively, to the formation of amyloids or amorphous aggregates. The relative extent of the two pathways is determined by pH, as amyloid aggregation is favored at high pH values ( approximately 9), while the formation of amorphous aggregates is favored at low pH ( approximately 5). At difference from amorphous aggregation, the formation of amyloid fibrils requires significant conformational changes on the protein, both at secondary and tertiary structural level. To our knowledge, this is the first observation of amyloid fibrils from concanavalin A.

Nanotools for megaproblems: probing protein misfolding diseases using nanomedicine modus operandi

Misfolding and self-assembly of proteins in nanoaggregates of different sizes and morphologies (nanoensembles, primary nanofilaments, nanorings, filaments, protofibrils, fibrils, etc.) is a common theme unifying a number of human pathologies termed protein misfolding diseases. Recent studies highlight increasing recognition of the public health importance of protein misfolding diseases, including various neurodegenerative disorders and amyloidoses. It is understood now that the first essential elements in the vast majority of neurodegenerative processes are misfolded and aggregated proteins. Altogether, the accumulation of abnormal protein nanoensembles exerts toxicity by disrupting intracellular transport, overwhelming protein degradation pathways, and/or disturbing vital cell functions. In addition, the formation of inclusion bodies is known to represent a major problem in the production of recombinant therapeutic proteins. Formulation of these therapeutic proteins into delivery systems and their in vivo delivery are often complicated by protein association. Thus, protein folding abnormalities and subsequent events underlie a multitude of human pathologies and difficulties with protein therapeutic applications. The field of medicine therefore can be greatly advanced by establishing a fundamental understanding of key factors leading to misfolding and self-assembly responsible for various protein folding pathologies. This article overviews protein misfolding diseases and outlines some novel and advanced nanotechnologies, including nanoimaging techniques, nanotoolboxes and nanocontainers, complemented by appropriate ensemble techniques, all focused on the ultimate goal to establish etiology and to diagnose, prevent, and cure these devastating disorders.

Prediction of amyloidogenic and disordered regions in protein chains

The determination of factors that influence protein conformational changes is very important for the identification of potentially amyloidogenic and disordered regions in polypeptide chains. In our work we introduce a new parameter, mean packing density, to detect both amyloidogenic and disordered regions in a protein sequence. It has been shown that regions with strong expected packing density are responsible for amyloid formation. Our predictions are consistent with known disease-related amyloidogenic regions for eight of 12 amyloid-forming proteins and peptides in which the positions of amyloidogenic regions have been revealed experimentally. Our findings support the concept that the mechanism of amyloid fibril formation is similar for different peptides and proteins. Moreover, we have demonstrated that regions with weak expected packing density are responsible for the appearance of disordered regions. Our method has been tested on datasets of globular proteins and long disordered protein segments, and it shows improved performance over other widely used methods. Thus, we demonstrate that the expected packing density is a useful value with which one can predict both intrinsically disordered and amyloidogenic regions of a protein based on sequence alone. Our results are important for understanding the structural characteristics of protein folding and misfolding.

Characterization of the nanoscale properties of individual amyloid fibrils

We report the detailed mechanical characterization of individual amyloid fibrils by atomic force microscopy and spectroscopy. These self-assembling materials, formed here from the protein insulin, were shown to have a strength of 0.6 +/- 0.4 GPa, comparable to that of steel (0.6-1.8 GPa), and a mechanical stiffness, as measured by Young's modulus, of 3.3 +/- 0.4 GPa, comparable to that of silk (1-10 GPa). The values of these parameters reveal that the fibrils possess properties that make these structures highly attractive for future technological applications. In addition, analysis of the solution-state growth kinetics indicated a breakage rate constant of 1.7 +/- 1.3 x 10(-8) s(-1), which reveals that a fibril 10 mum in length breaks spontaneously on average every 47 min, suggesting that internal fracturing is likely to be of fundamental importance in the proliferation of amyloid fibrils and therefore for understanding the progression of their associated pathogenic disorders.

Molecular alignment within beta-sheets in Abeta(14-23) fibrils: solid-state NMR experiments and theoretical predictions

We report investigations of the molecular structure of amyloid fibrils formed by residues 14-23 of the beta-amyloid peptide associated with Alzheimer's disease (Abeta(14-23)), using solid-state nuclear magnetic resonance (NMR) techniques in conjunction with electron microscopy and atomic force microscopy. The NMR measurements, which include two-dimensional proton-mediated (13)C-(13)C exchange and two-dimensional relayed proton-mediated (13)C-(13)C exchange spectra, show that Abeta(14-23) fibrils contain antiparallel beta-sheets with a registry of backbone hydrogen bonds that aligns residue 17+k of each peptide molecule with residue 22-k of neighboring molecules in the same beta-sheet. We compare these results, as well as previously reported experimental results for fibrils formed by other beta-amyloid fragments, with theoretical predictions of molecular alignment based on databases of residue-specific alignments in antiparallel beta-sheets in known protein structures. While the theoretical predictions are not in exact agreement with the experimental results, they facilitate the design of experiments by suggesting a small number of plausible alignments that are readily distinguished by solid-state NMR.