Implications for Alzheimer's disease of an atomic resolution structure of amyloid-β(1-42) fibrils

Bioinspired stormwater control measure for the enhanced removal of truly dissolved polycyclic aromatic hydrocarbons and heavy metals from urban runoff

Stormwater harvesting (SWH) addresses the UN's Sustainable Development Goals (SDGs). Conventional stormwater control measures (SCMs) effectively remove particulate and colloidal contaminants from urban runoff; however, they fail to retain dissolved contaminants, particularly substances of concern like polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs), thereby hindering the SWH applicability. Here, inspired by protein folding in nature, we reported a novel biomimetic SCM for the efficient removal of dissolved PAHs and HMs from urban runoff. Lab-scale tests were conducted together with a more mechanistic investigation on how the contaminants were removed. By integrating hydrophobic organic chains with low-cost hydrophilic flocculant matrixes, our biomimetic flocculants achieved a 1.4-9.5 times removal of all detected dissolved PAHs and HMs, while enhancing the removal of a wide-spectrum of particulate and colloidal contaminants, compared to existing SCMs. Ecotoxicity, as indicated by newborn Daphnia magna as experimental organisms, was reduced from "acute toxicity" of the original runoff sample (toxic unit of ∼2.6) to "non-toxicity" (toxic unit < 0.4) of the treated water. The improved performance is attributed to the protein-folding-like features of the bioinspired flocculants providing: (i) stronger binding to PAHs (via hydrophobic association) and HMs (via coordination), and (ii) the ability of spontaneous aggregation. The bio-inspired approach in this work holds strong promise as an alternative or supplementary component in SCM systems, and is expected to contribute to sustainable water management practices in relation to SDGs.

Protein-folding-inspired approach for UF fouling mitigation using elevated membrane cleaning temperature and residual hydrophobic-modified flocculant after flocculation-sedimentation pre-treatment

Hydrophobic-modified flocculants have demonstrated considerable promise in the removal of emerging contaminants by flocculation. However, there is a lack of information about the impacts of dosing such flocculants on the performance of subsequent treatment unit(s) in the overall water treatment process. In this work, inspired by the ubiquitous protein folding phenomenon, an innovative approach using an elevated membrane cleaning temperature as the means to induce residual hydrophobic-modified chitosan flocculant (TRC), after flocculation-sedimentation, to reduce membrane fouling in a subsequent ultrafiltration was proposed; this was evaluated in a continuous flocculation-sedimentation-ultrafiltration (FSUF) process treating samples of the Yangtze River. The hydrophobic chains of TRC had similar temperature-dependent hydrophobicity to those of natural proteins. In the 40-day operation of the FSUF system with combined dosing of alum and TRC, a moderately elevated cleaning water temperature (45 °C) of both backwash with air-bubbling and soaking with sponge-scrubbing cleaning, significantly reduced reversible and irreversible fouling resistance by 49.8%∼61.3% and 73.9%∼83.3%, respectively, compared to the system using cleaning water at 25 °C. Material flow analysis, statistical analysis, instrumental characterizations, and computational simulations, showed that the enhanced fouling mitigation originated from three factors: the reduced contaminant accumulation onto membranes, the strengthened membrane-surface-modification role of TRC, and the weakened structure of the fouling material containing TRC, at the elevated cleaning temperature. Other measures of the performance, these being water purification, membrane stability and economic aspects, also confirmed the potential and feasibility of the proposed approach. This work has provided new insights into the role of hydrophobic-modified flocculants in membrane fouling control, in addition to emerging contaminant removal, in a FSUF surface water treatment process.

Based on molecular structures: Amyloid-β generation, clearance, toxicity and therapeutic strategies

Amyloid-β (Aβ) has long been considered as one of the most important pathogenic factors in Alzheimer’s disease (AD), but the specific pathogenic mechanism of Aβ is still not completely understood. In recent years, the development of structural biology technology has led to new understandings about Aβ molecular structures, Aβ generation and clearance from the brain and peripheral tissues, and its pathological toxicity. The purpose of the review is to discuss Aβ metabolism and toxicity, and the therapeutic strategy of AD based on the latest progress in molecular structures of Aβ. The Aβ structure at the atomic level has been analyzed, which provides a new and refined perspective to comprehend the role of Aβ in AD and to formulate therapeutic strategies of AD.

Artemisia absinthium improves spatial performance and neuronal injury induced by amyloid- beta in the CA1 hippocampal area of male Wistar rats

Alzheimer's disease is a neurodegenerative disorder. It is characterized by the presence of two aberrant structures in the brain, those are, amyloid plaques and neurofibrillary tangles, along with neuronal death. Amyloid-beta further exacerbates the metabolic decline and results in cognitive impairments. Because of the favorable antioxidant and anti-inflammatory activities of Artemisia absinthium (wormwood), this study aimed to evaluate the effects of hydroalcoholic extract of this plant on spatial memory performance, neuronal injury, and apoptosis induced by amyloid-beta. Forty-eight male Wistar rats (220-250 g) were divided into the following groups: 1) control; 2) sham (solvent; ICV); 3) amyloid-beta 1-40 (ICV); and 4) amyloid-beta plus A. absinthium (10, 50, and 100 mg/kg/day; gavage). Congo red and TUNEL staining were performed to investigate the neuronal injury. Also, the Morris water maze (MWM) test was used to evaluate the spatial memory of the experimental groups. The results showed that spatial memory for finding the hidden platform in the MWM task decreased significantly in the amyloid-beta group, compared to the control and sham groups. In contrast, treatment with A. absinthium improved spatial memory dose-dependently and reduced tissue degeneration, amyloid plaques, and apoptosis. It seems that the hydroalcoholic extract of A. absinthium, due to its antioxidant and anti-inflammatory activities, can effectively reverse spatial memory deficits and reduce amyloid-beta plaques.

Protein Aggregation Landscape in Neurodegenerative Diseases: Clinical Relevance and Future Applications

Intrinsic disorder is a natural feature of polypeptide chains, resulting in the lack of a defined three-dimensional structure. Conformational changes in intrinsically disordered regions of a protein lead to unstable β-sheet enriched intermediates, which are stabilized by intermolecular interactions with other β-sheet enriched molecules, producing stable proteinaceous aggregates. Upon misfolding, several pathways may be undertaken depending on the composition of the amino acidic string and the surrounding environment, leading to different structures. Accumulating evidence is suggesting that the conformational state of a protein may initiate signalling pathways involved both in pathology and physiology. In this review, we will summarize the heterogeneity of structures that are produced from intrinsically disordered protein domains and highlight the routes that lead to the formation of physiological liquid droplets as well as pathogenic aggregates. The most common proteins found in aggregates in neurodegenerative diseases and their structural variability will be addressed. We will further evaluate the clinical relevance and future applications of the study of the structural heterogeneity of protein aggregates, which may aid the understanding of the phenotypic diversity observed in neurodegenerative disorders.

Fibril growth captured by electrical properties of amyloid-β and human islet amyloid polypeptide

The aggregation of amyloid-β (Aβ) and human islet amyloid polypeptide (hIAPP) proteins have attracted considerable attention because of their involvement in protein misfolding diseases. These proteins have mostly been investigated using atomic force microscopy, transmission electron microscopy, and fluorescence microscopy to study the directional growth of fibrils both perpendicular to and along the fibril axis. Here, we demonstrate the real-time monitoring of the directional growth of fibrils in terms of activation energy of proton transfer using an impedance spectroscopy technique. The activation energy is used to quantify the sensitivity of proton conduction to the different stages of protein aggregation. The decrement (increment) in activation energy is related to the fibril growth along (perpendicular to) the fibril axis in intrinsic protein aggregation. The entire aggregation process shows different phases of the directional growth for Aβ and hIAPP, indicating different pathways for their aggregation. The activation energy for hIAPP is found to be smaller than the activation energy of Aβ during the aggregation process. The oscillatory behavior of the activation energy of hIAPP reflects a rapid change in the directional growth of the protofilaments of hIAPP. The results indicate higher aggregation propensity of Aβ than hIAPP. In the presence of resveratrol, hIAPP exhibits slower aggregation compared to Aβ. Methods of this study may in general be used to reveal the modulated aggregation pathway of proteins in the presence of different ligands.

Rationally designed peptide-based inhibitor of Aβ42 fibril formation and toxicity: a potential therapeutic strategy for Alzheimer's disease

Amyloid beta peptide (Aβ42) aggregation in the brain is thought to be responsible for the onset of Alzheimer's disease, an insidious condition without an effective treatment or cure. Hence, a strategy to prevent aggregation and subsequent toxicity is crucial. Bio-inspired peptide-based molecules are ideal candidates for the inhibition of Aβ42 aggregation, and are currently deemed to be a promising option for drug design. In this study, a hexapeptide containing a self-recognition component unique to Aβ42 was designed to mimic the β-strand hydrophobic core region of the Aβ peptide. The peptide is comprised exclusively of D-amino acids to enhance specificity towards Aβ42, in conjunction with a C-terminal disruption element to block the recruitment of Aβ42 monomers on to fibrils. The peptide was rationally designed to exploit the synergy between the recognition and disruption components, and incorporates features such as hydrophobicity, β-sheet propensity, and charge, that all play a critical role in the aggregation process. Fluorescence assays, native ion-mobility mass spectrometry (IM-MS) and cell viability assays were used to demonstrate that the peptide interacts with Aβ42 monomers and oligomers with high specificity, leading to almost complete inhibition of fibril formation, with essentially no cytotoxic effects. These data define the peptide-based inhibitor as a potentially potent anti-amyloid drug candidate for this hitherto incurable disease.

BODIPY Dyes as Probes and Sensors to Study Amyloid-β-Related Processes

Amyloid formation plays a major role in a number of neurodegenerative diseases, including Alzheimer's disease. Amyloid-β peptides (Aβ) are one of the primary markers associated with this pathology. Aβ aggregates exhibit a diverse range of morphologies with distinct pathological activities. Recognition of the Aβ aggregates by using small molecule-based probes and sensors should not only enhance understanding of the underlying mechanisms of amyloid formation, but also facilitate the development of therapeutic strategies to interfere with amyloid neurotoxicity. BODIPY (boron dipyrrin) dyes are among the most versatile small molecule fluorophores. BODIPY scaffolds could be functionalized to tune their photophysical properties to the desired ranges as well as to adapt these dyes to various types of conditions and environments. Thus, BODIPY dyes could be viewed as unique platforms for the design of probes and sensors that are capable of detecting and tracking structural changes of various Aβ aggregates. This review summarizes currently available examples of BODIPY dyes that have been used to investigate conformational changes of Aβ peptides, self-assembly processes of Aβ, as well as Aβ interactions with various molecules.

Distinct Animal Food Allergens Form IgE-Binding Amyloids

Several animal food allergens assemble into amyloids under gastric-like environments. These aggregated structures provide Gad m 1 with an enhanced immunoglobulin E (IgE) interaction due to the fibrillation of the epitope regions. However, whether these properties are unique to Gad m 1 or shared by other food allergens has not yet been addressed. Using Bos d 5, Bos d 12 and Gal d 2 as allergen models and Gad m 1 as the control, aggregation reactions and the sera of milk, egg and fish allergic patients have been analyzed, assessing the IgE interactions of their amyloids. We found that amyloids formed by Bos d 12 and Gal d 2 full-length and truncated chains are recognized by the IgEs of milk and egg allergic patient sera. As with Gad m 1, in most cases amyloid recognition is higher than that of the native structure. Bos d 5 was not recognized under any fold by the IgE of the sera studied. These results suggest that the formation of IgE-binding amyloids could be a common feature to animal food allergens.

Half a century of amyloids: past, present and future

Amyloid diseases are global epidemics with profound health, social and economic implications and yet remain without a cure. This dire situation calls for research into the origin and pathological manifestations of amyloidosis to stimulate continued development of new therapeutics. In basic science and engineering, the cross-β architecture has been a constant thread underlying the structural characteristics of pathological and functional amyloids, and realizing that amyloid structures can be both pathological and functional in nature has fuelled innovations in artificial amyloids, whose use today ranges from water purification to 3D printing. At the conclusion of a half century since Eanes and Glenner's seminal study of amyloids in humans, this review commemorates the occasion by documenting the major milestones in amyloid research to date, from the perspectives of structural biology, biophysics, medicine, microbiology, engineering and nanotechnology. We also discuss new challenges and opportunities to drive this interdisciplinary field moving forward.

Identification and Nanomechanical Characterization of the HIV Tat-Amyloid β Peptide Multifibrillar Structures

HIV transactivator of transcription (Tat) protein could interact with amyloid β (Aβ) peptide which cause the growth of Aβ plaques in the brain and result in Alzheimer's disease in HIV-infected patients. Herein, we employ high-resolution atomic force microscopy and quantitative nanomechanical mapping to investigate the effects of Tat protein in Aβ peptide aggregation. Our results demonstrate that the Tat protein could bind to the Aβ fibril surfaces and result in the formation of Tat-Aβ multifibrillar structures. The resultant Tat-Aβ multifibrillar aggregates represent an increase in stiffness compared with Aβ fibrils due to the increase in β-sheet formation. The identification and characterization of the Tat-Aβ intermediate aggregates is important to understanding the interactions between Tat protein and Aβ peptide, and the development of novel therapeutic strategy for Alzheimer's disease-like disorder in HIV infected individuals.

Network-Based Classification and Modeling of Amyloid Fibrils

Amyloid fibrils are locally ordered protein aggregates that self-assemble under a variety of physiological and in vitro conditions. Their formation is of fundamental interest as a physical chemistry problem and plays a central role in Alzheimer's disease, Type II diabetes, and other human diseases. As the number of known amyloid fibril structures has grown, the need has arisen for a nomenclature for describing and classifying fibril types, as well as a theoretical description of the physics that gives rise to the self-assembly of these structures. Here, we introduce a systematic nomenclature and coarse-graining methodology for describing the topology of fibrils and other protein aggregates, along with a computational methodology for simulating protein aggregation. Both have mathematical underpinnings in graph theory and statistical mechanics and are consistent with available experimental data on the fibril structure and aggregation kinetics. Our graph representation of the fibril topology enables us to define a network Hamiltonian based on connectivity patterns among monomers rather than detailed intermolecular interactions, greatly speeding up the simulation of large ensembles. Our simulation strategy is capable of recapitulating the formation of all currently known amyloid fibril topologies found in the Protein Data Bank, as well as the formation kinetics of fibrils and oligomers.

Rational Structure-Based Design of Fluorescent Probes for Amyloid Folds

Amyloid fibrils are pathological hallmarks of various human diseases, including Parkinson's, Alzheimer's, amyotrophic lateral sclerosis (ALS or motor neurone disease), and prion diseases. Treatment of the amyloid diseases are hindered, among other factors, by timely detection and therefore, early detection of the amyloid fibrils would be beneficial for treatment against these disorders. Here, a small molecular fluorescent probe is reported that selectively recognize the fibrillar form of amyloid beta(1-42), α-synuclein, and HET-s(218-289) protein over their monomeric conformation. The rational design of the reporters relies on the well-known cross-β-sheet repetition motif, the key structural feature of amyloids.

Induced Lanthanide Circularly Polarized Luminescence as a Probe of Protein Fibrils

Protein fibrils are involved in a number of biological processes. Because their structure is very complex and not completely understood, different spectroscopic methods are used to monitor different aspects of fibril structure. We have explored circularly polarized luminescence (CPL) induced in lanthanide compounds to indicate fibril growth and discriminate among fibril types. For hen egg-white lysozyme and polyglutamic acid-specific CPL, spectral patterns were obtained and could be correlated with vibrational circular dichroism (VCD) spectra and thioflavin T fluorescence. The CPL spectra were measured on a Raman optical activity spectrometer, and its various polarization modes are discussed. The experiments indicate that the induced CPL is sensitive to more local aspects of the fibril structure than VCD. For CPL, smaller amounts of the sample are required for the analysis, and thus this method appears to be a good candidate for future spectroscopic characterization of these peptide and protein aggregates.

Recent Advances by In Silico and In Vitro Studies of Amyloid-β 1-42 Fibril Depicted a S-Shape Conformation

The amyloid-β 1-42 (Aβ1-42) peptide is produced by proteolytic cleavage of the amyloid precursor protein (APP) by sequential reactions that are catalyzed by γ and β secretases. Aβ1-42, together with the Tau protein are two principal hallmarks of Alzheimer's disease (AD) that are related to disease genesis and progression. Aβ1-42 possesses a higher aggregation propensity, and it is able to form fibrils via nucleated fibril formation. To date, there are compounds available that prevent Aβ1-42 aggregation, but none have been successful in clinical trials, possibly because the Aβ1-42 structure and aggregation mechanisms are not thoroughly understood. New molecules have been designed, employing knowledge of the Aβ1-42 structure and are based on preventing or breaking the ionic interactions that have been proposed for formation of the Aβ1-42 fibril U-shaped structure. Recently, a new Aβ1-42 fibril S-shaped structure was reported that, together with its aggregation and catalytic properties, could be helpful in the design of new inhibitor molecules. Therefore, in silico and in vitro methods have been employed to analyze the Aβ1-42 fibril S-shaped structure and its aggregation to obtain more accurate Aβ1-42 oligomerization data for the design and evaluation of new molecules that can prevent the fibrillation process.

Chiral modulation of amyloid beta fibrillation and cytotoxicity by enantiomeric carbon dots

Enantiomeric carbon dots (C-dots) synthesized from l-lysine or d-lysine, modulate aggregation and cytotoxicity of amyloid beta-42 (Aβ42), the primary constituent of the amyloid plaques associated with Alzheimer's disease. In particular, l-Lys-C-dots dramatically remodeled Aβ42 secondary structure and fibril morphologies, as well as inhibited Aβ42 cytotoxicity and membrane interactions.

Disorder at the Tips of a Disease-Relevant Aβ42 Amyloid Fibril: A Molecular Dynamics Study

We present a simulation study of the early events of peptide dissociation from a fibril of the Alzheimer's Aβ42 peptide. The fibril consists of layers of two adjacent Aβ42 peptides each folded in an S-shaped structure which has been determined by solid state NMR spectroscopy of a monomorphic disease-relevant species. Multiple molecular dynamics runs (16 at 310 K and 15 at 370 K) were carried out starting from an 18-peptide protofibril for a cumulative sampling of about 15 μs. The simulations show structural stability of the fibrillar core and an overall increase in the twist to about 3 degrees. The N-terminal segment 1-14 is disordered in all peptides. At both ends of the fibril, the central segment 21-29, which includes part of the β₂ strand, dissociates in some of the simulations. The β₁ and β₃ strands, residues 15-20 and 35-41, respectively, are structurally stable. The transient binding of the N-terminal stretch to the β₃ strand of the adjacent peptide at the tip is likely to contribute to the arrest phase of the stop-and-go mechanism.

Energy Landscapes for the Aggregation of Aβ17-42

The aggregation of the Aβ peptide (Aβ_1-42) to form fibrils is a key feature of Alzheimer's disease. The mechanism is thought to be a nucleation stage followed by an elongation process. The elongation stage involves the consecutive addition of monomers to one end of the growing fibril. The aggregation process proceeds in a stop-and-go fashion and may involve off-pathway aggregates, complicating experimental and computational studies. Here we present exploration of a well-defined region in the free and potential energy landscapes for the Aβ_17-42 pentamer. We find that the ideal aggregation process agrees with the previously reported dock-lock mechanism. We also analyze a large number of additional stable structures located on the multifunnel energy landscape, which constitute kinetic traps. The key contributors to the formation of such traps are misaligned strong interactions, for example the stacking of F19 and F20, as well as entropic contributions. Our results suggest that folding templates for aggregation are a necessity and that aggregation studies could employ such species to obtain a more detailed description of the process.

Small-molecule PET Tracers for Imaging Proteinopathies

In this chapter, we provide a review of the challenges and advances in developing successful PET imaging agents for 3 major types of aggregated amyloid proteins: amyloid-beta (Aβ), tau, and alpha-synuclein (α-syn). These 3 amyloids are involved in the pathogenesis of a variety of neurodegenerative diseases, referred to as proteinopathies or proteopathies, that include Alzheimer disease, Lewy body dementias, multiple system atrophy, and frontotemporal dementias, among others. In the Introduction section, we briefly discuss the history of amyloid in neurodegenerative diseases and describe why progress in developing effective imaging agents has been hampered by the failure of crystallography to provide definitive ligand-protein interactions for rational radioligand design efforts. Instead, the field has relied on largely serendipitous, trial-and-error methods to achieve useful and specific PET amyloid imaging tracers for Aβ, tau, and α-syn deposits. Because many of the proteopathies involve more than 1 amyloid protein, it is important to develop selective PET tracers for the different amyloids to help assess the relative contribution of each to total amyloid burden. We use Pittsburgh compound B to illustrate some of the critical steps in developing a potent and selective Aβ PET imaging agent. Other selective Aβ and tau PET imaging compounds have followed similar pathways in their developmental processes. Success for selective α-syn PET imaging agents has not been realized yet, but work is ongoing in multiple laboratories throughout the world. In the tau sections, we provide background regarding 3-repeat (3R) and 4-repeat (4R) tau proteins and how they can affect the binding of tau radioligands in different tauopathies. We review the ongoing efforts to assess the properties of tau ligands, which are useful in 3R, 4R, or combined 3R-4R tauopathies. Finally, we describe in the α-syn sections recent attempts to develop selective tracers to image α-synucleinopathies.

Effects of Mutations on the Aggregation Propensity of the Human Prion-Like Protein hnRNPA2B1

Hundreds of human proteins contain prion-like domains, which are a subset of low-complexity domains with high amino acid compositional similarity to yeast prion domains. A recently characterized mutation in the prion-like domain of the human heterogeneous nuclear ribonucleoprotein hnRNPA2B1 increases the aggregation propensity of the protein and causes multisystem proteinopathy. The mutant protein forms cytoplasmic inclusions when expressed in Drosophila, the mutation accelerates aggregation in vitro, and the mutant prion-like domain can substitute for a portion of a yeast prion domain in supporting prion activity. To examine the relationship between amino acid sequence and aggregation propensity, we made a diverse set of point mutations in the hnRNPA2B1 prion-like domain. We found that the effects on prion formation in Saccharomyces cerevisiae and aggregation in vitro could be predicted entirely based on amino acid composition. However, composition was an imperfect predictor of inclusion formation in Drosophila; while most mutations showed similar behaviors in yeast, in vitro, and in Drosophila, a few showed anomalous behavior. Collectively, these results demonstrate the significant progress that has been made in predicting the effects of mutations on intrinsic aggregation propensity while also highlighting the challenges of predicting the effects of mutations in more complex organisms.

Quenched hydrogen-deuterium exchange NMR of a disease-relevant Aβ(1-42) amyloid polymorph

Alzheimer’s disease is associated with the aggregation into amyloid fibrils of Aβ(1–42) and Aβ(1–40) peptides. Interestingly, these fibrils often do not obtain one single structure but rather show different morphologies, so-called polymorphs. Here, we compare quenched hydrogen-deuterium (H/D) exchange of a disease-relevant Aβ(1–42) fibril for which the 3D structure has been determined by solid-state NMR with H/D exchange previously determined on another structural polymorph. This comparison reveals secondary structural differences between the two polymorphs suggesting that the two polymorphisms can be classified as segmental polymorphs.

Stereoisomers Probe Steric Zippers in Amyloid-β

Shape complementarity between close-packed residues plays a critical role in the amyloid aggregation process. Here, we probe such "steric zipper" interactions in amyloid-β (Aβ₄₀), whose aggregation is linked to Alzheimer's disease, by replacing natural residues by their stereoisomers. Such mutations are expected to specifically destabilize the shape sensitive "packing" interactions, which may potentially increase their solubility and change other properties. We study the stereomutants DF19 and DL34 and also the DA2/DF4/DH6/DS8 mutant of Aβ₄₀. F19-L34 is a critical contact in a tightly packed region of Aβ, while residues 1-9 are known to be disordered. While both DF19 and DL34 slow down the kinetics of aggregation and form amyloid fibrils efficiently, only DL34 increases the final solubility. DF19 gives rise to additional off-pathway aggregation which results in large, kinetically stable aggregates, and has lower net solubility. DA2/DF4/DH6/DS8 does not have an effect on the kinetics or the solubility. Notably, both DF19 and DL34 oligomers have a significantly lower level of interactions with lipid vesicles and live cells. We conclude that stereoisomers can cause complex site dependent changes in amyloid properties, and provide an effective tool to determine the role of individual residues in shaping the packed interiors of amyloid aggregates.

The activities of amyloids from a structural perspective

The aggregation of proteins into structures known as amyloids is observed in many neurodegenerative diseases, including Alzheimer's disease. Amyloids are composed of pairs of tightly interacting, many stranded and repetitive intermolecular β-sheets, which form the cross-β-sheet structure. This structure enables amyloids to grow by recruitment of the same protein and its repetition can transform a weak biological activity into a potent one through cooperativity and avidity. Amyloids therefore have the potential to self-replicate and can adapt to the environment, yielding cell-to-cell transmissibility, prion infectivity and toxicity.

How the hydrophobic factor drives protein folding

How hydrophobicity (HY) drives protein folding is studied. The 1971 Nozaki-Tanford method of measuring HY is modified to use gases as solutes, not crystals, and this makes the method easy to use. Alkanes are found to be much more hydrophobic than rare gases, and the two different kinds of HY are termed intrinsic (rare gases) and extrinsic (alkanes). The HY values of rare gases are proportional to solvent-accessible surface area (ASA), whereas the HY values of alkanes depend on special hydration shells. Earlier work showed that hydration shells produce the hydration energetics of alkanes. Evidence is given here that the transfer energetics of alkanes to cyclohexane [Wolfenden R, Lewis CA, Jr, Yuan Y, Carter CW, Jr (2015) Proc Natl Acad Sci USA 112(24):7484-7488] measure the release of these shells. Alkane shells are stabilized importantly by van der Waals interactions between alkane carbon and water oxygen atoms. Thus, rare gases cannot form this type of shell. The very short (approximately picoseconds) lifetime of the van der Waals interaction probably explains why NMR efforts to detect alkane hydration shells have failed. The close similarity between the sizes of the opposing energetics for forming or releasing alkane shells confirms the presence of these shells on alkanes and supports Kauzmann's 1959 mechanism of protein folding. A space-filling model is given for the hydration shells on linear alkanes. The model reproduces the n values of Jorgensen et al. [Jorgensen WL, Gao J, Ravimohan C (1985) J Phys Chem 89:3470-3473] for the number of waters in alkane hydration shells.