Atlas of Science

Tag: Abeta peptide

  • Determination of regions involved in amyloid fibril formation for Aβ(1-40) peptide

    Determination of regions involved in amyloid fibril formation for Aβ(1-40) peptide

    Mechanisms of amyloid formation of Aβ peptide are studied intensively. Determination of regions responsible for aggregation of the peptide and formation of amyloid fibrils is one of the primary aims in studying the formation of such structures. Knowledge of these regions will facilitate the choice of compounds interacting with a given region and thus preventing its aggregation. Therefore, in this study our task was to find amyloidogenic regions in amyloid fibrils formed by Aβ(1-40) peptide and to compare the data with the theoretical prediction. The FoldAmyloid method (http://bioinfo.protres.ru/fold-amyloid/) developed specially for this purpose was used to predict amyloidogenic regions of the Aβ(1-40) peptide.

    Fig. 1. Sets of peptides accumulated after hydrolysis of Abeta(1-40) with a mixture of proteases (trypsin, chymotrypsin, proteinase K). The regions of Abeta(1-40) most protected from proteolysis in the amyloid structure are presented.

    As known, the core of an amyloid fibril is resistant to the action of proteases. Therefore, it is possible to suggest that regions of the polypeptide chain that are involved in the core of the amyloid structure will be protected from the action of proteases, while the other parts of the polypeptide chain will be cleaved by proteases. Fibrils formed by this peptide were treated with a mixture of proteases consisting of trypsin, chymotrypsin, and proteinase K. When proteolysis was terminated, the mixture was centrifuged. The cleaved peptides (not included in the core of the amyloid fibril) remained in the supernatant, whereas amyloid structures were precipitated. The precipitate was washed, dried in a vacuum concentrator, and dissolved in formic acid. The sample was then layered on a reversed-phase column and eluted with an acetonitrile gradient. A mass spectrometer was used as the detector. The eluted peptides were ionized in the mass spectrometer, after which ions with the same mass were isolated and fragmented in an automatic mode using a specific algorithm. As a result, sets of masses of ions and their fragmentation spectra were obtained. After the analysis of the mass spectra and their fragments, the PEAKS Studio program was used to determine amino acid sequences of Aβ peptide fragments precipitated in the complex of amyloid fibrils.

    Figure 1 shows peptides accumulated after hydrolysis of Aβ(1–40). It is seen that peptides of the C-terminal region in the Ab peptide are accumulated. In all C-terminal peptides, the region from amino acid residues 28 to 40 is resistant to the action of proteases. In addition, peptides are accumulated where the region from amino acid residues 16 to 22 also has increased resistance to the action of the proteases. In this case, control monomer (unassociated) structures of Aβ(1–40) are hydrolyzed completely into very short di-, tri-, and tetrapeptides.

    Fig. 2. Amyloidogenic regions predicted by the FoldAmyloid program are underlined by green color (http://bioinfo.protres.ru/fold-amyloid/).

    Thus, using mass-spectrometry we determined regions of the chain that are protected from the action of proteases in amyloid fibrils formed by the Aβ(1–40) peptide. We demonstrated that for the synthetic Aβ(1–40) peptide, amino acid regions 16-22 and 28-40 are protected from the action of proteases upon formation of the amyloid structure. These data are in agreement with the amyloidogenic regions (amino acid residues 16-21 and 32-36) in the sequence of the Aβ(1–40) peptide predicted theoretically (Fig. 2).

    Alexey K. Surin, Oxana V. Galzitskaya
    Institute of Protein Research, Russian Academy of sciences

     

    Publication

    Determination of Regions Involved in Amyloid Fibril Formation for Aβ(1-40) Peptide.
    Surin AK, Grigorashvili EI, Suvorina MY, Selivanova OM, Galzitskaya OV
    Biochemistry (Mosc). 2016 Jul

  • Unusual structure of aggregates formed by the fragment of Аβ(16-25) peptide

    Unusual structure of aggregates formed by the fragment of Аβ(16-25) peptide

    By the moment, a large number of proteins and peptides, polymerization of which in fibril formations leads to emergence of different diseases (amyloidosis), have been identified. But it is not always that fibril formations are toxic for organisms. A multitude of the so-called functional amyloids are known. Such amyloids have been found in many animals and plants as well in yeasts and bacteria. For several peptide and protein hormones, the functional state is their continued storage in secretary granules of the endocrine system (glucagon, somatostatin etc.). Many microorganisms have amyloid proteins on their cell surfaces. They help microorganisms not only interact with inert surfaces (plastic, glass) but also are required for adhesion to the host-cell surfaces. In this case, the risk of development of some diseases, such as tuberculosis, increases. Much attention has been recently focused on studying biofilms formed by amyloid proteins from microorganisms, for example, curlin from E. coli. Biofilms are intended for facilitating the adhesion of bacterial cells to the host-cell surface, which helps microorganisms to colonize host organisms. Lately it has been noticed that biofilms can be used as nanobiomaterials for studying different biological processes, for example, for enhancing retroviral transduction or direct visualization on the surface of nanofilms of viral particles. This is just the beginning of the usage of nanofilms. However their design could allow producing nanofilms with different programmed properties which is indisputably a promising range of research.

    Fig. 1. Electron microscopic images of peptide Аβ(16-25) at large magnification. a, Polymer films of different width are seen in the field; b, Films are thin and nearly merge with the background. The film thickness in the places of their twisting is about 3 nm (arrows).

    Our experience of studying different amyloidogenic proteins and peptides (insulin, Аβ(1-40) and Аβ(1-42) peptides including the different predicted amyloidogenic fragments of Аβ(1-42) peptide (Аβ(16-25), Аβ(31-40), Аβ(33-42)), and also the predicted amyloidogenic fragments of protein Bgl2p–glucantransferase from S. cerevisiae cell walls) has shown that the morphology of amyloid fibrils changes depending on the protein sequence. However, with the diversity of the objects studied, it is for the first time that we have observed polymers as films for the Аβ(16-25) peptide (Fig. 1). The process of amyloid formation for all investigated samples follows by the next pathway: destabilized monomer ® ring-like oligomer ® amyloid fibril. We have found that the main building block of a fibril of any morphology is a ring oligomer (Fig. 2). Despite on the similar morphology of the general structural blocks upon amyloid formation the structure of oligomer is determined mainly by their amino acid sequence. The interaction of ring oligomers with each other in different ways in the peptides studied by us makes it possible to explain their polymorphism.

    Fig. 2. Schematic representation of the process of nanofilm formation by the Аβ(16-25) fragment of Aβ. А – destabilized monomers; B – ring oligomers; C – short thin fibrils; D – films (on the enlarged image of the film fragment, the ring oligomers are indicated by arrows); E – molecular structure of nanofilm consisting of ring-like oligomer structures.

    Nanofilms are of great interest for nanotechnology which is being intensely developed now. Biofilms open wide possibilities for studying biological, biochemical, and biophysical processes occurring in the organism at the molecular level. For example, they can be used as biosurfaces for fixing some short-lived intermediate processes upon interactions of proteins, protein complexes etc. The importance of methods of bioinformatics becomes obvious because they will make it possible to predict bionanomaterials with a priori determined properties. In the first place this concerns the production of differently charged nanofilms Due to their unique chemical and physical properties, amyloid nanomaterials have an inviting potential as a novel class of bionanomaterials. Nanostructures offer many potential applications from electronics to biologically active materials.

    Olga M. Selivanova, Oxana V. Galzitskaya
    Institute of Protein Research, Russian Academy of sciences

     

    Publication

    Peptide Aβ(16-25) Forms Nanofilms in the Process of Its Aggregation.
    Selivanova OM, Gorbunova EY, Mustaeva LG, Grigorashvili EI, Suvorina MY, Surin AK, Galzitskaya OV
    Biochemistry (Mosc). 2016 Jul