Protein aggregation results in beta-sheet-like assemblies that adopt either a variety of amorphous morphologies or ordered amyloid-like structures. These differences in structure also reflect biological differences; amyloid and amorphous beta-sheet aggregates have different chaperone affinities, accumulate in different cellular locations and are degraded by different mechanisms. Further, amyloid function depends entirely on a high intrinsic degree of order. Here we experimentally explored the sequence space of amyloid hexapeptides and used the derived data to build Waltz, a web-based tool that uses a position-specific scoring matrix to determine amyloid-forming sequences. Waltz allows users to identify and better distinguish between amyloid sequences and amorphous beta-sheet aggregates and allowed us to identify amyloid-forming regions in functional amyloids.
The amyloid peptides Ab 40 and Ab 42 of Alzheimer's disease are thought to contribute differentially to the disease process. Although Ab 42 seems more pathogenic than Ab 40 , the reason for this is not well understood. We show here that small alterations in the Ab 42 :Ab 40 ratio dramatically affect the biophysical and biological properties of the Ab mixtures reflected in their aggregation kinetics, the morphology of the resulting amyloid fibrils and synaptic function tested in vitro and in vivo. A minor increase in the Ab 42 :Ab 40 ratio stabilizes toxic oligomeric species with intermediate conformations. The initial toxic impact of these Ab species is synaptic in nature, but this can spread into the cells leading to neuronal cell death. The fact that the relative ratio of Ab peptides is more crucial than the absolute amounts of peptides for the induction of neurotoxic conformations has important implications for anti-amyloid therapy. Our work also suggests the dynamic nature of the equilibrium between toxic and non-toxic intermediates.
The empirical force field Fold-X was developed previously to allow rapid free energy calculations in proteins. Here, we present an enhanced version of the force field allowing prediction of the position of structural water molecules and metal ions, together called single atom ligands. Fold-X picks up 76% of water molecules found to interact with two or more polar atoms of proteins in high-resolution crystal structures and predicts their position to within 0.8 Å on average. The prediction of metal ion-binding sites have success rates between 90% and 97% depending on the metal, with an overall standard deviation on the position of binding of 0.3-0.6 Å. The following metals were included in the force field: Mg 2؉ , Ca 2؉ , Zn 2؉ , Mn 2؉ , and Cu 2؉ . As a result, the current version of Fold-X can accurately decorate a protein structure with biologically important ions and water molecules. Additionally, the free energy of binding of Ca 2؉ and Zn 2؉ (i.e., the natural logarithm of the dissociation constant) and its dependence on ionic strength correlate reasonably well with the experimental data available in the literature, allowing one to discriminate between high-and low-affinity binding sites. Importantly, the accuracy of the energy prediction presented here is sufficient to efficiently discriminate between Mg 2؉ , Ca 2؉ , and Zn 2؉ binding.ion ͉ water bridge ͉ calcium ͉ zinc ͉ structural water A wide range of strategies have been developed for estimating interaction energies in proteins. These methods generally either derive pseudoenergies from the statistical analysis of protein structural databases or, alternatively, aim at calculating energies based on explicit physical models (1, 2). Empirical force fields such as Fold-X, conversely, rely directly on structureactivity data from protein-engineering experiments to calculate interaction energies (1, 3). There are multiple advantages to empirical force fields. First, they are perfectly geared to the simulation of biological macromolecules, because the calibration data and simulated model systems are on a similar scale of complexity. Second, because empirical force fields rely on structure-activity information, they provide a rationale for the physical interpretation of changes in free energy. Finally, empirical force fields such as Fold-X are designed to allow fast and accurate estimations of free energy changes upon mutation in proteins or protein complexes. Fold-X has similar accuracy as physical force fields for prediction of free energy changes, yet it is many orders of magnitude faster, because the estimation of entropic contributions to protein interactions is directly derived from the structure using a statistical thermodynamics approach. As such, Fold-X provides a powerful tool for high-throughput structure-activity analyses of proteomes (4, 5), prediction of protein-folding pathways (6, 7), or protein design (8). The Fold-X force field is composed of a solvation term, a van der Waals term, H-bond, and electrostatic terms and entropic terms for the backbo...
Although soluble oligomeric and protofibrillar assemblies of Aβ-amyloid peptide cause synaptotoxicity and potentially contribute to Alzheimer's disease (AD), the role of mature Aβ-fibrils in the amyloid plaques remains controversial. A widely held view in the field suggests that the fibrillization reaction proceeds ‘forward' in a near-irreversible manner from the monomeric Aβ peptide through toxic protofibrillar intermediates, which subsequently mature into biologically inert amyloid fibrils that are found in plaques. Here, we show that natural lipids destabilize and rapidly resolubilize mature Aβ amyloid fibers. Interestingly, the equilibrium is not reversed toward monomeric Aβ but rather toward soluble amyloid protofibrils. We characterized these ‘backward' Aβ protofibrils generated from mature Aβ fibers and compared them with previously identified ‘forward' Aβ protofibrils obtained from the aggregation of fresh Aβ monomers. We find that backward protofibrils are biochemically and biophysically very similar to forward protofibrils: they consist of a wide range of molecular masses, are toxic to primary neurons and cause memory impairment and tau phosphorylation in mouse. In addition, they diffuse rapidly through the brain into areas relevant to AD. Our findings imply that amyloid plaques are potentially major sources of soluble toxic Aβ-aggregates that could readily be activated by exposure to biological lipids.
Self-assembling amyloid-like peptides and proteins give rise to promising biomaterials with potential applications in many fields. Amyloid structures are formed by the process of molecular recognition and self-assembly, wherein a peptide or protein monomer spontaneously self-associates into dimers and oligomers and subsequently into supramolecular aggregates, finally resulting in condensed fibrils. Mature amyloid fibrils possess a quasi-crystalline structure featuring a characteristic fiber diffraction pattern and have well-defined properties, in contrast to many amorphous protein aggregates that arise when proteins misfold. Core sequences of four to seven amino acids have been identified within natural amyloid proteins. They are capable to form amyloid fibers and fibrils and have been used as amyloid model structures, simplifying the investigations on amyloid structures due to their small size. Recent studies have highlighted the use of self-assembled amyloid-based fibers as nanomaterials. Here, we discuss the latest advances and the major challenges in developing amyloids for future applications in nanotechnology and nanomedicine, with the focus on development of sensors to study protein-ligand interactions.
Dengue virus (DENV) affects millions of people, causing more than 20,000 deaths annually. No effective treatment for the disease caused by DENV infection is currently available, partially due to the lack of knowledge on the basic aspects of the viral life cycle, including the molecular basis of the interaction between viral components and cellular compartments. Here, we characterized the properties of the interaction between the DENV capsid (C) protein and hepatic lipid droplets (LDs), which was recently shown to be essential for the virus replication cycle. Zeta potential analysis revealed a negative surface charge of LDs, with an average surface charge of ؊19 mV. The titration of LDs with C protein led to an increase of the surface charge, which reached a plateau at ؉13.7 mV, suggesting that the viral protein-LD interaction exposes the protein cationic surface to the aqueous environment. Atomic force microscopy (AFM)-based force spectroscopy measurements were performed by using C proteinfunctionalized AFM tips. The C protein-LD interaction was found to be strong, with a single (un)binding force of 33.6 pN. This binding was dependent on high intracellular concentrations of potassium ions but not sodium. The inhibition of Na ؉ /K ؉ -ATPase in DENV-infected cells resulted in the dissociation of C protein from LDs and a 50-fold inhibition of infectious virus production but not of RNA replication, indicating a biological relevance for the potassium-dependent interaction. Limited proteolysis of the LD surface impaired the C protein-LD interaction, and force measurements in the presence of specific antibodies indicated that perilipin 3 (TIP47) is the major DENV C protein ligand on the surface of LDs. Dengue virus (DENV) causes the most important arthropodborne human viral disease, with 2.5 billion people at risk, 100 million infections, and more than 20,000 deaths annually, primarily in tropical developing countries (20). Four genetically distinct serotypes (DENV1 to DENV4) have been identified, which are transmitted among humans through the bite of an infected mosquito of the genus Aedes. DENV belongs to the family Flaviviridae, together with other important human pathogens, such as yellow fever virus (YFV), West Nile virus (WNV), and hepatitis C virus (HCV). The clinical manifestations of DENV infection range from a mild illness to a severe and potentially life-threatening disease for which no treatment is available so far, due at least in part to the limited understanding of the molecular mechanisms that underlie the interaction between DENV and its host cells.The DENV genome is a single-stranded positive-sense RNA molecule of approximately 11 kb that is translated from a single open reading frame, generating a polyprotein associated with the endoplasmic reticulum (ER) membrane (34). The polyprotein is cleaved co-and posttranslationally by cellular and viral proteases into three structural proteins (capsid [C], premembrane [prM], and envelope [E]) and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B,...
Dengue is the major arthropod-borne human viral disease, for which no vaccine or specific treatment is available. We used NMR, zeta potential measurements and atomic force microscopy to study the structural features of the interaction between dengue virus C (capsid) protein and LDs (lipid droplets), organelles crucial for infectious particle formation. C protein-binding sites to LD were mapped, revealing a new function for a conserved segment in the N-terminal disordered region and indicating that conformational selection is involved in recognition. The results suggest that the positively charged N-terminal region of C protein prompts the interaction with negatively charged LDs, after which a conformational rearrangement enables the access of the central hydrophobic patch to the LD surface. Taken together, the results allowed the design of a peptide with inhibitory activity of C protein-LD binding, paving the way for new drug development approaches against dengue.
α-Synuclein misfolding and aggregation is a hallmark in Parkinson's disease and in several other neurodegenerative diseases known as synucleinopathies. The toxic properties of α-synuclein are conserved from yeast to man, but the precise underpinnings of the cellular pathologies associated are still elusive, complicating the development of effective therapeutic strategies. Combining molecular genetics with target-based approaches, we established that glycation, an unavoidable age-associated post-translational modification, enhanced α-synuclein toxicity in vitro and in vivo, in Drosophila and in mice. Glycation affected primarily the N-terminal region of α-synuclein, reducing membrane binding, impaired the clearance of α-synuclein, and promoted the accumulation of toxic oligomers that impaired neuronal synaptic transmission. Strikingly, using glycation inhibitors, we demonstrated that normal clearance of α-synuclein was re-established, aggregation was reduced, and motor phenotypes in Drosophila were alleviated. Altogether, our study demonstrates glycation constitutes a novel drug target that can be explored in synucleinopathies as well as in other neurodegenerative conditions.
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