RESUMEN
Antibiotic-resistant strains are an emerging threat to public health. The usage of antimicrobial peptides (AMPs) is one of the promising approaches to solve this problem. For the development of new AMPs, it is necessary to have reliable prediction methods. Recently, deep learning approaches have been used to predict AMP. In this paper, we want to compare simple and complex methods for these purposes. We used the BERT transformer to create sequence embeddings and the multilayer perceptron (MLP) and light attention (LA) approaches for classification. One of them reached about 80 % accuracy and specificity in benchmark testing, which is on par with the best available methods. For comparison, we proposed a simple method using only the amino acid composition of proteins or peptides. This method has shown good results, at the level of the best methods. We have prepared a special server for predicting the ability of AMPs by amino acid composition: http://bioproteom.protres.ru/antimicrob/.
RESUMEN
Meisl et al. have recently observed an anomalous dependence of the amyloid formation rate on the protein concentration. A novel mechanism of fibril growth has been proposed by Meisl et al. to explain the abnormality; it consists in the fibril-catalyzed initiation of fibril formation with saturation of catalytic sites at high concentrations of substrates. Our article describes an alternative explanation of the anomalous kinetics, assuming that the formation of metastable oligomers competes with fibril formation by decreasing the concentration of free monomers. Oligomers are indeed observed in the course of amyloid formation, but are usually considered as seeds of amyloid fibrils rather as their competitors. However, the oligomers visually detectable by electron microscopy were shown to be close in size to those that can be derived from the anomalous dependence of the amyloid growth rate on the protein concentration, given that the anomaly results from competition between oligomer formation and amyloidogenesis.
Asunto(s)
Péptidos beta-Amiloides/química , Amiloide/química , Amiloide/ultraestructura , Péptidos beta-Amiloides/ultraestructura , CinéticaRESUMEN
We have developed a highly efficient method for purification of the recombinant product Aß(1-40) peptide. The concentration dependence of amyloid formation by recombinant Aß(1-40) peptide was studied using fluorescence spectroscopy and electron microscopy. We found that the process of amyloid formation is preceded by lag time, which indicates that the process is nucleation-dependent. Further exponential growth of amyloid fibrils is followed by branching scenarios. Based on the experimental data on the concentration dependence, the sizes of the folding nuclei of fibrils were calculated. It turned out that the size of the primary nucleus is one "monomer" and the size of the secondary nucleus is zero. This means that the nucleus for new aggregates can be a surface of the fibrils themselves. Using electron microscopy, we have demonstrated that fibrils of these peptides are formed by the association of rounded ring structures.
Asunto(s)
Péptidos beta-Amiloides/metabolismo , Amiloide/metabolismo , Fragmentos de Péptidos/metabolismo , Amiloide/química , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/genética , Cinética , Microscopía Electrónica , Fragmentos de Péptidos/química , Fragmentos de Péptidos/genética , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/aislamiento & purificación , Espectrometría de Fluorescencia , Espectrometría de Masa por Ionización de ElectrosprayRESUMEN
Amyloid and amyloid-like aggregates are elongated unbranched fibrils consisting of ß-structures of separate monomers positioned perpendicular to the fibril axis and stacked strictly above each other. In their physicochemical properties, amyloid fibrils are reminiscent of synthetic polymers rather than usual proteins because they are stable to the action of denaturing agents and proteases. Their mechanical stability can be compared to a spider's web, that in spite of its ability to stretch, is stronger than steel. It is not surprising that a large number of diseases are accompanied with amyloid fibril depositing in different organs. Pathologies provoked by depositing of incorrectly folded proteins include Alzheimer's, Parkinson's, and Huntington's diseases. In addition, this group of diseases involves mucoviscidosis, some types of diabetes, and hereditary cataracts. Each type of amyloidosis is characterized by aggregation of a certain type of protein that is soluble in general, and thus leads to specific distortions of functions of the corresponding organs. Therefore, it is important to understand the process of transformation of "native" proteins to amyloid fibrils to clarify how these molecules acquire such strength and what key elements of this process determine the pathway of erroneous protein folding. This review presents our analysis of complied information on the mechanisms of formation and biochemical properties of amyloid fibrils.
Asunto(s)
Amiloide/química , Amiloidosis/etiología , Enfermedad de Alzheimer/etiología , Fibrosis Quística/etiología , Humanos , Enfermedad de Huntington/etiología , Enfermedad de Parkinson/etiología , Conformación Proteica , Pliegue de ProteínaRESUMEN
The number of protons available for hydrogen-deuterium exchange was predicted for ten globular proteins using a method described elsewhere by the authors. The average number of protons replaced by deuterium was also determined by mass spectrometry of the intact proteins in their native conformations. Based on these data, we find that two models proposed earlier agree with each other in estimation of the number of protons replaced by deuterium. Using a model with a probability scale for hydrogen bond formation, we estimated a number of protons replaced by deuterium that is close to the experimental data for long-term incubation in D(2)O (24 h). Using a model based on estimations with a scale of the expected number of contacts in globular proteins there is better agreement with the experimental data obtained for a short period of incubation in D(2)O (15 min). Therefore, the former model determines weakly fluctuating parts of a protein that are in contact with solvent only for a small fraction of the time. The latter model (based on the scale of expected number of contacts) predicts either flexible parts of a protein chain exposed to interactions with solvent or disordered parts of the protein.
Asunto(s)
Medición de Intercambio de Deuterio/métodos , Globulinas/química , Aminoácidos/química , Animales , Bovinos , Deuterio/química , Humanos , Hidrógeno/química , Enlace de Hidrógeno , Espectrometría de Masas/métodos , Modelos Químicos , Conformación Molecular , Probabilidad , Estructura Secundaria de Proteína , Protones , SolventesRESUMEN
No detailed step-by-step model of protein rearrangements during amyloid structure formation has been presented in the literature. The aim of this work was to design a kinetic model for description of the amyloid formation process on the basis of the most recent experimental data. A general kinetic model is proposed for description of the amyloid formation process including the nucleation mechanism of polymerization with consecutive monomer attachment to oligomer and autocatalytic growth of amyloid aggregates implying all types of exponential growth such as branching, fragmentation, and growth from the surface. Computer simulations have shown that the model correctly describes experimentally observed growth stages of amyloid fibrils and that the presence of exponential growth stage in the model is critical for modeling amyloid fibril formation. The key feature of the proposed model is the stage of the exponential growth of the aggregate. Such stage can simultaneously describe several versions of aggregate enlargement by branching, fragmentation, or growth from the surface. Data obtained using this model suggest conclusions concerning the significance of each stage in amyloid fibril assembly.
Asunto(s)
Amiloide/química , Modelos Biológicos , Multimerización de Proteína , Biocatálisis , Cinética , Estructura Secundaria de ProteínaRESUMEN
We have investigated the possibility to predict protection of amino acid residues from hydrogen-deuterium exchange. A database containing experimental hydrogen-deuterium exchange data for 14 proteins for which these data are known has been compiled. Different structural parameters related to flexibility of amino acid residues and their amide groups have been analyzed to answer the question whether these parameters can be used for predicting the protection of amino acid residues from hydrogen-deuterium exchange. A method for prediction of protection of amino acid residues, which uses only the amino acid sequence of a protein, has been elaborated.
Asunto(s)
Proteínas Bacterianas/química , Deuterio/química , Hidrógeno/química , Proteínas de Plantas/química , Proteínas/química , Secuencia de Aminoácidos , Animales , CinéticaRESUMEN
We have created a database of two-domain proteins with homology less than 25% (452 proteins). Based on one half of this set of proteins statistics of appearance of amino acid residues on the domain boundaries of multiple domain proteins has been obtained. Small and hydrophilic amino acids (proline, glycine, asparagine, glutamic acid, arginine and others) appear on the domain boundaries more often than in the whole protein. Opposite, hydrophobic amino acid residues (tryptophane, methionine, phenylalanine and others) appear on the domain boundaries more rarely. The obtained scales of the appearance of amino acid residues on the boundary regions from the statistics have been used for calculation of domain boundaries in the proteins of the second half of the database. The probability scale obtained by averaging the appearance of amino acid residues on the domain boundary region including 8 residues (+/-4 residues from the real domain boundary) gives the best result: for 57% of proteins the predicted boundary was closer than 40 residues to the boundary assigned from three-dimensional structures, for 41% it was closer than 20 residues from the real boundary. The probability scale was used to predict domain boundaries for proteins with unknown three-dimensional structure (international competition CASP6).