Specific Mutations Reverse Regulatory Effects of Adenosine Phosphates and Increase Their Binding Stoichiometry in CBS Domain-Containing Pyrophosphatase.

Regulatory cystathionine ß-synthase (CBS) domains are widespread in proteins; however, difficulty in structure determination prevents a comprehensive understanding of the underlying regulation mechanism. Tetrameric microbial inorganic pyrophosphatase containing such domains (CBS-PPase) is allosterically inhibited by AMP and ADP and activated by ATP and cell alarmones diadenosine polyphosphates. Each CBS-PPase subunit contains a pair of CBS domains but binds cooperatively to only one molecule of the mono-adenosine derivatives. We used site-directed mutagenesis of Desulfitobacterium hafniense CBS-PPase to identify the key elements determining the direction of the effect (activation or inhibition) and the "half-of-the-sites" ligand binding stoichiometry. Seven amino acid residues were selected in the CBS1 domain, based on the available X-ray structure of the regulatory domains, and substituted by alanine and other residues. The interaction of 11 CBS-PPase variants with the regulating ligands was characterized by activity measurements and isothermal titration calorimetry. Lys100 replacement reversed the effect of ADP from inhibition to activation, whereas Lys95 and Gly118 replacements made ADP an activator at low concentrations but an inhibitor at high concentrations. Replacement of these residues for alanine increased the stoichiometry of mono-adenosine phosphate binding by twofold. These findings identified several key protein residues and suggested a "two non-interacting pairs of interacting regulatory sites" concept in CBS-PPase regulation.

The Structure and Nucleotide-Binding Characteristics of Regulated Cystathionine ß-Synthase Domain-Containing Pyrophosphatase without One Catalytic Domain.

Regulatory adenine nucleotide-binding cystathionine ß-synthase (CBS) domains are widespread in proteins; however, information on the mechanism of their modulating effects on protein function is scarce. The difficulty in obtaining structural data for such proteins is ascribed to their unusual flexibility and propensity to form higher-order oligomeric structures. In this study, we deleted the most movable domain from the catalytic part of a CBS domain-containing bacterial inorganic pyrophosphatase (CBS-PPase) and characterized the deletion variant both structurally and functionally. The truncated CBS-PPase was inactive but retained the homotetrameric structure of the full-size enzyme and its ability to bind a fluorescent AMP analog (inhibitor) and diadenosine tetraphosphate (activator) with the same or greater affinity. The deletion stabilized the protein structure against thermal unfolding, suggesting that the deleted domain destabilizes the structure in the full-size protein. A "linear" 3D structure with an unusual type of domain swapping predicted for the truncated CBS-PPase by Alphafold2 was confirmed by single-particle electron microscopy. The results suggest a dual role for the CBS domains in CBS-PPase regulation: they allow for enzyme tetramerization, which impedes the motion of one catalytic domain, and bind adenine nucleotides to mitigate or aggravate this effect.

Mutant Cytochrome C as a Potential Detector of Superoxide Generation: Effect of Mutations on the Function and Properties.

Cytochrome c (CytC) is a single-electron carrier between complex bc1 and cytochrome c-oxidase (CcO) in the electron transport chain (ETC). It is also known as a good radical scavenger but its participation in electron flow through the ETC makes it impossible to use CytC as a radical sensor. To solve this problem, a series of mutants were constructed with substitutions of Lys residues in the universal binding site (UBS) which interact electrostatically with negatively charged Asp and Glu residues at the binding sites of CytC partners, bc1 complex and CcO. The aim of this study was to select a mutant that had lost its function as an electron carrier in the ETC, retaining the structure and ability to quench radicals. It was shown that a mutant CytC with substitutions of five (8Mut) and four (5Mut) Lys residues in the UBS was almost inactive toward CcO. However, all mutant proteins kept their antioxidant activity sufficiently with respect to the superoxide radical. Mutations shifted the dipole moment of the CytC molecule due to seriously changed electrostatics on the surface of the protein. In addition, a decrease in the redox potential of the protein as revealed by the redox titrations of 8Mut was detected. Nevertheless, the CD spectrum and dynamic light scattering suggested no significant changes in the secondary structure or aggregation of the molecules of CytC 8Mut. Thus, a variant 8Mut with multiple mutations in the UBS which lost its ability to electron transfer and saved most of its physico-chemical properties can be effectively used as a detector of superoxide generation both in mitochondria and in other systems.

Chitosan polyplexes: Energetics of formation and conformational changes in DNA upon binding and release.

Energetics of chitosan (CS) polyplexes and conformational stability of bound DNA were studied at pH 5.0 by ITC and HS-DSC, respectively. The CS-DNA binding isotherm was well approximated by the McGhee-von Hippel model suggesting the binding mechanism to be a cooperative attachment of interacting CS ligands to the DNA matrix. Melting thermograms of polyplexes revealed the transformation of different conformational forms of bound DNA in dependence on the CS/DNA weight ratio rw. At 0

Complexation between chitosan and carboxymethyl cellulose in weakly acidic, neutral, and weakly alcaline media.

The interaction between carboxymethyl cellulose and partially reacetylated chitosan soluble in acidic and alkaline aqueous media is studied by light scattering and isothermal titration calorimetry in a wide pH range. It is shown that the formation of polyelectrolyte complexes (PEC) can occur in the pH range of 6-8, while this pair of polyelectrolytes loses the ability to complexation upon transition to a more alkaline medium. The revealed dependence of the observed enthalpy of interaction on the ionization enthalpy of the buffer indicates the participation of proton transfer from the buffer substance to chitosan and its additional ionization in the binding process. This phenomenon is first observed in a mixture of a weak polybase chitosan and a weak polyacid. The possibility to obtain soluble nonstoichiometric PEC by a direct mixing of the components in a weakly alkaline medium is shown. The resulting PECs are polymolecular particles in shape close to homogeneous spheres with a radius of about 100 nm. The obtained results are promising for creating of biocompatible and biodegradable drug delivery systems.

Pre-steady-state kinetics and solvent isotope effects support the "billiard-type" transport mechanism in Na+ -translocating pyrophosphatase.

Membrane-bound pyrophosphatase (mPPase) found in microbes and plants is a membrane H+ pump that transports the H+ ion generated in coupled pyrophosphate hydrolysis out of the cytoplasm. Certain bacterial and archaeal mPPases can in parallel transport Na+ via a hypothetical "billiard-type" mechanism, also involving the hydrolysis-generated proton. Here, we present the functional evidence supporting this coupling mechanism. Rapid-quench and pulse-chase measurements with [32 P]pyrophosphate indicated that the chemical step (pyrophosphate hydrolysis) is rate-limiting in mPPase catalysis and is preceded by a fast isomerization of the enzyme-substrate complex. Na+ , whose binding is a prerequisite for the hydrolysis step, is not required for substrate binding. Replacement of H2 O with D2 O decreased the rates of pyrophosphate hydrolysis by both Na+ - and H+ -transporting bacterial mPPases, the effect being more significant than with a non-transporting soluble pyrophosphatase. We also show that the Na+ -pumping mPPase of Thermotoga maritima resembles other dimeric mPPases in demonstrating negative kinetic cooperativity and the requirement for general acid catalysis. The findings point to a crucial role for the hydrolysis-generated proton both in H+ -pumping and Na+ -pumping by mPPases.

Peculiarities of the interaction of sodium dodecyl sulfate with chitosan in acidic and alkaline media.

In this work, the interaction between the negatively charged surfactant sodium dodecyl sulfate (SDS) and partially N-reacetylated chitosan (RA-CHI), which is soluble at pH range up to pH 12, is studied in a wide pH range including alkaline media by light scattering (LS) and isothermic titration calorimetry (ITC). It is shown that in the weakly alkaline medium (pH 7.4), RA-CHI/SDS interaction is exothermic and cooperative. This interaction is found to be coupled with proton transfer from the buffer substance to chitosan as it is revealed by the dependence of the measured heat release on the ionization enthalpy of the buffer. At higher pH values (pH > 8), another mechanism of interaction is observed that include SDS micellization induced by hydrophobic interactions with polymer segments, so that no phase separation occurred in these mixtures. The results obtained can contribute to expand the knowledge about application of chitosan for preparation of pharmaceutical and cosmetic compositions containing anionic surfactants.

Unusual chromosomal polymorphism of the common shrew, Sorex araneus L., in southern Belarus.

Analysis of the frequency of karyotypes and chromosomal rearrangements in the distributional ranges of four metacentric races of Sorex araneus Linnaeus, 1758 has revealed features that are not typical for polymorphic populations of this species. The frequency of the acrocentric karyotype and heterozygotes for fusion of acrocentric chromosomes turned out to be significantly higher than expected in case of random crossing. As an explanation for the unusual polymorphism, it has been suggested that metacentric races may hybridize with acrocentric populations that remained from the ancient chromosomal form.

Poly(Ethylene Glycol) Interacts with Hyaluronan in Aqueous Media.

We report here the first evidence for the interaction of poly(ethylene glycol) (PEG) with hyaluronan (HA) in aqueous solutions. PEG-HA complexes (Kapp = 45,000 ± 8000 M-1) contained about 3.3 ± 0.1 of ethylene glycol units per disaccharide of HA. The carboxyl of the D-glucuronic acid and the amide of the N-acetyl-D-glucosamine did not participate in PEG binding. Similar experiments performed with dextran and monosaccharides showed that multiple free primary hydroxyls regularly distributed along the polysaccharide chain are necessary for PEG binding. Another novelty of our study is contraction of HA upon PEG binding. The effect was observed with HA in solution or adsorbed on positively charged liposomes. The thickness of the HA layer on the liposomes decreased 2-fold upon PEG addition. HA compaction induced by PEG may underlie the changes in the plasma membrane properties and resealing of mechanical injuries induced by Pluronics.

The tetrameric structure of nucleotide-regulated pyrophosphatase and its modulation by deletion mutagenesis and ligand binding.

A quarter of prokaryotic Family II inorganic pyrophosphatases (PPases) contain a regulatory insert comprised of two cystathionine ß-synthase (CBS) domains and one DRTGG domain in addition to the two catalytic domains that form canonical Family II PPases. The CBS domain-containing PPases (CBS-PPases) are allosterically activated or inhibited by adenine nucleotides that cooperatively bind to the CBS domains. Here we use chemical cross-linking and analytical ultracentrifugation to show that CBS-PPases from Desulfitobacterium hafniense and four other bacterial species are active as 200-250-kDa homotetramers, which seems unprecedented among the four PPase families. The tetrameric structure is stabilized by Co2+, the essential cofactor, pyrophosphate, the substrate, and adenine nucleotides, including diadenosine tetraphosphate. The deletion variants of dhPPase containing only catalytic or regulatory domains are dimeric. Co2+ depletion by incubation with EDTA converts CBS-PPase into inactive tetrameric and dimeric forms. Dissociation of tetrameric CBS-PPase and its catalytic part by dilution renders them inactive. The structure of CBS-PPase tetramer was modelled from the structures of dimeric catalytic and regulatory parts. These findings signify the role of the unique oligomeric structure of CBS-PPase in its multifaced regulation.

Biodegradable thermoresponsive oligochitosan nanoparticles: Mechanisms of phase transition and drug binding-release.

Oligochitosan, a low molecular weight derivative of the cationic biopolymer, chitosan, currently shows a great potential of application as a biodegradable non-toxic stimuli-sensitive drug carrier. This paper aimed to elucidate the thermoresponsive potential of oligochitosan and the temperature-controlled drug binding and release to shed light on oligochitosan potential in stimuli-responsive drug delivery. Mechanisms of thermoresponsive behavior of oligochitosan induced by ß-glycerophosphate (GP) were investigated using ITC, DSC, and DLS. Upon heating, the aqueous oligochitosan solution underwent a cooperative transition of the microphase separation type resulting in the formation of stable nano-sized particles. Energetics of the GP-oligochitosan interaction (evaluated by ITC) revealed a positive enthalpy of the GP binding to oligochitosan, which pointed to a notable contribution of dehydration and the related rearrangement of the polysaccharide hydration shell. Energetics of the thermal phase transition of oligochitosan was investigated by DSC upon variation of the solvent dielectric constant and GP concentration. The dependences of the transition parameters on these variables were determined and used for the analysis of the oligochitosan thermoresponsivity mechanism. The binding of ibuprofen to the thermotropic oligochitosan nanogel particles and its release from them were evaluated under near-physiological conditions. Relevantly, the oligochitosan nanoparticles surpassed some reference macromolecular adsorbers by the affinity for the drug and by the delayed release kinetics.

An arginine residue involved in allosteric regulation of cystathionine ß-synthase (CBS) domain-containing pyrophosphatase.

Inorganic pyrophosphatase containing a pair of regulatory CBS domains (CBS-PPase1) is allosterically inhibited by AMP and ADP and activated by ATP and diadenosine polyphosphates. Mononucleotide binding to CBS domains and substrate binding to catalytic domains are characterized by positive co-operativity. Bioinformatics analysis pinpointed a conserved arginine residue at the interface of the regulatory and catalytic domains in bacterial CBS-PPases as potentially involved in enzyme regulation. The importance of this residue was assessed by site-directed mutagenesis using the CBS-PPase from Desulfitobacterium hafniense (dhPPase) as a model. The mutants R276A, R276K and R276E were constructed and purified, and the impact of the respective mutation on catalysis, nucleotide binding and regulation was analysed. Overall, the effects decreased in the following order R276A > R276E > R276K. The variants retained ≥50% catalytic efficiency but exhibited reduced kinetic co-operativity or even its inversion (R276A). Negative co-operativity was retained in the R276A variant in the presence of mononucleotides but was reversed by diadenosine tetraphosphate. Positive nucleotide-binding co-operativity was retained in all variants but the R276A and R276E variants exhibited a markedly reduced affinity to AMP and ADP and greater residual activity at their saturating concentrations. The R276A substitution abolished activation by ATP and diadenosine tetraphosphate, while preserving the ability to bind them. The results suggest that the H-bond formed by the Arg276 sidechain is essential for signal transduction between the regulatory and catalytic domains within one subunit and between the catalytic but not regulatory domains of different subunits.

Karyotypic differentiation of populations of the common shrew Sorex araneus L. (Mammalia) in Belarus.

The common shrews, Sorex araneus Linnaeus, 1758, inhabiting the territory of Belarus, are characterized by a significant variation in the frequency of Robertsonian (Rb) translocations. The frequency clines for translocations specific of three chromosome races: the West Dvina (gm, hk, ip, no, qr), Kiev (g/m, hi, k/o, n, p, q, r), and Bialowieza (g/r, hn, ik, m/p, o, q) have already been studied in this territory. In this communication we report new data on polymorphic populations with Rb metacentrics specific of the Neroosa race (go, hi, kr, mn, p/q) in south-eastern Belarus, analyse the distribution of karyotypes in southern and central Belarus and draw particular attention to the fixation of the acrocentric variants of chromosomes in this area. The results show that certain Rb metacentrics specific of the Neroosa, West Dvina, Kiev, and Bialowieza races (namely, go and pq; ip; ko; hn and ik, respectively) are absent in many polymorphic populations. Thus, the karyotypic differentiation of S. araneus in the studied area is determined by unequal spread of different Rb translocations and by fixation of acrocentric variants of specific chromosomes.

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. Experimental investigation of putative GroEL-like chaperonin proteins has been continued by physicochemical and functional characterization of gp246 encoded by the genome of Pseudomonas fluorescens bacteriophage OBP. Unlike the more usual double-ring architecture of chaperonins, including the EL gp146, the recombinant gp246 produced by Escherichia coli cells has been purified as a single heptameric ring. It possesses ATPase activity and does not require a co-chaperonin for its function. In vitro experiments demonstrated that gp246 is able to suppress the thermal protein inactivation and aggregation in an ATP-dependent manner, thus indicating chaperonin function. Single-particle electron microscopy analysis revealed the different conformational states of OBP chaperonin, depending on the bound nucleotide.

Cationic nanogels as Trojan carriers for disruption of endosomes.

The comparison study of interaction of linear poly(2-dimethyl amino)ethyl methacrylate and its cationic nanogels of various cross-linking with both DNA and sodium poly(styrene sulfonate) has been performed. Although all amino groups of the nanogels proved to be susceptible for protonation, their accessibility for ion pairing with the polyanions was controlled and impaired with the cross-linking. The investigation of nanogels complexes with cells in culture that was accomplished by using of calcein pH-sensitive probe revealed a successive increase in the cytoplasmic fluorescence upon the growth in the cross-linking due to calceine leakage from acidic compartments to cytosol. This regularity implies that amino groups which are buried presumably inside the nanogel are protected against the ion-pairing with polyanions of plasma membrane and hence are able to manifest buffer properties while captured into acidic endosomes, i.e. possess lyso/endosomolytic capacity. These findings suggest that network architecture makes an important contribution to proton sponge properties of weak polycations.

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. We also compared by isothermal titration calorimetry the binding affinity of HBM and the control oligolysine peptide to several natural polyanions including heparan sulfate (HS), heparin, the bacterial dextran sulfate and salmon sperm DNA, and demonstrated that HBM significantly exceeds oligolysine peptide in the affinity to HS, heparin and DNA. By contrast, oligolysine peptide bound with higher affinity to dextran sulfate. We speculate that such a difference may ensure specificity of the morphogen binding to HSPG and could be explained by steric constrains imposed by different distribution of the negative charges along a given polymeric molecule. Finally, by using EGFP-HBM recombinant protein we have visualized the natural pattern of the Noggin1 binding sites within the X. laevis gastrula and demonstrated that these sites forms a dorsal-ventral concentration gradient, with a maximum in the dorsal blastopore lip. In sum, our data provide a quantitative basis for modeling the process of Noggin1 diffusion in embryonic tissues, considering its interaction with HSPG.

Cystathionine ß-Synthase (CBS) Domain-containing Pyrophosphatase as a Target for Diadenosine Polyphosphates in Bacteria.

Among numerous proteins containing pairs of regulatory cystathionine ß-synthase (CBS) domains, family II pyrophosphatases (CBS-PPases) are unique in that they generally contain an additional DRTGG domain between the CBS domains. Adenine nucleotides bind to the CBS domains in CBS-PPases in a positively cooperative manner, resulting in enzyme inhibition (AMP or ADP) or activation (ATP). Here we show that linear P(1),P(n)-diadenosine 5'-polyphosphates (ApnAs, where n is the number of phosphate residues) bind with nanomolar affinity to DRTGG domain-containing CBS-PPases of Desulfitobacterium hafniense, Clostridium novyi, and Clostridium perfringens and increase their activity up to 30-, 5-, and 7-fold, respectively. Ap4A, Ap5A, and Ap6A bound noncooperatively and with similarly high affinities to CBS-PPases, whereas Ap3A bound in a positively cooperative manner and with lower affinity, like mononucleotides. All ApnAs abolished kinetic cooperativity (non-Michaelian behavior) of CBS-PPases. The enthalpy change and binding stoichiometry, as determined by isothermal calorimetry, were ~10 kcal/mol nucleotide and 1 mol/mol enzyme dimer for Ap4A and Ap5A but 5.5 kcal/mol and 2 mol/mol for Ap3A, AMP, ADP, and ATP, suggesting different binding modes for the two nucleotide groups. In contrast, Eggerthella lenta and Moorella thermoacetica CBS-PPases, which contain no DRTGG domain, were not affected by ApnAs and showed no enthalpy change, indicating the importance of the DTRGG domain for ApnA binding. These findings suggest that ApnAs can control CBS-PPase activity and hence affect pyrophosphate level and biosynthetic activity in bacteria.

Effect of disulfide crosslinking on thermal transitions and chaperone-like activity of human small heat shock protein HspB1.

Temperature-induced conformational changes of reduced and oxidized HspB1 crosslinked by disulfide bond between single Cys137 of neighboring monomers were analyzed by means of different techniques. Heating of reduced HspB1 was accompanied by irreversible changes of Trp fluorescence, whereas oxidized HspB1 underwent completely reversible changes of fluorescence. Increase of the temperature in the range of 20-70 °C was accompanied by self-association of both reduced and oxidized protein. Further increase of the temperature led to formation of heterogeneous mixture of large self-associated complexes of reduced HspB1 and to formation of smaller and less heterogeneous complexes of oxidized HspB1. Heat-induced changes of oligomeric state of reduced HspB1 were only partially reversible, whereas the corresponding changes of oligomeric state of oxidized HspB1 were almost completely reversible. Oxidation resulted in decrease of chaperone-like activity of HspB1. It is concluded that oxidative stress, inducing formation of disulfide bond, can affect stability and conformational mobility of human HspB1.

Expression and functional characterization of the first bacteriophage-encoded chaperonin.

Chaperonins promote protein folding in vivo and are ubiquitously found in bacteria, archaea, and eukaryotes. The first viral chaperonin GroEL ortholog, gene product 146 (gp146), whose gene was earlier identified in the genome of bacteriophage EL, has been shown to be synthesized during phage propagation in Pseudomonas aeruginosa cells. The recombinant gp146 has been expressed in Escherichia coli and characterized by different physicochemical methods for the first time. Using serum against the recombinant protein, gp146's native substrate, the phage endolysin gp188, has been immunoprecipitated from the lysate of EL-infected bacteria and identified by mass spectrometry. In vitro experiments have shown that gp146 has a protective effect against endolysin thermal inactivation and aggregation, providing evidence of its chaperonin function. The phage chaperonin has been found to have the architecture and some properties similar to those of GroEL but not to require cochaperonin for its functional activity.

A comparison of the chromosome G-banding pattern in two Sorex species, S. satunini and S. araneus (Mammalia, Insectivora).

The G-banded karyotype of Sorex satunini was compared with the karyotype of Sorex araneus. Extensive homology was revealed. The major chromosomal rearrangements involved in the evolutionary divergence of these species have been identified as centric fusions and centromeric shifts. From the known palaeontological age of Sorex satunini it is obvious that the vast chromosomal polymorphism of the Sorex araneus group originated during the middle Pleistocene.