Cytotoxic PSMα3 inhibits the aggregation of human insulin .

Phenol-soluble modulins (PSMs) are extracellular short amphipathic peptides secreted by the bacteria (). They play an essential role in the bacterial lifecycle, biofilm formation, and stabilisation. From the PSM family, PSMα3 has been of special interest recently due to its cytotoxicity and highly stable α-helical conformation, which also remains in its amyloid fibrils.

Structural effects of charge destabilization and amino acid substitutions in amyloid fragments of CsgA.

The most studied functional amyloid is the CsgA, major curli subunit protein, which is produced by numerous strains of Enterobacteriaceae. Although CsgA sequences are highly conserved, they exhibit species diversity, which reflects the specific evolutionary and functional adaptability of the major curli subunit. Herein, we performed bioinformatics analyses to uncover the differences in the amyloidogenic properties of the R4 fragments in Escherichia coli and Salmonella enterica and proposed four mutants for more detailed studies: M1, M2, M3, and M4.

PACT - Prediction of amyloid cross-interaction by threading.

Amyloid proteins are often associated with the onset of diseases, including Alzheimer's, Parkinson's and many others. However, there is a wide class of functional amyloids that are involved in physiological functions, e.g.

The role of tandem repeats in bacterial functional amyloids.

Repetitivity and modularity of proteins are two related notions incorporated into multiple evolutionary concepts. We discuss whether they may also be essential for functional amyloids. Amyloids are proteins that create very regular and usually highly insoluble fibrils, which are often associated with neurodegeneration.

A spatiotemporal reconstruction of the pharyngeal cuticle reveals a structure rich in phase-separating proteins.

How the cuticles of the roughly 4.5 million species of ecdysozoan animals are constructed is not well understood. Here, we systematically mine gene expression datasets to uncover the spatiotemporal blueprint for how the chitin-based pharyngeal cuticle of the nematode is built.

AmyloGraph: a comprehensive database of amyloid-amyloid interactions.

Information about the impact of interactions between amyloid proteins on their fibrillization propensity is scattered among many experimental articles and presented in unstructured form. We manually curated information located in almost 200 publications (selected out of 562 initially considered), obtaining details of 883 experimentally studied interactions between 46 amyloid proteins or peptides. We also proposed a novel standardized terminology for the description of amyloid-amyloid interactions, which is included in our database, covering all currently known types of such a cross-talk, including inhibition of fibrillization, cross-seeding and other phenomena.

Topological analysis as a tool for detection of abnormalities in protein-protein interaction data.

Motivation: Protein-protein interaction datasets, which can be modeled as networks, constitute an essential layer in multi-omics approach to biomedical knowledge. This representation gives insight into molecular pathways, help to uncover novel potential drug targets or predict a therapy outcome. Nevertheless, the data that constitute such systems are frequently incomplete, error-prone and biased by scientific trends.

Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins.

Several computational methods have been developed to predict amyloid propensity of a protein or peptide. These bioinformatics tools are time- and cost-saving alternatives to expensive and laborious experimental methods which are used to confirm self-aggregation of a protein. Computational approaches not only allow preselection of reliable candidates for amyloids but, most importantly, are capable of a thorough and informative analysis of a protein, indicating the sequence determinants of protein aggregation, identifying the potential causal mutations and likely mechanisms.

Variability of Amyloid Propensity in Imperfect Repeats of CsgA Protein of and .

CsgA is an aggregating protein from bacterial biofilms, representing a class of functional amyloids. Its amyloid propensity is defined by five fragments (R1-R5) of the sequence, representing non-perfect repeats. Gate-keeper amino acid residues, specific to each fragment, define the fragment's propensity for self-aggregation and aggregating characteristics of the whole protein.

Water Pores in Planar Lipid Bilayers at Fast and Slow Rise of Transmembrane Voltage.

Basic understanding of the barrier properties of biological membranes can be obtained by studying model systems, such as planar lipid bilayers. Here, we study water pores in planar lipid bilayers in the presence of transmembrane voltage. Planar lipid bilayers were exposed to fast and slow linearly increasing voltage and current signals.

Bioinformatics methods for identification of amyloidogenic peptides show robustness to misannotated training data.

Several disorders are related to amyloid aggregation of proteins, for example Alzheimer's or Parkinson's diseases. Amyloid proteins form fibrils of aggregated beta structures. This is preceded by formation of oligomers-the most cytotoxic species.

Ultrathin glass fiber microprobe for electroporation of arbitrary selected cell groups.

A new type of ultrathin fiber microprobe for selective electroporation is reported. The microprobe is 10 cm long and has a diameter of 350 µm. This microprobe is a low cost tool, which allows electroporation of an arbitrary selected single cell or groups of cells among population with use of a standard microscope and cell culture plates.

PATH - Prediction of Amyloidogenicity by Threading and Machine Learning.

Amyloids are protein aggregates observed in several diseases, for example in Alzheimer's and Parkinson's diseases. An aggregate has a very regular beta structure with a tightly packed core, which spontaneously assumes a steric zipper form. Experimental methods enable studying such peptides, however they are tedious and costly, therefore inappropriate for genomewide studies.

Proapoptotic activity induced by photodynamic reaction with novel cyanine dyes in caspase-3-deficient human breast adenocarcinoma cell lines (MCF/WT and MCF/DX).

Photodynamic therapy (PDT) is currently one of the cancer treatment options. PDT requires the application of a photosensitizer (such as: porphyrins, chlorines, and phthalocyanines) that selectively targets malignant cells. It is a dilemma to find a proper photosensitizer.

Effect of electrochemotherapy with betulinic acid or cisplatin on regulation of heat shock proteins in metastatic human carcinoma cells in vitro.

Betulinic acid (BTA) is naturally occurring triterpene that has received interest as a novel therapeutic substance with cytotoxicity towards a number of cancer cell lines. Despite the wide spectrum of biological and pharmacological effects, its effect may be limited its lipophobic properties. Therefore, strategies to improve the access of BTA to the cells are required to enhance the anticancer effects.

Automated method to differentiate between native and mirror protein models obtained from contact maps.

Mirror protein structures are often considered as artifacts in modeling protein structures. However, they may soon become a new branch of biochemistry. Moreover, methods of protein structure reconstruction, based on their residue-residue contact maps, need methodology to differentiate between models of native and mirror orientation, especially regarding the reconstructed backbones.

Biological effects in photodynamic treatment combined with electropermeabilization in wild and drug resistant breast cancer cells.

Electrochemotherapy became one of the therapeutic protocols successfully used in oncology. However, biological effects occurring in cells, especially those which are drug resistant, have not been studied thoroughly. This study presents response of wild and drug resistant breast cancer cells to classical photodynamic therapy with Photofrin or experimental photodynamic therapy with cyanine IR-775, combined with electroporation.

Amyloidogenic motifs revealed by n-gram analysis.

Amyloids are proteins associated with several clinical disorders, including Alzheimer's, and Creutzfeldt-Jakob's. Despite their diversity, all amyloid proteins can undergo aggregation initiated by short segments called hot spots. To find the patterns defining the hot spots, we trained predictors of amyloidogenicity, using n-grams and random forest classifiers.

The Effect of Millisecond Pulsed Electric Fields (msPEF) on Intracellular Drug Transport with Negatively Charged Large Nanocarriers Made of Solid Lipid Nanoparticles (SLN): In Vitro Study.

Drug delivery technology is still a dynamically developing field of medicine. The main direction in nanotechnology research (nanocarriers, nanovehicles, etc.) is efficient drug delivery to target cells with simultaneous drug reduction concentration.

Applying PyRosetta molecular energies to separate properly oriented protein models from mirror models, obtained from contact maps.

Reconstructing protein structure based on contact maps leads to two types of models: properly oriented models and mirror models. This is due to the fact that contact maps do not include information on protein chirality. Therefore, both types of model orientations share the same contact map and are geometrically allowed.

Electroporation and lipid nanoparticles with cyanine IR-780 and flavonoids as efficient vectors to enhanced drug delivery in colon cancer.

Nanocarriers and electroporation (also named electropermeabilization) are convenient methods to increase drug transport. In the current study, we present an effective support of drug delivery into cancer cells, utilizing these methods. We compare the efficiency of each of them and their combination.

Fast assessment of structural models of ion channels based on their predicted current-voltage characteristics.

Computational prediction of protein structures is a difficult task, which involves fast and accurate evaluation of candidate model structures. We propose to enhance single-model quality assessment with a functionality evaluation phase for proteins whose quantitative functional characteristics are known. In particular, this idea can be applied to evaluation of structural models of ion channels, whose main function - conducting ions - can be quantitatively measured with the patch-clamp technique providing the current-voltage characteristics.

AmyLoad: website dedicated to amyloidogenic protein fragments.

Unlabelled: Analyses of amyloidogenic sequence fragments are essential in studies of neurodegenerative diseases. However, there is no one internet dataset that collects all the sequences that have been investigated for their amyloidogenicity. Therefore, we have created the AmyLoad website which collects the amyloidogenic sequences from all major sources.

Comparative modeling of hypothetical amyloid pores based on cylindrin.

Cylindrin is a six-stranded antiparallel beta barrel obtained from amyloidogenic strands of crystallin. It induces cell toxicity through an unknown mechanism. In this work, the potential use of the structure of cylindrin as a template for modeling amyloid pores-hypothetical transmembrane structures which appear during amyloid diseases-was studied.