Photophysical properties of popular fluorescent adenosine nucleotide analogs used in enzyme mechanism probing

Nucleotide Exchange Factors for Hsp70 Chaperones

The ATPase cycle of Hsp70 chaperones controls their transient association with substrates and thus governs their function in protein folding. Nucleotide exchange factors (NEFs) accelerate ADP release from Hsp70, which results in rebinding of ATP and release of the substrate, thereby regulating the lifetime of the Hsp70-substrate complex. This chapter describes several methods suitable to study NEFs of Hsp70 chaperones. On the one hand, steady-state ATPase assays provide information on how the NEF influences progression of the Hsp70 through the entire ATPase cycle. On the other hand, nucleotide release can be measured directly using labeled nucleotides, which enables identification and further characterization of NEFs.

PI(3,4,5)P3 Engagement Restricts Akt Activity to Cellular Membranes

Protein kinase B/Akt regulates cellular metabolism, survival, and proliferation in response to hormones and growth factors. Hyperactivation of Akt is frequently observed in cancer, while Akt inactivation is associated with severe diabetes. Here, we investigated the molecular and cellular mechanisms that maintain Akt activity proportional to the activating stimulus. We show that binding of phosphatidylinositol-3,4,5-trisphosphate (PIP₃) or PI(3,4)P₂ to the PH domain allosterically activates Akt by promoting high-affinity substrate binding. Conversely, dissociation from PIP₃ was rate limiting for Akt dephosphorylation, dependent on the presence of the PH domain. In cells, active Akt associated primarily with cellular membranes. In contrast, a transforming mutation that uncouples kinase activation from PIP₃ resulted in the accumulation of hyperphosphorylated, active Akt in the cytosol. Our results suggest that intramolecular allosteric and cellular mechanisms cooperate to restrict Akt activity to cellular membranes, thereby enhancing the fidelity of Akt signaling and the specificity of downstream substrate phosphorylation.

A viologen phosphorus dendritic molecule as a carrier of ATP and Mant-ATP: spectrofluorimetric and NMR studies

A viologen phosphorus dendritic molecule is able to create non-covalent interactions with model molecules of drugs belonging to the group of nucleoside analogues.

Studying complexes between PPI dendrimers and Mant-ATP

The aim of this study was to investigate the interactions between poly(propylene imine) (PPI) dendrimers and 2'-/3'-O-(N'-methylanthraniloyl)-ATP (Mant-ATP). Mant-ATP was used as a model molecule. Purine and pyrimidine nucleoside analogues are antimetabolites commonly used in therapy for cancer. Drug molecules can complex with dendrimers in two ways: therapeutic agents may be attached in dendrimer interior or bind to functional groups on the surface. Drugs attached to nanoparticles are characterized by improved solubility, pharmacokinetics and stability. Here, we have used poly(propylene imine) dendrimers of the 4th and 5th generations (PPI G4 and PPI G5) with primary amino surface groups partially modified with maltose (PPI-m) or without modification (PPI). We assessed the efficiency of complex formation in relation to dendrimer generation, pH of solution and the type of dendrimer used. A double fluorimetric titration method was used to estimate the binding constant (K b ) and the number of binding centers per molecule of the binding agent (n).

Allosteric communication between the nucleotide binding domains of caseinolytic peptidase B

ClpB is a hexameric chaperone that solubilizes and reactivates protein aggregates in cooperation with the Hsp70/DnaK chaperone system. Each of the identical protein monomers contains two nucleotide binding domains (NBD), whose ATPase activity must be coupled to exert on the substrate the mechanical work required for its reactivation. However, how communication between these sites occurs is at present poorly understood. We have studied herein the affinity of each of the NBDs for nucleotides in WT ClpB and protein variants in which one or both sites are mutated to selectively impair nucleotide binding or hydrolysis. Our data show that the affinity of NBD2 for nucleotides (K(d) = 3-7 μm) is significantly higher than that of NBD1. Interestingly, the affinity of NBD1 depends on nucleotide binding to NBD2. Binding of ATP, but not ADP, to NBD2 increases the affinity of NBD1 (the K(d) decreases from ≈160-300 to 50-60 μm) for the corresponding nucleotide. Moreover, filling of the NBD2 ring with ATP allows the cooperative binding of this nucleotide and substrates to the NBD1 ring. Data also suggest that a minimum of four subunits cooperate to bind and reactivate two different aggregated protein substrates.

A small fluorophore reporter of protein conformation and redox state

A new thiol-specific reagent introduces a small bis(methylamino)terephthalic acid fluorophore into proteins. The noninvasive probe with distinct spectroscopic properties offers many advantages for protein labeling, purification, and mechanistic work promising to serve as a powerful tool in studies of protein folding and heme redox reactions.

Fluorescence polarization analysis for revealing molecular mechanism of nucleotide-dependent phospholipid membrane binding of MinD adenosine 5'-triphosphate, adenosine triphosphatase

Membrane binding of Walker type adenosine 5'-triphosphate, adenosine triphosphatase (ATPase), MinD, is a key step in regulating the site of cell division in Escherichia coli. Two lysine residues (K11, K16) in the Walker A motif of MinD have been suggested to be essential for both membrane binding and ATPase activity, but the relationship between the membrane binding of MinD and its ATPase activity is still unclear. To reveal the role of K11 and K16 in MinD membrane interaction and ATP-binding, we compared the functionality of wild-type MinD (WT) and two MinD mutants that lack ATPase activity, where alanine was substituted for lysine at positions 11 and 16 (K11A, K16A), using liposomes and fluorescent-labeled ATP. The ATP dissociation constant (K(d)) of wild-type MinD was 4.9 µM. Unexpectedly, the K(d) values of the two lysine mutants were almost the same as that of wild type, indicating that ATP can bind to MinD mutants, even though these mutants showed no ATPase activity and membrane binding ability. Our results presumed that K11 and K16 residues might play an important role in dimmer formation of MinD, but not ATP binding step, for recruiting to membrane.

Nucleotide exchange factors for Hsp70 chaperones

The ATPase cycle of Hsp70 chaperones controls their transient association with substrate and, thus, governs their function in protein folding. Nucleotide exchange factors (NEFs) accelerate ADP release from Hsp70 which results in rebinding of ATP and release of the substrate. This chapter describes several methods suitable to study NEFs of Hsp70 chaperones. On the one hand, steady-state ATPase assays provide information on how the NEF influences progression of the Hsp70 through the entire ATPase cycle. On the other hand, nucleotide release can be measured directly using labeled nucleotides, which enables identification and further characterization of NEFs.