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Protein Science : a Publication of the... Sep 2019Free-standing single-layer β-sheets are extremely rare in naturally occurring proteins, even though β-sheet motifs are ubiquitous. Here we report the crystal...
Free-standing single-layer β-sheets are extremely rare in naturally occurring proteins, even though β-sheet motifs are ubiquitous. Here we report the crystal structures of three homologous, single-layer, anti-parallel β-sheet proteins, comprised of three or four twisted β-hairpin repeats. The structures reveal that, in addition to the hydrogen bond network characteristic of β-sheets, additional hydrophobic interactions mediated by small clusters of residues adjacent to the turns likely play a significant role in the structural stability and compensate for the lack of a compact hydrophobic core. These structures enabled identification of a family of secreted proteins that are broadly distributed in bacteria from the human gut microbiome and are putatively involved in the metabolism of complex carbohydrates. A conserved surface patch, rich in solvent-exposed tyrosine residues, was identified on the concave surface of the β-sheet. These new modular single-layer β-sheet proteins may serve as a new model system for studying folding and design of β-rich proteins.
Topics: Bacteria; Bacterial Proteins; Crystallography, X-Ray; Gastrointestinal Microbiome; Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Models, Molecular; Protein Conformation, beta-Strand; Protein Folding; Tyrosine
PubMed: 31306512
DOI: 10.1002/pro.3683 -
Viruses Jan 2019The mechanism of prion strain diversity remains unsolved. Investigation of inheritance and diversification of protein-based pathogenic information demands the... (Review)
Review
The mechanism of prion strain diversity remains unsolved. Investigation of inheritance and diversification of protein-based pathogenic information demands the identification of the detailed structures of abnormal isoforms of the prion protein (PrP); however, achieving purification is difficult without affecting infectivity. Similar prion-like properties are recognized also in other disease-associated in-register parallel β-sheet amyloids including Tau and α-synuclein (αSyn) amyloids. Investigations into structures of those amyloids via solid-state nuclear magnetic resonance spectroscopy and cryo-electron microscopy recently made remarkable advances due to their relatively small sizes and lack of post-translational modifications. Herein, we review advances regarding pathogenic amyloids, particularly Tau and αSyn, and discuss implications about strain diversity mechanisms of prion/PrP from the perspective that PrP is an in-register parallel β-sheet amyloid. Additionally, we present our recent data of molecular dynamics simulations of αSyn amyloid, which suggest significance of compatibility between β-sheet propensities of the substrate and local structures of the template for stability of amyloid structures. Detailed structures of αSyn and Tau amyloids are excellent models of pathogenic amyloids, including PrP, to elucidate strain diversity and pathogenic mechanisms.
Topics: Amyloid; Animals; Humans; Mice; Molecular Dynamics Simulation; PrPSc Proteins; Prion Diseases; Prion Proteins; Prions; Protein Conformation, beta-Strand; alpha-Synuclein; tau Proteins
PubMed: 30696005
DOI: 10.3390/v11020110 -
Protein and Peptide Letters 2019The self-assembly of short peptide building blocks into well-ordered nanostructures is a key direction in bionanotechnology. The formation of β -sheet organizations by... (Review)
Review
The self-assembly of short peptide building blocks into well-ordered nanostructures is a key direction in bionanotechnology. The formation of β -sheet organizations by short peptides is well explored, leading to the development of a wide range of functional assemblies. Likewise, many natural proteinaceous materials, such as silk and amyloid fibrils, are based on β-sheet structures. In contrast, collagen, the most abundant protein in mammals, is based on helical arrangement. Similar to β-sheet structures, short helical peptides have been recently discovered to possess a diverse set of functionalities with the potential to fabricate artificial self-assembling materials. Here, we outline the functional roles of self-assembled nanostructures formed by short helical peptides and their potential as artificial materials. We focus on the association between self-assembled mesoscale structures and their material function and demonstrate the way by which this class of building blocks bears the potential for diverse applications, such as the future fabrication of smart devices.
Topics: Amyloid; Collagen; Drug Delivery Systems; Nanostructures; Peptides; Protein Conformation; Protein Conformation, beta-Strand; Protein Multimerization; Surface Properties
PubMed: 30227810
DOI: 10.2174/0929866525666180917163142 -
Annual Review of Biochemistry Jun 2017Lipids are produced site-specifically in cells and then distributed nonrandomly among membranes via vesicular and nonvesicular trafficking mechanisms. The latter... (Review)
Review
Lipids are produced site-specifically in cells and then distributed nonrandomly among membranes via vesicular and nonvesicular trafficking mechanisms. The latter involves soluble amphitropic proteins extracting specific lipids from source membranes to function as molecular solubilizers that envelope their insoluble cargo before transporting it to destination sites. Lipid-binding and lipid transfer structural motifs range from multi-β-strand barrels, to β-sheet cups and baskets covered by α-helical lids, to multi-α-helical bundles and layers. Here, we focus on how α-helical proteins use amphipathic helical layering and bundling to form modular lipid-binding compartments and discuss the functional consequences. Preformed compartments generally rely on intramolecular disulfide bridging to maintain conformation (e.g., albumins, nonspecific lipid transfer proteins, saposins, nematode polyprotein allergens/antigens). Insights into nonpreformed hydrophobic compartments that expand and adapt to accommodate a lipid occupant are few and provided mostly by the three-layer, α-helical ligand-binding domain of nuclear receptors. The simple but elegant and nearly ubiquitous two-layer, α-helical glycolipid transfer protein (GLTP)-fold now further advances understanding.
Topics: Albumins; Allergens; Animals; Antigens; Binding Sites; Biological Transport; Carrier Proteins; Gene Expression; Humans; Lipid Metabolism; Lipids; Models, Molecular; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Domains
PubMed: 28375742
DOI: 10.1146/annurev-biochem-061516-044445 -
International Journal of Molecular... Mar 2022Our work discusses the investigation of 75 peptide-based drugs with the potential ability to break the β-sheet structures of amyloid-beta peptides from senile plaques....
Our work discusses the investigation of 75 peptide-based drugs with the potential ability to break the β-sheet structures of amyloid-beta peptides from senile plaques. Hence, this study offers a unique insight into the design of neuropeptide-based drugs with β-sheet breaker potential in the amyloid-beta cascade for Alzheimer's disease (AD). We started with five peptides (QKLVFF, KLVFF, LVFF, KLVF and QKLV), to which 14 different organic acids were attached at the N-terminal. It was necessary to evaluate the physiochemical features of these sequences due to the biological correlation with our proposal. Hence, the preliminary analysis of different pharmacological features provided the necessary data to select the peptides with the best biocompatibility for administration purposes. Our approaches demonstrated that the peptides LVFF, NA-LVFF, KLVF and NA-KLVF (NA-nicotinic acid) have the ability to interfere with fibril formation and hence improve the neuro and cognitive functions. Moreover, the peptide conjugate NA-KLVF possesses attractive pharmacological properties, demonstrated by in silico and in vitro studies. Tandem mass spectrometry showed no fragmentation for the spectra of KLVF. Such important results suggest that under the action of protease, the peptide cleavage does not occur at all. Additionally, circular dichroism confirmed docking simulations and showed that NA-KLVF may improve the β-sheet breaker mechanism, and thus the entanglement process of amyloid-beta peptides can be more effective.
Topics: Alzheimer Disease; Amyloid beta-Peptides; Humans; Neuropeptides; Peptide Fragments; Pharmaceutical Preparations; Plaque, Amyloid; Protein Conformation, beta-Strand
PubMed: 35269999
DOI: 10.3390/ijms23052857 -
Biochemistry Feb 2022Aβ dimers are a basic building block of many larger Aβ oligomers and are among the most neurotoxic and pathologically relevant species in Alzheimer's disease....
Aβ dimers are a basic building block of many larger Aβ oligomers and are among the most neurotoxic and pathologically relevant species in Alzheimer's disease. Homogeneous Aβ dimers are difficult to prepare, characterize, and study because Aβ forms heterogeneous mixtures of oligomers that vary in size and can rapidly aggregate into more stable fibrils. This paper introduces Aβ as a disulfide-stabilized analogue of Aβ that forms stable homogeneous dimers in lipid environments but does not aggregate to form insoluble fibrils. The Aβ peptide is readily expressed in and purified by reverse-phase HPLC to give ca. 8 mg of pure peptide per liter of bacterial culture. SDS-PAGE establishes that Aβ forms homogeneous dimers in the membrane-like environment of SDS and that conformational stabilization of the peptide with a disulfide bond prevents the formation of heterogeneous mixtures of oligomers. Mass spectrometric (MS) studies in the presence of dodecyl maltoside (DDM) further confirm the formation of stable noncovalent dimers. Circular dichroism (CD) spectroscopy establishes that Aβ adopts a β-sheet conformation in detergent solutions and supports a model in which the intramolecular disulfide bond induces β-hairpin folding and dimer formation in lipid environments. Thioflavin T (ThT) fluorescence assays and transmission electron microscopy (TEM) studies indicate that Aβ does not undergo fibril formation in aqueous buffer solutions and demonstrate that the intramolecular disulfide bond prevents fibril formation. The recently published NMR structure of an Aβ tetramer (PDB: 6RHY) provides a working model for the Aβ dimer, in which two β-hairpins assemble through hydrogen bonding to form a four-stranded antiparallel β-sheet. It is anticipated that Aβ will serve as a stable, nonfibrilizing, and noncovalent Aβ dimer model for amyloid and Alzheimer's disease research.
Topics: Alzheimer Disease; Amyloid; Amyloid beta-Peptides; Circular Dichroism; Disulfides; Humans; Hydrogen Bonding; Microscopy, Electron, Transmission; Models, Molecular; Peptide Fragments; Protein Conformation; Protein Conformation, beta-Strand
PubMed: 35080857
DOI: 10.1021/acs.biochem.1c00739 -
Journal of the American Chemical Society Oct 2016In Alzheimer's disease, aggregation of the β-amyloid peptide (Aβ) results in the formation of oligomers and fibrils that are associated with neurodegeneration....
In Alzheimer's disease, aggregation of the β-amyloid peptide (Aβ) results in the formation of oligomers and fibrils that are associated with neurodegeneration. Aggregation of Aβ occurs through interactions between different regions of the peptide. This paper and the accompanying paper constitute a two-part investigation of two key regions of Aβ: the central region and the C-terminal region. These two regions promote aggregation and adopt β-sheet structure in the fibrils, and may also do so in the oligomers. In this paper, we study the assembly of macrocyclic β-sheet peptides that contain residues 17-23 (LVFFAED) from the central region and residues 30-36 (AIIGLMV) from the C-terminal region. These peptides assemble to form tetramers. Each tetramer consists of two hydrogen-bonded dimers that pack through hydrophobic interactions in a sandwich-like fashion. Incorporation of a single N isotopic label into each peptide provides a spectroscopic probe with which to elucidate the β-sheet assembly and interaction: H,N HSQC studies facilitate the identification of the monomers and tetramers; N-edited NOESY studies corroborate the pairing of the dimers within the tetramers. In the following paper, J. Am. Chem. Soc. 2016, DOI: 10.1021/jacs.6b06001 , we will extend these studies to elucidate the coassembly of the peptides to form heterotetramers.
Topics: Amyloid beta-Peptides; Drug Design; Molecular Dynamics Simulation; Peptide Fragments; Protein Conformation, beta-Strand; Protein Multimerization
PubMed: 27642651
DOI: 10.1021/jacs.6b06000 -
The Journal of Physical Chemistry... Oct 2021The aggregation of the amyloid beta (Aβ) protein into plaques is a pathological feature of Alzheimer's disease (AD). While amyloid aggregates have been extensively...
The aggregation of the amyloid beta (Aβ) protein into plaques is a pathological feature of Alzheimer's disease (AD). While amyloid aggregates have been extensively studied in vitro, their structural aspects and associated chemistry in the brain are not fully understood. In this report, we demonstrate, using infrared spectroscopic imaging, that Aβ plaques exhibit significant heterogeneities in terms of their secondary structure and phospholipid content. We show that the capabilities of discrete frequency infrared imaging (DFIR) are ideally suited for characterization of amyloid deposits in brain tissues and employ DFIR to identify nonplaque β-sheet aggregates distributed throughout brain tissues. We further demonstrate that phospholipid-rich β-sheet deposits exist outside of plaques in all diseased tissues, indicating their potential clinical significance. This is the very first application of DFIR toward a characterization of protein aggregates in an AD brain and provides a rapid, label-free approach that allows us to uncover β-sheet heterogeneities in the AD, which may be significant for targeted therapeutic strategies in the future.
Topics: Alzheimer Disease; Amyloid beta-Peptides; Brain; Humans; Protein Aggregates; Protein Conformation, beta-Strand; Spectrophotometry, Infrared
PubMed: 34590866
DOI: 10.1021/acs.jpclett.1c02306 -
Scientific Reports Jul 2019Although multiple hydrophobic, aromatic π-π, and electrostatic interactions are proposed to be involved in amyloid fibril formation, the precise interactions within...
Although multiple hydrophobic, aromatic π-π, and electrostatic interactions are proposed to be involved in amyloid fibril formation, the precise interactions within amyloid structures remain poorly understood. Here, we carried out detailed quantum theory of atoms-in-molecules (QTAIM) analysis to examine the hydrophobic core of amyloid parallel and antiparallel β-sheet structures, and found the presence of multiple inter-strand and intra-strand topological neighborhoods, represented by networks of through-space bond paths. Similar bond paths from side chain to side chain and from side chain to main chain were found in a single β-strand and in di- and tripeptides. Some of these bond-path networks were enhanced upon β-sheet formation. Overall, our results indicate that the cumulative network of weak interactions, including various types of hydrogen bonding (X-H-Y; X, Y = H, C, O, N, S), as well as non-H-non-H bond paths, is characteristic of amyloid β-sheet structure. The present study postulated that the presence of multiple through-space bond-paths, which are local and directional, can coincide with the attractive proximity effect in forming peptide assemblies. This is consistent with a new view of the van der Waals (vdW) interactions, one of the origins of hydrophobic interaction, which is updating to be a directional intermolecular force.
Topics: Amyloid beta-Peptides; Dipeptides; Humans; Hydrogen Bonding; Peptide Fragments; Protein Conformation, beta-Strand; Quantum Theory
PubMed: 31341215
DOI: 10.1038/s41598-019-47151-2 -
European Journal of Nuclear Medicine... May 2023Knowledge about pancreatic cancer (PC) biology has been growing rapidly in recent decades. Nevertheless, the survival of PC patients has not greatly improved. The...
PURPOSE
Knowledge about pancreatic cancer (PC) biology has been growing rapidly in recent decades. Nevertheless, the survival of PC patients has not greatly improved. The development of a novel methodology suitable for deep investigation of the nature of PC tumors is of great importance. Molecular imaging techniques, such as Fourier transform infrared (FTIR) spectroscopy and Raman hyperspectral mapping (RHM) combined with advanced multivariate data analysis, were useful in studying the biochemical composition of PC tissue.
METHODS
Here, we evaluated the potential of molecular imaging in differentiating three groups of PC tumors, which originate from different precursor lesions. Specifically, we comprehensively investigated adenocarcinomas (ACs): conventional ductal AC, intraductal papillary mucinous carcinoma, and ampulla of Vater AC. FTIR microspectroscopy and RHM maps of 24 PC tissue slides were obtained, and comprehensive advanced statistical analyses, such as hierarchical clustering and nonnegative matrix factorization, were performed on a total of 211,355 Raman spectra. Additionally, we employed deep learning technology for the same task of PC subtyping to enable automation. The so-called convolutional neural network (CNN) was trained to recognize spectra specific to each PC group and then employed to generate CNN-prediction-based tissue maps. To identify the DNA methylation spectral markers, we used differently methylated, isolated DNA and compared the observed spectral differences with the results obtained from cellular nuclei regions of PC tissues.
RESULTS
The results showed significant differences among cancer tissues of the studied PC groups. The main findings are the varying content of β-sheet-rich proteins within the PC cells and alterations in the relative DNA methylation level. Our CNN model efficiently differentiated PC groups with 94% accuracy. The usage of CNN in the classification task did not require Raman spectral data preprocessing and eliminated the need for extensive knowledge of statistical methodologies.
CONCLUSIONS
Molecular spectroscopy combined with CNN technology is a powerful tool for PC detection and subtyping. The molecular fingerprint of DNA methylation and β-sheet cytoplasmic proteins established by our results is different for the main PC groups and allowed the subtyping of pancreatic tumors, which can improve patient management and increase their survival. Our observations are of key importance in understanding the variability of PC and allow translation of the methodology into clinical practice by utilizing liquid biopsy testing.
Topics: Humans; DNA Methylation; Protein Conformation, beta-Strand; Pancreatic Neoplasms; Spectrum Analysis
PubMed: 36757432
DOI: 10.1007/s00259-023-06121-7