Search

The number of atomic-resolution structures of disease-associated amyloids has greatly increased in recent years. These structures have confirmed not only the polymorphic nature of amyloids but also the association of specific polymorphs to particular proteinopathies. These observations are strengthening the view that amyloid polymorphism is a marker for specific pathological subtypes (e.g. in tauopathies or synucleinopathies). The nature of this association and how it relates to the selective cellular vulnerability of amyloid nucleation, propagation and toxicity are still unclear. Here, we provide an overview of the mechanistic insights provided by recent patient-derived amyloid structures. We discuss the framework organisation of amyloid polymorphism and how heterotypic amyloid interactions with the physiological environment could modify the solubility and assembly of amyloidogenic proteins. We conclude by hypothesising how such interactions could contribute to selective cellular vulnerability. • Cross-interplay of amyloids with other biomolecules affects their structure, function and toxicity. • Heterotypic interactions, APRs and structurally frustrated regions mediate the formation of polymorphic amyloid structures. • Interfaces promoting amyloid heterotypic interactions share different levels of specificity. • Cell-specific proteomic backgrounds can modulate amyloid toxicity and functionality through heterotypic-based assembly mechanisms. [ABSTRACT FROM AUTHOR]

The molecular cause of severe congenital neutropenia (SCN) is unknown in 30% to 50% of patients. SEC61A1 encodes the α-subunit of the Sec61 complex, which governs endoplasmic reticulum protein transport and passive calcium leakage. Recently, mutations in SEC61A1 were reported to be pathogenic in common variable immunodeficiency and glomerulocystic kidney disease. Our aim was to expand the spectrum of SEC61A1 -mediated disease to include autosomal dominant SCN. Whole exome sequencing findings were validated, and reported mutations were compared by Western blotting, Ca2+ flux assays, differentiation of transduced HL-60 cells, in vitro differentiation of primary CD34 cells, quantitative PCR for unfolded protein response (UPR) genes, and single-cell RNA sequencing on whole bone marrow. We identified a novel de novo missense mutation in SEC61A1 (c.A275G;p.Q92R) in a patient with SCN who was born to nonconsanguineous Belgian parents. The mutation results in diminished protein expression, disturbed protein translocation, and an increase in calcium leakage from the endoplasmic reticulum. In vitro differentiation of CD34+ cells recapitulated the patient's clinical arrest in granulopoiesis. The impact of Q92R-Sec61α1 on neutrophil maturation was validated by using HL-60 cells, in which transduction reduced differentiation into CD11b+CD16+ cells. A potential mechanism for this defect is the uncontrolled initiation of the unfolded protein stress response, with single-cell analysis of primary bone marrow revealing perturbed UPR in myeloid precursors and in vitro differentiation of primary CD34+ cells revealing upregulation of CCAAT/enhancer-binding protein homologous protein and immunoglobulin heavy chain binding protein UPR-response genes. Specific mutations in SEC61A1 cause SCN through dysregulation of the UPR. [ABSTRACT FROM AUTHOR]

Recent years have witnessed major advances in our understanding of the structural basis of protein aggregation on several fronts. Firstly, high-resolution structural information that remained elusive for many years was provided by a series of studies of amyloid fibers using NMR, X-ray crystallography and electron microscopy, thereby confirming earlier models based on lower resolution observations. Secondly, studies of the sequence determinants of protein aggregation culminated in the development of computer algorithms that predict aggregation-prone sequences with good accuracy, allowing the design of mutations that reduce aggregation. Thirdly, based on the first results from such predictions and on statistical analysis of naturally occurring aggregating sequences, a picture is emerging in which aggregation-prone sequences are capped by gatekeeper residues that oppose aggregation. In addition to their aggregation-opposing function, it seems that gatekeeper residues are also important in determining chaperone selectivity for strongly aggregating regions. Finally, recent computational and experimental work shows that preventing aggregation does not necessarily mean that amyloid formation is prevented and vice versa. Thus, although aggregation and amyloidosis correlate to a certain extent, they are different processes and should be treated as such. [Copyright &y& Elsevier]

The functional dynamics of signal transduction through protein interaction networks are determined both by network topology and by the signal processing properties of component proteins. In order to understand the emergent properties of signal transduction networks in terms of information processing, storage and decision making, we not only need to map the so-called ‘interactome’ but, perhaps more importantly, we also have to understand how the structural dynamics of constituent proteins shape non-linear responses through cooperativity and allostery. Several in silico methods have been developed to identify networks of cooperative residues in proteins and help infer their mode of action. Applying this type of analysis to important classes of modular signal transduction domains should, in principle, allow the function of these proteins to be abstracted in terms of their information processing characteristics, permitting better comprehension of the systemic properties of biological networks. [Copyright &y& Elsevier]

Three-dimensional domain swapping is the event by which a monomer exchanges part of its structure with identical monomers to form an oligomer where each subunit has a similar structure to the monomer. The accumulating number of observations of this phenomenon in crystal structures has prompted speculation as to its biological relevance. Domain swapping was originally proposed to be a mechanism for the emergence of oligomeric proteins and as a means for functional regulation, but also to be a potentially harmful process leading to misfolding and aggregation. We highlight experimental studies carried out within the last few years that have led to a much greater understanding of the mechanism of domain swapping and of the residue- and structure-specific features that facilitate the process. We discuss the potential biological implications of domain swapping in light of these findings. [Copyright &y& Elsevier]

suc1 has two native states, a monomer and a domain-swapped dimer, in which one molecule exchanges a β strand with an identical partner. Thus, monomer and dimer have the same structures but are topologically distinct. Importantly, residues that exchange are part of the folding nucleus of the monomer and therefore forming these interactions in the dimer would be expected to incur a large entropic cost. Here we present the transition state for folding/unfolding of domain-swapped dimeric suc1 and compare it with its monomeric counterpart. The same overall structure is observed in the two transition states but the φ values are consistently higher for the domain-swapped dimer. Thus, a greater entropic penalty for bringing together the key interactions in the dimer is overcome by mobilizing more contacts in the transition state, thereby achieving a greater enthalpic gain. [Copyright &y& Elsevier]

The amyloid-like aggregation propensity present in most globular proteins is generally considered to be a secondary side effect resulting from the requirements of protein stability. Here, we demonstrate, however, that mutations in the globular and amyloid state are thermodynamically correlated rather than simply associated. In addition, we show that the standard genetic code couples this structural correlation into a tight evolutionary relationship. We illustrate the extent of this evolutionary entanglement of amyloid propensity and globular protein stability. Suppressing a 600-Ma-conserved amyloidogenic segment in the p53 core domain fold is structurally feasible but requires 7-bp substitutions to concomitantly introduce two aggregation-suppressing and three stabilizing amino acid mutations. We speculate that, rather than being a corollary of protein evolution, it is equally plausible that positive selection for amyloid structure could have been a driver for the emergence of globular protein structure. • Mutations in the globular and amyloid state are thermodynamically correlated • The genetic code tightens this relationship between the amyloid and native state • Strongly amyloidogenic sequences in globular proteins are deeply conserved • Positive selection of amyloid propensity will favor globular protein stability Langenberg et al. show that amyloid propensity favors protein stability. This results from the energetic correlation of mutation in the native and amyloid state. The genetic code tightens this relationship so that stable amyloidogenic sequences are deeply conserved. Positive selection of amyloidogenic sequences could therefore have favored the evolution of globular structure. [ABSTRACT FROM AUTHOR]

• Introducing current methods and strategies involving nanomaterials to manage protein aggregation and related diseases. • Surface properties of nanomaterials can allow a control of protein aggregation. • Stimuli-responsive nanomaterials are efficient to destroy protein aggregates. • Extensive efforts are still needed for a clinical translation. Aggregation of proteins is involved in many disorders. Besides amyloid fibrils, which mostly form in the brain, other kind of protein aggregates can lead, for example, to clots in the blood or floaters in the vitreous of the eye. This review aims to overview on how nanomaterials could be employed to avoid and destroy most diverse protein aggregates. Indeed, thanks to their recognized versatility, (stimuli-responsive) nanomaterials may offer attractive features against harmful protein aggregates. However, despite the many conceptually interesting strategies it appears that most important information on both the in vivo efficacy and safety of nanotechnology based prevention or destruction of protein aggregates, which is highly needed to pave the way to clinically relevant therapies, remains missing. [ABSTRACT FROM AUTHOR]

Prions of lower eukaryotes are self-templating protein aggregates with cores formed by parallel in-register beta strands. Short aggregation-prone glutamine (Q)- and asparagine (N)-rich regions embedded in longer disordered domains have been proposed to act as nucleation sites that initiate refolding of soluble prion proteins into highly ordered fibrils, termed amyloid. We demonstrate that a short Q/N-rich peptide corresponding to a proposed nucleation site in the prototype Saccharomyces cerevisiae prion protein Sup35 is sufficient to induce infectious cytosolic prions in mouse neuroblastoma cells ectopically expressing the soluble Sup35 NM prion domain. Embedding this nucleating core in a non-native N-rich sequence that does not form amyloid but acts as an entropic bristle quadruples seeding efficiency. Our data suggest that large disordered sequences flanking an aggregation core in prion proteins act as not only solubilizers of the monomeric protein but also breakers of the formed amyloid fibrils, enhancing infectivity of the prion seeds. • A short peptide derived from Sup35 (p103–113) forms rigid amyloid fibrils • p103–113 fibrils can induce infectious Sup35 NM prions in mammalian cells • Embedding p103–113 in an N-rich sequence increases fibril brittleness • Increased fibril brittleness enhances prion-inducing capacity A protein aggregate can contain infective properties, prions being the prime example. Michiels et al. show that these infective properties are encoded in the specific amino acid sequence flanking the aggregation core of a protein. These so-called entropic bristle sequences drive fiber brittleness, a crucial feature for amyloid infectivity. [ABSTRACT FROM AUTHOR]

Protein aggregation propensity is a pervasive and seemingly inescapable property of proteomes. Strikingly, a significant fraction of the proteome is supersaturated, meaning that, for these proteins, their native conformation is less stable than the aggregated state. Maintaining the integrity of a proteome under such conditions is precarious and requires energy-consuming proteostatic regulation. Why then is aggregation propensity maintained at such high levels over long evolutionary timescales? Here, we argue that the conformational stability of the native and aggregated states are correlated thermodynamically and that codon usage strengthens this correlation. As a result, the folding of stable proteins requires kinetic control to avoid aggregation, provided by aggregation gatekeepers. These unique residues are evolutionarily selected to kinetically favor native folding, either on their own or by coopting chaperones. Aggregation is a universal property of natural polypeptides and constitutes a large energy drain for cellular homeostasis. Evolution cannot eliminate aggregation because of deep entanglement with native state thermodynamics. Supersaturation theory proposes that native states of many proteins are not thermodynamic minima. This renders the Anfinsen postulate a local property of the native side of the folding funnel, but not a global property of the entire energy landscape. To maintain natively folded proteomes, kinetic partitioning is essential and is achieved by a conjunction of protein-intrinsic gatekeepers and external chaperones. [ABSTRACT FROM AUTHOR]

Summary RNA-binding protein aggregation is a pathological hallmark of several neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). To gain better insight into the molecular interactions underlying this process, we investigated FUS, which is mutated and aggregated in both ALS and FTLD. We generated a Drosophila model of FUS toxicity and identified a previously unrecognized synergistic effect between the N-terminal prion-like domain and the C-terminal arginine-rich domain to mediate toxicity. Although the prion-like domain is generally considered to mediate aggregation of FUS, we find that arginine residues in the C-terminal low-complexity domain are also required for maturation of FUS in cellular stress granules. These data highlight an important role for arginine-rich domains in the pathology of RNA-binding proteins. [ABSTRACT FROM AUTHOR]

The increasing number of amyloid structures offers an opportunity to investigate the general principles determining amyloid stability and polymorphism. We find that amyloid stability is dominated by ∼30% of residues localized in segments that favor the cross-β conformation. These correspond to known aggregation-nucleating regions and constitute a stabilizing cross-β structural framework that is shared among polymorphs. Alternative packing of these segments with structurally frustrated regions within the protofilament results in conformationally different, but energetically similar, polymorphs. Differential analysis of distributions of interatomic distances in amyloid and globular structures revealed that unconventional residue contacts, such as identical charges in close proximity, are located in energetically frustrated segments of amyloids. These observations suggest that polymorphism results from a framework mechanism consisting of conserved stabilizing regions of high cross-β propensity. These are interspersed by structurally suboptimal regions that are potential sites of conformational plasticity and interaction with stabilizing cofactors such as (poly)ions. [Display omitted] • Structurally distinct amyloid polymorphs share a common thermodynamic framework • A fraction (30%) of amyloid-core residues contribute to this stabilizing framework • Frustrated fibril regions are enriched in atypical contacts compared with globular folds • Destabilizing interactions may be compensated by cofactors, such as metal or water Many proteins adopt an amyloid conformation, either as a pathogenic alternative to the native globular structure or as a functional state. Van der Kant et al. capitalize on the recent explosion in amyloid structures to begin unravelling the architecture of this poorly understood conformation. [ABSTRACT FROM AUTHOR]

Hen egg white protein (EWP) is an ingredient in many food products. EWP containing amyloid-like fibrils (ALFs) can be prepared under food processing relevant conditions and have specific techno-functional properties which advantageously can be exploited in specific food products. Here, we investigated whether combinations of heating and NaCl addition or trypsin treatment improve EWP fibrillation and gel properties. Heating (75 °C, 150 min) control 0.2% EWP solutions resulted in limited fibrillation unless they also contained 150 mM NaCl, in which case increased levels of curly ALFs were observed. When similarly heated control EWP solutions were submitted to trypsin treatment (37 °C, 24 h, 150 rpm), both straight and curly ALFs were formed. Gels [5.0%–6.0% (w/v) EWP] prepared by heating (75 °C, 150 min) of 150 mM NaCl containing dispersions or by similar heating without NaCl addition but with trypsin treatment contained ALFs of similar morphology but shorter than those in control EWP solutions. Increased levels of curly or of both straight and curly ALFs in NaCl containing gels or gels prepared with trypsin treatment, respectively, resulted in higher EWP gel stiffness than when the EWP gels were prepared in water. While the presence of straight ALFs in trypsin-derived EWP gels resulted in fast gel breakdown, the presence of both curly and straight ALFs reduced the amount of EWP needed for gel formation. The level and morphology of EWP ALFs can thus be modulated by specific food relevant processing and the resultant ALFs have specific gelling properties. [Display omitted] • Heating egg white protein solutions in the presence of salt improved their fibrillation. • Trypsin treatment of heated egg white protein solutions resulted in both straight and curly fibrils. • The presence of curly fibrils in heat-derived egg white protein gels containing salt increased their stiffness. • The presence of straight fibrils in trypsin-derived white protein gels resulted in fast gel breakdown. [ABSTRACT FROM AUTHOR]

Proteins are well known stabilisers for emulsions, gels and foams. Hereby, the protein (supra)molecular structure may play an important role. In order to investigate that effect, 0.5% unheated (UH), heated (H) and combined heat and trypsin treated (H TT) ovalbumin (OVA) dispersions were evaluated for their capacity to stabilize 20–60% oil-in-water (O/W) emulsions. Such emulsions contained native OVA (UH OVA), amorphous and short fibrillar aggregates (H OVA) or long fibrils and peptides (H TT OVA). The experimental results indicated that emulsions containing UH OVA showed larger droplet sizes than those containing H OVA or H TT OVA and revealed a high extent of oiling-off. Although the emulsions containing H OVA contained smaller oil droplets, still a remarkable amount of oil separated upon centrifugation. In contrast, the H TT OVA stabilized emulsions did not display any oiling-off upon centrifugation, which was suggested to be due to the increased viscosity of the (gelled) H TT OVA dispersions used as continuous phase. Nevertheless, the viscosity of the latter emulsions was negatively affected by breakdown of the fibrillary (gel) structure during emulsification. When 60% O/W emulsions containing 1.6% H OVA were subjected to tryptic treatment only after emulsification, the emulsion gels were significantly stronger than the H TT OVA emulsions. Both emulsion types only showed the onset of creaming after several hours of centrifugation, whereas only the emulsions submitted to the enzymatic treatment after emulsification showed no evidence of coalescence. Overall, the experimental results show that emulsions containing long OVA fibrils, as obtained by trypsin treatment after heating, hold great promise for structured food applications. [Display omitted] • ovalbumin dispersions were made containing different supramolecular structures. • these dispersions were used as aqueous phase in emulsions with 20–60% oil. • emulsion gels were obtained upon trypsin treatment of 4% heated ovalbumin dispersions. • the emulsion gels induced a largely improved creaming as well as coalescence stability. • trypsin treatment after emulsification prevented shear-induced breakdown. [ABSTRACT FROM AUTHOR]

Cellular compartments and organelles organize biological matter. Most well-known organelles are separated by a membrane boundary from their surrounding milieu. There are also many so-called membraneless organelles and recent studies suggest that these organelles, which are supramolecular assemblies of proteins and RNA molecules, form via protein phase separation. Recent discoveries have shed light on the molecular properties, formation, regulation, and function of membraneless organelles. A combination of techniques from cell biology, biophysics, physical chemistry, structural biology, and bioinformatics are starting to help establish the molecular principles of an emerging field, thus paving the way for exciting discoveries, including novel therapeutic approaches for the treatment of age-related disorders. [ABSTRACT FROM AUTHOR]

Heating aqueous solutions of ovalbumin (OVA) may cause gel formation. When heated at pH conditions close to the protein's isoelectric point (towards neutral pH), turbid particulate gels are formed, whereas at acidic pH fine-stranded, transparent gels are formed already at lower concentrations. Here, transparent gels were formed when subjecting 2.0% OVA to a combined heat (78 °C for 22 h at pH 7) and trypsin (37 °C for 48 h) treatment. Transmission electron microscopy clearly revealed the presence of long, straight OVA fibrils which contributed to the gel formation. Quartz crystal microbalance with dissipation (adsorption of small structures), size exclusion – HPLC (presence of both structures larger and smaller than native OVA) and atomic force microscopy (presence of long fibrils with a higher thickness, whereas heated OVA mainly showed amorphous aggregates) analyses confirmed that the additional enzymatic treatment was able to break down the amorphous aggregates formed by heating OVA into peptides, which then partly re-assembled into longer OVA fibrils. The above mentioned heat and enzymatic treatment conditions brought about gelation after 17 h with a gel strength of 68 Pa which broke at a stress of 38 Pa. By varying the temperature during heat (58–88 °C) and enzymatic (27–67 °C) treatments, gels were formed the fastest when heated at 78 °C followed by enzymatic treatment at 57 °C. A design of experiments for evaluating the impact of OVA and trypsin concentration revealed that the fastest gelation occurred at the higher considered OVA and trypsin concentrations. Additionally, the gel strength was also higher under the latter conditions. It is clear that different gel characteristics can be reached when varying the different process conditions, creating the opportunity for reconsidering the formulation of various foods such as jellies, marmalades and desserts. [Display omitted] • Combined heat and tryptic treatment of ovalbumin (OVA) induces gelation. • Trypsin hydrolyzes amorphous aggregates of OVA. • The resultant peptides can form amyloid-like fibrils. • Preheating and trypsin-incubation temperatures influence the gelation. • Increasing OVA and trypsin concentrations result in rapid formation of strong gels. [ABSTRACT FROM AUTHOR]

Recently, a number of aggregation disease polypeptides have been shown to spread from cell to cell, thereby displaying prionoid behavior. Studying aggregate internalization, however, is often hampered by the complex kinetics of the aggregation process, resulting in the concomitant uptake of aggregates of different sizes by competing mechanisms, which makes it difficult to isolate pathway-specific responses to aggregates. We designed synthetic aggregating peptides bearing different aggregation propensities with the aim of producing modes of uptake that are sufficiently distinct to differentially analyze the cellular response to internalization. We found that small acidic aggregates (≤500 nm in diameter) were taken up by nonspecific endocytosis as part of the fluid phase and traveled through the endosomal compartment to lysosomes. By contrast, bigger basic aggregates (>1 µm) were taken up through a mechanism dependent on cytoskeletal reorganization and membrane remodeling with the morphological hallmarks of phagocytosis. Importantly, the properties of these aggregates determined not only the mechanism of internalization but also the involvement of the proteostatic machinery (the assembly of interconnected networks that control the biogenesis, folding, trafficking, and degradation of proteins) in the process; whereas the internalization of small acidic aggregates is HSF1-independent, the uptake of larger basic aggregates was HSF1-dependent, requiring Hsp70. Our results show that the biophysical properties of aggregates determine both their mechanism of internalization and proteostatic response. It remains to be seen whether these differences in cellular response contribute to the particular role of specific aggregated proteins in disease. [ABSTRACT FROM AUTHOR]

Missense mutations in alanine 673 of the amyloid precursor protein (APP), which corresponds to the second alanine of the amyloid β (Aβ) sequence, have dramatic impact on the risk for Alzheimer disease; A2V is causative, and A2T is protective. Assuming a crucial role of amyloid-Aβ in neurodegeneration, we hypothesized that both A2V and A2T mutations cause distinct changes in Aβ properties that may at least partially explain these completely different phenotypes. Using human APP-overexpressing primary neurons, we observed significantly decreased Aβ production in the A2T mutant along with an enhancedAβ generation in the A2V mutant confirming earlier data from non-neuronal cell lines. More importantly, thioflavin T fluorescence assays revealed that the mutations, while having little effect on Aβ42 peptide aggregation, dramatically change the properties of the Aβ40 pool with A2V accelerating and A2T delaying aggregation of the Aβ peptides. In line with the kinetic data, Aβ A2Tdemonstrated an increase in the solubility at equilibrium, an effect that was also observed in all mixtures of the A2T mutant with the wild type Aβ40. We propose that in addition to the reduced β-secretase cleavage of APP, the impaired propensity to aggregate may be part of the protective effect conferred by A2T substitution. The interpretation of the protective effect of this mutation is thus much more complicated than proposed previously. [ABSTRACT FROM AUTHOR]

Summary: The number of protein-peptide interactions in a cell is so large that experimental determination of all these complex structures would be a daunting task. Although homology modeling and refinement protocols have vastly improved the number and quality of predicted structural models, ab initio methods are still challenged by both the large number of possible docking sites and the conformational space accessible to flexible peptides. We present a method that addresses these challenges by sampling the entire accessible surface of a protein with a reduced conformational space of interacting backbone fragment pairs from unrelated structures. We demonstrate its potential by predicting ab initio the bound structure for a variety of protein-peptide complexes. In addition, we show the potential of our method for the discovery of domain interaction sites and domain-domain docking. [Copyright &y& Elsevier]

Summary: The fibroblast growth factor (FGF)/fibroblast growth factor receptor (FGFR) signaling network plays an important role in cell growth, survival, differentiation, and angiogenesis. Deregulation of FGFR signaling can lead to cancer development. Here, we report an FGFR inhibitor, SSR128129E (SSR), that binds to the extracellular part of the receptor. SSR does not compete with FGF for binding to FGFR but inhibits FGF-induced signaling linked to FGFR internalization in an allosteric manner, as shown by crystallography studies, nuclear magnetic resonance, Fourier transform infrared spectroscopy, molecular dynamics simulations, free energy calculations, structure-activity relationship analysis, and FGFR mutagenesis. Overall, SSR is a small molecule allosteric inhibitor of FGF/FGFR signaling, acting via binding to the extracellular part of the FGFR. [Copyright &y& Elsevier]

Fabry disease is a lysosomal storage disorder caused by loss of α-galactosidase function. More than 500 Fabry disease mutants have been identified, the majority of which are structurally destabilized. A therapeutic strategy under development for lysosomal storage diseases consists of using pharmacological chaperones to stabilize the structure of the mutant protein, thereby promoting lysosomal delivery over retrograde degradation. The substrate analog 1-deoxygalactonojirimycin (DGJ) has been shown to restore activity of mutant α-galactosidase and is currently in clinical trial for treatment of Fabry disease. However, only ∼65% of tested mutants respond to treatment in cultured patient fibroblasts, and the structural underpinnings of DGJ response remain poorly explained. Using computational modeling and cell culture experiments, we show that the DGJ response is negatively affected by protein aggregation of α-galactosidase mutants, revealing a qualitative difference between misfolding-associated and aggregation-associated loss of function. A scoring function combining predicted thermodynamic stability and intrinsic aggregation propensity of mutants captures well their aggregation behavior under overexpression in HeLa cells. Interestingly, the same classifier performs well on DGJ response data of patient-derived cultured lymphoblasts, showing that protein aggregation is an important determinant of chemical chaperone efficiency under endogenous expression levels as well. Our observations reinforce the idea that treatment of aggregation-associated loss of function observed for the more severe α-galactosidase mutants could be enhanced by combining pharmacological chaperone treatment with the suppression of mutant aggregation, e.g. via proteostatic regulator compounds that increase cellular chaperone expression. [ABSTRACT FROM AUTHOR]

Theβ-amyloid peptide (Aβ) is directly related to neurotoxicity in Alzheimer disease (AD). The two most abundant alloforms of the peptide co-exist under normal physiological conditions in the brain in an Aβ42:Aβ40 ratio of ~1:9. This ratio is often shifted to a higher percentage of Aβ42 in brains of patients with familial AD and this has recently been shown to lead to increased synaptotoxicity. The molecular basis for this phenomenon is unclear. Although the aggregation characteristics of Aβ40 and Aβ42 individually are well established, little is known about the properties of mixtures. We have explored the biophysical and structural properties of physiologically relevant Aβ42: Aβ40 ratios by several techniques. We show that Aβ40 and Aβ42 directly interact as well as modify the behavior of the other. The structures of monomeric and fibrillar assemblies formed from Aβ40 and Aβ42 mixtures do not differ from those formed from either of these peptides alone. Instead, the co-assembly of Aβ40 andAβ42 influences the aggregation kinetics by altering the pattern of oligomer formation as evidenced by a unique combination of solution nuclear magnetic resonance spectroscopy, high molecular weight mass spectrometry, and cross-seeding experiments. We relate these observations to the observed enhanced toxicity of relevant ratios of Aβ42:Aβ40 in synaptotoxicity assays and in AD patients. [ABSTRACT FROM AUTHOR]

Structure-based computational methods are popular tools for designing proteins and interactions between proteins because they provide the necessary insight and details required for rational engineering. Here, we first argue that large-scale databases of fragments contain a discrete but complete set of building blocks that can be used to design structures. We show that these structural alphabets can be saturated to provide conformational ensembles that sample the native structure space around energetic minima. Second, we show that catalogs of interaction patterns hold the key to overcome the lack of scaffolds when computationally designing protein interactions. Finally, we illustrate the power of database-driven computational protein design methods by recent successful applications and discuss what challenges remain to push this field forward. [ABSTRACT FROM AUTHOR]

Peptides possess several attractive features when compared to small molecule and protein therapeutics, such as high structural compatibility with target proteins, the ability to disrupt protein–protein interfaces, and small size. Efficient design of high-affinity peptide ligands via rational methods has been a major obstacle to the development of this potential drug class. However, structural insights into the architecture of protein–peptide interfaces have recently culminated in several computational approaches for the rational design of peptides that target proteins. These methods provide a valuable alternative to experimental high-resolution structures of target protein–peptide complexes, bringing closer the dream of in silico designed peptides for therapeutic applications. [Copyright &y& Elsevier]

Summary: We compared the modes of interaction between protein-peptide interfaces and those observed within monomeric proteins and found surprisingly few differences. Over 65% of 731 protein-peptide interfaces could be reconstructed within 1 Å RMSD using solely fragment interactions occurring in monomeric proteins. Interestingly, more than 80% of interacting fragments used in reconstructing a protein-peptide binding site were obtained from monomeric proteins of an entirely different structural classification, with an average sequence identity below 15%. Nevertheless, geometric properties perfectly match the interaction patterns observed within monomeric proteins. We show the usefulness of our approach by redesigning the interaction scaffold of nine protein-peptide complexes, for which five of the peptides can be modeled within 1 Å RMSD of the original peptide position. These data suggest that the wealth of structural data on monomeric proteins could be harvested to model protein-peptide interactions and, more importantly, that sequence homology is no prerequisite. [Copyright &y& Elsevier]

Abstract: 2,6-Dibromophenol (DBP) was reported as an auxin-like molecule using molecular quantum similarity measures. In this study, the auxin activity of this molecule and its chlorinated homologue is further determined using a bacterial biosensor: the auxin-inducible ipdC promoter of Azospirillum brasilense. We were able to demonstrate that DBP can induce gene expression, but to a lesser extent than the auxin indole-3-acetic acid (IAA) and that DBP is not an antagonist for the IAA signalling pathway. To investigate the role of the bromine groups, the molecule 2,6-dichlorophenol (DCP) was also tested for gene expression induction. However, no induction could be observed. In a second part, DBP and other molecules were modelled in the auxin-binding pocket of the plant auxin receptor TIR1 to evaluate theoretical binding energies. Both DBP and its chlorinated homologue DCP are not strong ligands compared to other known auxins such as IAA. The importance of a carboxylated side chain for optimal binding (and probably auxin activity) was demonstrated. [Copyright &y& Elsevier]

The extent of hydrothermally induced denaturation and aggregation of native quinoa protein depends on the process conditions. Proteins in quinoa extracts containing water-extractable albumins and dilute salt-extractable globulins aggregate when heated at pH 5.0 to 7.0. An I-optimal experimental design was used to investigate the impact of heating temperature (45–100 °C), time (1–15 min), pH (5.0–7.0) and protein content (25.0–100.0 mg/ml) on the total and covalent aggregation of aqueous quinoa extracts. These were evaluated by determining protein solubility losses in water and a sodium dodecyl sulfate containing medium, respectively, using size separation chromatography. Both protein solubility loss types were independent of the protein content during the treatment. While heating time only had an impact on the intensity of protein aggregation, temperature and pH also influenced the type of aggregates formed. Non-covalent protein aggregation was important when heating at temperatures not exceeding 70 °C and when the pH was close to the iso-electric point (pH 5.0). Covalent protein aggregation was maximal (ca. 25%) after heating 15 min at 100 °C and pH 7.0. Under these conditions, oligomeric protein structures (ca. 100–500 kDa) had been formed already after 1 min of heating which further had polymerized to larger ones (>500 kDa) after 5 min of heating. Mainly 7S and 11S globulins aggregated (predominantly by disulfide cross-links), while 2S albumins were not involved in covalent protein aggregation. Furthermore, intact 11S globulin monomers were most prone to covalently aggregate. The new insights allow tailoring quinoa protein aggregation by adjusting the hydrothermal treatment conditions. Image 1 • Proteins in aqueous quinoa extracts aggregate when heated at pH 5.0 to 7.0 • Non-covalent protein aggregation is dominant when heating at ≤ 70 °C and pH 5.0 • Covalent protein aggregation is maximal when heating at 100 °C and pH 7.0 • Covalent aggregates consist of disulfide linked globulins, not albumins. • Intact 11 S globulin monomers are most prone to covalently aggregate. [ABSTRACT FROM AUTHOR]

The recipe of some food products contains dried hen egg white (EW). It is convenient in use and available with a range of functionalities as a result of being stored under different time, temperature and moisture conditions following drying. Amyloid fibrils are fibrillary protein structures composed of highly ordered stacking of cross-β sheets. They can contribute to the foaming and gelling capacity of EW proteins. We here for the first time report that dried EW contains amyloid-like fibrils and that such fibrils in spray-dried EW (EW SD) are longer (ca. 100–200 nm) than those in freeze-dried EW [EW FD ] (ca. 20–100 nm). In addition, conditions for optimal fibrillation were determined for both EW FD and freeze-dried ovalbumin (OVA FD) using a response surface design. Dilute solutions of OVA FD and EW FD were incubated at different pH values, times and temperatures. After storage at optimal conditions OVA FD [2.0% (w protein /v), pH 7.0, 23 h, 76 °C] and EW FD [0.5% (w protein /v), pH 7.0, 24 h, 85 °C], a higher level of cross-β sheet structures and larger worm-like protein fibrils were observed for OVA FD than for EW FD. Lastly, when EW SD stored for one week at either 50 °C and 50% relative humidity (RH) [EW SD 50°C/50% ] or at 60 °C and 80% RH (EW SD 60°C/80%) was submitted to heating [0.5% (w protein /v), pH 7.0, 24 h, 85 °C], a higher extent of fibrillation was found for EW SD 60°C/80% than for EW SD 50°C/50%. Thus, drying induces EW amyloid-like protein fibrillation. Also dry heating EW SD at 60 °C and 80% RH further enhances such fibrillation during heating in excess of water. Image 1 • Spray-drying & freeze-drying egg white (EW) produce amyloid-like fibrils. • The drying mode influences the length of the amyloid-like fibrils formed. • Dried EW protein fibrillation in excess water was optimized. • Dry heating of dried EW has a limited impact on protein fibrillation. • Dry heated EW powders show increased fibrillation when heated in excess water. [ABSTRACT FROM AUTHOR]