Alexander A. Makarov

The effect of net charge on the solubility, activity, and stability of ribonuclease Sa

The net charge and isoelectric pH (pI) of a protein depend on the content of ionizable groups and their pK values. Ribonuclease Sa (RNase Sa) is an acidic protein with a pI = 3.5 that contains no Lys residues. By replacing Asp and Glu residues on the surface of RNase Sa with Lys residues, we have created a 3K variant (D1K, D17K, E41K) with a pI = 6.4 and a 5K variant (3K + D25K, E74K) with a pI = 10.2. We show that pI values estimated using pK values based on model compound data can be in error by >1 pH unit, and suggest how the estimation can be improved. For RNase Sa and the 3K and 5K variants, the solubility, activity, and stability have been measured as a function of pH. We find that the pH of minimum solubility varies with the pI of the protein, but that the pH of maximum activity and the pH of maximum stability do not.

Cytotoxic ribonucleases: molecular weapons and their targets

Many ribonucleases (RNases) are highly cytotoxic. In some cases, they attack selectively malignant cells, triggering apoptotic response, and therefore are considered as alternative chemotherapeutic drugs. Factors that determine the cytotoxicity of RNases, primarily of those of microbial origin, are reviewed here. These factors include catalytic activity, ability to escape natural inhibitors, stability, and efficiency of internalization. The latter is, in turn, determined by positive charge on the molecule and interaction with cell membrane. Cellular targets and molecular determinants of RNases decisive for their cytotoxic action are characterized.

Binding of ATP to Heat Shock Protein 90 EVIDENCE FOR AN ATP-BINDING SITE IN THE C-TERMINAL DOMAIN

The presence of a nucleotide binding site on hsp90 was very controversial until x-ray structure of the hsp90 N-terminal domain, showing a nonconventional nucleotide binding site, appeared. A recent study suggested that the hsp90 C-terminal domain also binds ATP (Marcu, M. G., Chadli, A., Bouhouche, I., Catelli, M. G., and Neckers, L. M. (2000) J. Biol. Chem. 275, 37181–37186). In this paper, the interactions of ATP with native hsp90 and its recombinant N-terminal (positions 1–221) and C-terminal (positions 446–728) domains were studied by isothermal titration calorimetry, scanning differential calorimetry, and fluorescence spectroscopy. Results clearly demonstrate that hsp90 possesses a second ATP-binding site located on the C-terminal part of the protein. The association constant between this domain of hsp90 and ATP-Mg and a comparison with the binding constant on the full-length protein are reported for the first time. Secondary structure prediction revealed motifs compatible with a Rossmann fold in the C-terminal part of hsp90. It is proposed that this potential Rossmann fold may constitute the C-terminal ATP-binding site. This work also suggests allosteric interaction between N- and C-terminal domains of hsp90.

Why 3‐D? Gel‐based microarrays in proteomics

Gel‐based microarrays (biochips) consisting of nanoliter and sub‐nanoliter gel drops on hydrophobic substrate are a versatile technology platform for immobilization of proteins and other biopolymers. Biochips provide a highly hydrophilic environment, which stabilizes immobilized molecules and facilitates their interactions with analytes. The probes are immobilized simultaneously with gel polymerization, evenly distributed throughout individual elements, and are easily accessible because of large pores. Each element is an isolated nanotube. Applications of biochips in the studies of protein interactions with other proteins, nucleic acids, and glycans are described. In particular, biochips are compatible with MALDI‐MS. Biochip‐based assay of prostate‐specific antigen became the first protein microarray approved for clinical use by a national regulatory agency. In this review, 3‐D immobilization is compared with mainstream technologies based on surface immobilization.

S-glutathionylation of the Na,K-ATPase catalytic α subunit is a determinant of the enzyme redox-sensitivity

Background: Na,K-ATPase activity is extremely sensitive to changes in the redox state. Results: Binding of glutathione to the regulatory cysteine residues of the catalytic subunit completely inhibits the Na,K-ATPase by blocking the ATP-binding site. Conclusion: S-Glutathionylation of the catalytic subunit is revealed as a mechanism controlling the Na,K-ATPase function. Significance: Regulatory S-glutathionylation adjusts Na,K-ATPase activity to the changes in intracellular redox state and ATP levels. Na,K-ATPase is highly sensitive to changes in the redox state, and yet the mechanisms of its redox sensitivity remain unclear. We have explored the possible involvement of S-glutathionylation of the catalytic α subunit in redox-induced responses. For the first time, the presence of S-glutathionylated cysteine residues was shown in the α subunit in duck salt glands, rabbit kidneys, and rat myocardium. Exposure of the Na,K-ATPase to oxidized glutathione (GSSG) resulted in an increase in the number of S-glutathionylated cysteine residues. Increase in S-glutathionylation was associated with dose- and time-dependent suppression of the enzyme function up to its complete inhibition. The enzyme inhibition concurred with S-glutathionylation of the Cys-454, -458, -459, and -244. Upon binding of glutathione to these cysteines, the enzyme was unable to interact with adenine nucleotides. Inhibition of the Na,K-ATPase by GSSG did not occur in the presence of ATP at concentrations above 0.5 mm. Deglutathionylation of the α subunit catalyzed by glutaredoxin or dithiothreitol resulted in restoration of the Na,K-ATPase activity. Oxidation of regulatory cysteines made them inaccessible for glutathionylation but had no profound effect on the enzyme activity. Regulatory S-glutathionylation of the α subunit was induced in rat myocardium in response to hypoxia and was associated with oxidative stress and ATP depletion. S-Glutathionylation was followed by suppression of the Na,K-ATPase activity. The rat α2 isoform was more sensitive to GSSG than the α1 isoform. Our findings imply that regulatory S-glutathionylation of the catalytic subunit plays a key role in the redox-induced regulation of Na,K-ATPase activity.

Binase and other microbial RNases as potential anticancer agents

Some RNases possess preferential cytotoxicity against malignant cells. The best known of these RNases, onconase, was isolated from frog oocytes and is in clinical trials as anticancer therapy. Here we propose an alternative platform for anticancer therapy based on T1 RNases of microbial origin, in particular binase from Bacillus intermedius and RNase Sa from Streptomyces aureofaciens. We discuss their advantages and the most promising directions of research for their potential clinical applications.

Termination of translation in eukaryotes is mediated by the quaternary eRF1•eRF3•GTP•Mg2+ complex. The biological roles of eRF3 and prokaryotic RF3 are profoundly distinct

GTP hydrolysis catalyzed in the ribosome by a complex of two polypeptide release factors, eRF1 and eRF3, is required for fast and efficient termination of translation in eukaryotes. Here, isothermal titration calorimetry is used for the quantitative thermodynamic characterization of eRF3 interactions with guanine nucleotides, eRF1 and Mg2+. We show that (i) eRF3 binds GDP (Kd = 1.9 μM) and this interaction depends only minimally on the Mg2+ concentration; (ii) GTP binds to eRF3 (Kd = 0.5 μM) only in the presence of eRF1 and this interaction depends on the Mg2+ concentration; (iii) GTP displaces GDP from the eRF1•eRF3•GDP complex, and vice versa; (iv) eRF3 in the GDP-bound form improves its ability to bind eRF1; (v) the eRF1•eRF3 complex binds GDP as efficiently as free eRF3; (vi) the eRF1•eRF3 complex is efficiently formed in the absence of GDP/GTP but requires the presence of the C-terminus of eRF1 for complex formation. Our results show that eRF1 mediates GDP/GTP displacement on eRF3. We suggest that after formation of eRF1•eRF3•GTP•Mg2+, this quaternary complex binds to the ribosomal pretermination complex containing P-site-bound peptidyl-tRNA and the A-site-bound stop codon. The guanine nucleotide binding properties of eRF3 and of the eRF3•eRF1 complex profoundly differ from those of prokaryotic RF3.

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process

A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange.

Isomerization of the Asp7 Residue Results in Zinc-Induced Oligomerization of Alzheimer’s Disease Amyloid β(1–16) Peptide

Alzheimer’s disease (AD)—a fatal neurodegenerative disorder that primarily affects the elderly—is pathophysiologically characterized by the extracellular deposition of a 40/42-aminoacid-long protein, referred to as amyloid-b peptide (Ab), in the brains of AD victims. Although the molecular mechanism of AD onset is unknown, the transformation of Ab from its native monomer conformation via soluble dimers and higher oligomers into insoluble fibrillar b-sheet aggregates, which finally accumulate into the amyloid plaques, is believed to be a key event in AD pathogenesis. One plausible hypothesis suggests that the amyloid neuropathology of AD depends on zinc ions released during neurotransmission, and so it is assumed that binding of zinc to Ab might play an important role in initiating pathogenic amyloid deposition, as well as some additional still unidentified proteinaceous factors. The Ab molecules isolated from AD brain lesions have numerous endogenous post-translational modifications (PTMs), which should profoundly affect both the Ab conformation and its oligomeric state and make up a pool of potential pathogenic agents in AD. The most abundant PTM of Ab is isomerization of the Asp7 residue; this results in the formation of an lisoAsp7 isoform (isoaspartate). This nonenzymatic modification occurs spontaneously in polypeptides through an intramolecular rearrangement of aspartate or asparagine residues and is generally regarded as a degradation reaction that occurs in vivo during tissue ageing. In the case of isomerized Ab (isoAb) it is still unclear whether the isoaspartyl residues are the cause or the result of the pathological accumulation of Ab. Nevertheless, recent in vitro experimental evidence indicates that isoAb might potentially be involved in the onset of AD. To investigate the role of the Asp7 isomerization in zinc-induced oligomerization of Ab we have studied the thermodynamics of zinc binding and the oligomeric states of two synthetic model peptides that correspond to region 1–16 in Ab and in isoAb : Ab16 and isoAb16, respectively. Earlier, this region was identified as the zinc-binding domain of Ab, which binds Zn with 1:1 stoichiometry and a 6 mm dissociation constant. Both Ab16 and its complex with Zn 2+ were found to be monomeric under physiological conditions for at least six months over a wide concentration range, and so were used as monomer reference standards throughout this work. The isoAb16 was also shown to possess zinc-binding ability; [11] however, the properties of the Zn–isoAb16 complex have not been studied previously. To compare Zn binding to Ab16 and to isoAb16 (in 50 mm Tris buffer at pH 7.3), isothermal titration calorimetry (ITC) was used. The thermodynamic data demonstrate that Ab16 binds one zinc ion with an association constant of 1.7ACHTUNGTRENNUNG( 0.4)A10m 1 (Figure 1), which corresponds to previously published da ACHTUNGTRENNUNGta.

DNA microarrays in the clinic: infectious diseases.

We argue that the most-promising area of clinical application of microarrays in the foreseeable future is the diagnostics and monitoring of infectious diseases. Microarrays for the detection and characterization of human pathogens have already found their way into clinical practice in some countries. After discussing the persistent, yet often underestimated, importance of infectious diseases for public health, we consider the technologies that are best suited for the detection and clinical investigation of pathogens. Clinical application of microarray technologies for the detection of mycobacteria, Bacillus anthracis, HIV, hepatitis and influenza viruses, and other major pathogens, as well as the analysis of their drug-resistance patterns, illustrate our main thesis.