Changes in the Structure of Potato Virus A Virions after Limited in situ Proteolysis According to Tritium Labeling Data and Computer Simulation.

Coat proteins (CP) of the potato virus A virions (PVA) contain partially disordered N-terminal domains, which are necessary for performing vital functions of the virus. Comparative analysis of the structures of coat proteins (CPs) in the intact PVA virions and in the virus particles lacking N-terminal 32 amino acids (PVAΔ32) was carried out in this work based on the tritium planigraphy data. Using atomic-resolution structure of the potato virus Y potyvirus (PVY) protein, which is a homolog of the CP PVA, the available CP surfaces in the PVY virion were calculated and the areas of intersubunit/interhelix contacts were determined.

Alpha-synuclein phosphorylation induces amyloid conversion via enhanced electrostatic bridging: Insights from molecular modeling of the full-length protein.

Fibril formation from alpha-synuclein is a key point in Parkinson's disease, multiple system atrophy, and other synucleinopathies. The mechanism of the amyloid-like conversion followed by the formation of pre-fibrillar soluble oligomers and fibrils is not completely clear; furthermore, it is unclear how the Parkinson's disease-related point mutations located in the pre-NAC region enhance fibrillation. In the present paper, atomistic replica exchange molecular dynamics simulations of the full-length alpha-synuclein and its two mutants, A53T and E46K, elucidated amyloid conversion intermediates.

pH-Sensitive Liposomes with Embedded 3-(isobutylamino)cholan-24-oic Acid: What Is the Possible Mechanism of Fast Cargo Release?

pH-sensitive liposomes have great potential for biomedical applications, in particular as nanocontainers for the delivery of biologically active compounds to specific areas of the human body. In this article, we discuss the possible mechanism of fast cargo release from a new type of pH-sensitive liposomes with embedded ampholytic molecular switch (AMS, 3-(isobutylamino)cholan-24-oic acid) with carboxylic anionic groups and isobutylamino cationic ones attached to the opposite ends of the steroid core. AMS-containing liposomes demonstrated the rapid release of the encapsulated substance when altering the pH of an outer solution, but the exact mechanism of the switch action has not yet been accurately determined.

Effect of the Coat Protein N-Terminal Domain Structure on the Structure and Physicochemical Properties of Virions of Potato Virus X and Alternanthera Mosaic Virus.

The amino acid sequences of the coat proteins (CPs) of the potexviruses potato virus X (PVX) and alternanthera mosaic virus (AltMV) share ~40% identity. The N-terminal domains of these proteins differ in the amino acid sequence and the presence of the N-terminal fragment of 28 residues (ΔN peptide) in the PVX CP. Here, we determined the effect of the N-terminal domain on the structure and physicochemical properties of PVX and AltMV virions.

Local Flexibility of a New Single-Ring Chaperonin Encoded by Bacteriophage AR9 .

Chaperonins, a family of molecular chaperones, assist protein folding in all domains of life. They are classified into two groups: bacterial variants and those present in endosymbiotic organelles of eukaryotes belong to group I, while group II includes chaperonins from the cytosol of archaea and eukaryotes. Recently, chaperonins of a prospective new group were discovered in giant bacteriophages; however, structures have been determined for only two of them.

Polyelectrolytes for Enzyme Immobilization and the Regulation of Their Properties.

In this review, we considered aspects related to the application of polyelectrolytes, primarily synthetic polyanions and polycations, to immobilize enzymes and regulate their properties. We mainly focused on the description of works in which polyelectrolytes were used to create complex and unusual systems (self-regulated enzyme-polyelectrolyte complexes, artificial chaperones, polyelectrolyte brushes, layer-by-layer immobilization and others). These works represent the field of "smart polymers", whilst the trivial use of charged polymers as carriers for adsorption or covalent immobilization of proteins is beyond the scope of this short review.

REMD Simulations of Full-Length Alpha-Synuclein Together with Ligands Reveal Binding Region and Effect on Amyloid Conversion.

Alpha-synuclein is a key protein involved in the development and progression of Parkinson's disease and other synucleinopathies. The intrinsically disordered nature of alpha-synuclein hinders the computational screening of new drug candidates for the treatment of these neurodegenerative diseases. In the present work, replica exchange molecular dynamics simulations of the full-length alpha-synuclein together with low-molecular ligands were utilized to predict the binding site and effect on the amyloid-like conversion of the protein.

Structural and Functional Features of Viral Chaperonins.

Chaperonins provide proper folding of proteins in vivo and in vitro and, as was thought until recently, are characteristic of prokaryotes, eukaryotes, and archaea. However, it turned out that some bacteria viruses (bacteriophages) encode their own chaperonins. This review presents results of the investigations of the first representatives of this new chaperonin group: the double-ring EL chaperonin and the single-ring OBP and AR9 chaperonins.

Thermocontrolled Reversible Enzyme Complexation-Inactivation-Protection by Poly(-acryloyl glycinamide).

A prospective technology for reversible enzyme complexation accompanied with its inactivation and protection followed by reactivation after a fast thermocontrolled release has been demonstrated. A thermoresponsive polymer with upper critical solution temperature, poly(-acryloyl glycinamide) (PNAGA), which is soluble in water at elevated temperatures but phase separates at low temperatures, has been shown to bind lysozyme, chosen as a model enzyme, at a low temperature (10 °C and lower) but not at room temperature (around 25 °C). The cooling of the mixture of PNAGA and lysozyme solutions from room temperature resulted in the capturing of the protein and the formation of stable complexes; heating it back up was accompanied by dissolving the complexes and the release of the bound lysozyme.

Effect of Polyphosphorylation on Behavior of Protein Disordered Regions.

Proteins interact with many charged biological macromolecules (polyelectrolytes), including inorganic polyphosphates. Recently a new protein post-translational modification, polyphosphorylation, or a covalent binding of polyphosphate chain to lysine, was demonstrated in human and yeast. Herein, we performed the first molecular modeling study of a possible effect of polyphosphorylation on behavior of the modified protein using replica exchange molecular dynamics simulations in atomistic force field with explicit water.

Glycation of glyceraldehyde-3-phosphate dehydrogenase inhibits the binding with α-synuclein and RNA.

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) shows great diversity of functions, interaction partners and post-translational modifications. GAPDH undergoes glycation of positively charged residues in diabetic patient's tissues and therefore may change interaction with partners. The influence of GAPDH glycation on interaction with two important partners, α-synuclein and RNA, has been investigated in silico using molecular dynamics simulations and in vitro using surface plasmon resonance measurements.

Interaction of Ionenes with Lipid Membrane: Unusual Impact of Charge Density.

Synthetic water-soluble polymers are increasingly used for gene delivery, stabilization, and delivery of proteins, and as prospective antimicrobial and antiviral agents. Therefore, study of their interaction with lipid membranes is of special importance. Herein, we studied interaction of aliphatic cationic ionenes (recently tested for gene delivery efficiency) differed in the length of spacer between charged groups (and therefore in charge density) with anionic lipid membrane.

Structural and functional diversity of novel and known bacteriophage-encoded chaperonins.

A bioinformatics analysis of the currently predicted GroEL-like proteins encoded by bacteriophage genomes was carried out in comparison with the phage double-ring EL and single-ring OBP chaperonins, previously described by us, as well as with the known chaperonins of group I and group II. A novel GroEL-like protein predicted in the genome of phage AR9 Bacillus subtilis was expressed in E. coli cells, purified and characterised by various physicochemical methods.

Cryo-EM reveals an asymmetry in a novel single-ring viral chaperonin.

Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They are classified into group I (bacterial, mitochondrial, chloroplast chaperonins) and group II (archaeal and eukaryotic cytosolic variants). However, both of these groups do not include recently discovered viral chaperonins.

Tightly bound polyelectrolytes enhance enzyme proteolysis and destroy amyloid aggregates.

The use of polyelectrolytes is a prospective approach to form nanocomplexes to transport different compounds including proteins. In many cases, the bound protein should be digested after delivery to the target. In the present work, we studied proteolysis of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in the complexes with polyelectrolytes.

Sensitizing tumor cells to conventional drugs: HSP70 chaperone inhibitors, their selection and application in cancer models.

Hsp70 chaperone controls proteostasis and anti-stress responses in rapidly renewing cancer cells, making it an important target for therapeutic compounds. To date several Hsp70 inhibitors are presented with remarkable anticancer activity, however their clinical application is limited by the high toxicity towards normal cells. This study aimed to develop assays to search for the substances that reduce the chaperone activity of Hsp70 and diminish its protective function in cancer cells.

The unique two-component tail sheath of giant Pseudomonas phage PaBG.

Myoviridae bacteriophages have a special contractile tail machine that facilitates high viral infection efficiency. The major component of this machine is a tail sheath that contracts during infection, allowing delivery of viral DNA into the host cell. Tail sheaths of Myoviridae phages are composed of multiple copies of individual proteins.

Peptide fragments of Hsp70 modulate its chaperone activity and sensitize tumor cells to anti-cancer drugs.

Most Hsp70 chaperone inhibitors exert anti-cancer effects; however, their high cytotoxicity proposed the use of peptide fragments of the chaperone as safer modulators of its activity and as complements to customary drugs. One such peptide, ICit-2, was found to inhibit substrate-binding and refolding activities of the chaperone. Using various approaches, we established that ICit-2 binds Hsp70, which may explain its inhibitory action.

Chaperone-like activity of synthetic polyanions can be higher than the activity of natural chaperones at elevated temperature.

Polyelectrolytes are a prospective tool for protection of proteins against aggregation. We compared synthetic polyanion, poly(styrene sulfonate), and natural chaperones of different types, namely, GroEL-like chaperonin from Pseudomonas aeruginosa phage EL and human small heat shock protein HspB5 (αB-crystallin), in their ability to prevent aggregation of client proteins. At 45 °C, all three agents efficiently suppressed thermal aggregation of phage endolysin.

New GroEL-like chaperonin of bacteriophage OBP Pseudomonas fluorescens suppresses thermal protein aggregation in an ATP-dependent manner.

Recently, we discovered and studied the first virus-encoded chaperonin of bacteriophage EL Pseudomonas aeruginosa, gene product (gp) 146. In the present study, we performed bioinformatics analysis of currently predicted GroEL-like proteins encoded by phage genomes in comparison with cellular and mitochondrial chaperonins. Putative phage chaperonins share a low similarity and do not form a monophyletic group; nevertheless, they are closer to bacterial chaperonins in the phylogenetic tree.

Glyceraldehyde-3-phosphate dehydrogenase: Aggregation mechanisms and impact on amyloid neurodegenerative diseases.

The review analyses data on specific features of aggregation of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and possible role of this enzyme in the development of neurodegenerative diseases. Different post-translational modifications of the enzyme are considered: oxidation, nitrosylation, and S-glutathionylation of the active site sulfhydryl groups, as well as phosphorylation, glycation and homocysteinylation of other amino acid residues. Modification of the sulfhydryl groups of the enzyme inhibits the enzymatic activity of GAPDH, resulting in slowdown of glycolysis, and may lead to the dissociation of the cofactor NAD from the active site of the enzyme.

Properties of substances inhibiting aggregation of oxidized GAPDH: Data on the interaction with the enzyme and the impact on its intracellular content.

This data is related to our paper "Small molecules preventing GAPDH aggregation are therapeutically applicable in cell and rat models of oxidative stress" (Lazarev et al. [1]) where we explore therapeutic properties of small molecules preventing GAPDH aggregation in cell and rat models of oxidative stress. The present article demonstrates a few of additional properties of the chemicals shown to block GAPDH aggregation such as calculated site for targeting the enzyme, effects on GAPDH glycolytic activity, influence on GAPDH intracellular level and anti-aggregate activity of pure polyglutamine exemplifying a denatured protein.

Small molecules preventing GAPDH aggregation are therapeutically applicable in cell and rat models of oxidative stress.

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is one of the most abundant targets of the oxidative stress. Oxidation of the enzyme causes its inactivation and the formation of intermolecular disulfide bonds, and leads to the accumulation of GAPDH aggregates and ultimately to cell death. The aim of this work was to reveal the ability of chemicals to break the described above pathologic linkage by inhibiting GAPDH aggregation.

Affinity of the heparin binding motif of Noggin1 to heparan sulfate and its visualization in the embryonic tissues.

Heparin binding motifs were found in many secreted proteins and it was suggested that they are responsible for retardation of the protein diffusion within the intercellular space due to the binding to heparan sulfate proteoglycanes (HSPG). Here we used synthetic FITC labeled heparin binding motif (HBM peptide) of the Xenopus laevis secreted BMP inhibitor Noggin1 to study its diffusion along the surface of the heparin beads by FRAP method. As a result, we have found out that diffusivity of HBM-labeled FITC was indeed much lesser than those predicted by theoretical calculations even for whole protein of the Noggin size.

Structural basis for regulation of stability and activity in glyceraldehyde-3-phosphate dehydrogenases. Differential scanning calorimetry and molecular dynamics.

Tissue specific isoforms of human glyceraldehyde-3-phosphate dehydrogenase, somatic (GAPD) and sperm-specific (GAPDS), have been reported to display different levels of both stability and catalytic activity. Here we apply MD simulations to investigate molecular basis of this phenomenon. The protein is a tetramer where each subunit consists of two domains - catalytic and NAD-binding one.