Interaction of an Antituberculosis Drug with a Nanoscopic Macromolecular Assembly: Temperature-Dependent Förster Resonance Energy Transfer Studies on Rifampicin in an Anionic Sodium Dodecyl Sulfate Micelle

In this contribution, we report studies on the nature of binding of a potent antituberculosis drug, Rifampicin (RF) with a model drug delivery system, sodium dodecyl sulfate (SDS) micelle. Temperature dependent dynamic light scattering (DLS), conductometry, and circular dichroism (CD) spectroscopy have been employed to study the binding interaction of the drug with the micelle. The absorption spectrum of the drug RF in the visible region has been employed to study Förster resonance energy transfer (FRET) from another fluorescent drug Hoechst 33258 (H33258), bound to the micelle. Picosecond-resolved FRET studies at room temperature confirm the simultaneous binding of the two drugs to the micelle and the distance between the donor−acceptor pair is found to be 34 Å. The temperature dependent FRET study also confirms that the location and efficiency of drug binding to the micelle changes significantly at the elevated temperature. The energy transfer efficiency of the donor H33258, as measured from time-resolved studies, decreases significantly from 76% at 20 °C to 60% at 55 °C. This reveals detachment of some amount of the drug molecules from the micelles and increased donor−acceptor distance at elevated temperatures. The estimated donor−acceptor distance increases from a value of 33 Å at 20 °C to 37 Å at 55 °C. The picosecond resolved FRET studies on a synthesized DNA bound H33258 in RF solution have been performed to explore the interaction between the two. Our studies are expected to find relevance in the exploration of a potential vehicle for the vital drug rifampicin

Aha1 regulates Hsp90's conformation and function in a stoichiometry-dependent way

The heat shock protein 90 (Hsp90) is a molecular chaperone, which plays a key role in eukaryotic protein homeostasis. Co-chaperones assist Hsp90 in client maturation and in regulating essential cellular processes such as cell survival, signal transduction, gene regulation, hormone signaling and neurodegeneration. Aha1 (activator of Hsp90 ATPase) is a unique co-chaperone known to stimulate the ATP hydrolysis of Hsp90, but the mechanism of their interaction is still unclear. In this report, we show that one or two Aha1 can bind to one Hsp90 dimer and that the binding stoichiometry affects Hsp90's conformation, kinetics, ATPase activity and stability. In particular, a coordination of two Aha1 molecules can be seen in stimulating the ATPase activity of Hsp90 and the unfolding of the middle domain, while the conformational equilibrium and kinetics are hardly affected by the stoichiometry of bound Aha1. Altogether, we show a regulation mechanism through the stoichiometry of Aha1 going far beyond a regulation of Hsp90's conformation.</p

Simultaneous binding of anti-tuberculosis and anti-thrombosis drugs to a human transporter protein: A FRET study

Although rifampicin (Rf) is one of the most effective antibiotics against infection caused by Mycobacterium tuberculosis, interaction of the drug with universal carrier protein in human blood plasma is not fully understood. Reduction of medicinal efficacy of other drugs, including anti-thrombosis drug warfarin (Wf), to the patients on Rf therapy also needs molecular understanding. In the present work we have studied interaction of Rf with one of the model carrier protein (human serum albumin). By using circular dichroism (CD) spectroscopy we have characterized the change in the secondary structure of the protein. The consequence of the simultaneous binding of the two drugs, Rf and Wf, on the structure of the protein has also been explored. Picosecond resolved Förster resonance energy transfer (FRET) from Wf to Rf explores possible binding sites of the anti-tuberculosis drug on the protein. In this report, we have discussed the potential problem of using the single tryptophan of the protein (Trp 214) as energy donor in FRET experiment for the characterization of the binding site of the drug Rf on the protein

Human Copper Chaperone Atox1 Translocates to the Nucleus but does not Bind DNA In Vitro.

After Ctr1-mediated cell uptake, copper (Cu) is transported by the cytoplasmic Cu chaperone Atox1 to P1B type ATPases ATP7A and ATP7B in the Golgi network, for incorporation into Cudependent enzymes. Atox1 is a small 68-residue protein that binds Cu in a conserved CXXC motif; it delivers Cu to target domains in ATP7A/B via direct protein-protein interactions. Specific transcription factors regulating expression of the human Cu transport proteins have not been reported although Atox1 was recently suggested to have dual functionality such that it, in addition to its cytoplasmic chaperone function, acts as a transcription factor in the nucleus. To examine this hypothesis, here we investigated the localization of Atox1 in HeLa cells using fluorescence imaging in combination with in vitro binding experiments to fluorescently labeled DNA duplexes harboring the proposed promotor sequence. We found that whereas Atox1 is present in the nucleus in HeLa cells, it does not bind to DNA in vitro. It appears that Atox1 mediates transcriptional regulation via additional (unknown) proteins

Ultrafast electron transfer in the recognition of different DNA sequences by a DNA-binding protein with different dynamical conformations

<div><p>Ultrafast electron transfer (ET) phenomenon in protein and protein–DNA complex is very much crucial and often leads to the regulation of various kinds of redox reactions in biological system. Although, the conformation of the protein in protein–DNA complex is concluded to play the key role in the ET process, till date very little evidences exist in the literature. λ-repressor–operator DNA interaction, particularly O_R1 and O_R2, is a key component of the λ-genetic switch and is a model system for understanding the chemical principles of the conformation-dependent ET reaction, governed by differential protein dynamics upon binding with different DNA target sequences. Here, we have explored the photoinduced electron transfer from the tryptophan moieties of the protein λ-repressor to two operators DNA of different sequences (O_R1 and O_R2) using picosecond-resolved fluorescence spectroscopy. The enhanced flexibility and different conformation of the C-terminal domain of the repressor upon complexation with O_R1 DNA compared to O_R2 DNA are found to have pronounced effect on the rate of ET. We have also observed the ET phenomenon from a dansyl chromophore, bound to the lysine residue, distal from the DNA-binding domain of the protein to the operator DNA with a specific excitation at 299 nm wavelength. The altered ET dynamics as a consequence of differential protein conformation upon specific DNA sequence recognition may have tremendous biological implications.</p> </div

Human Copper Chaperone Atox1 Translocates to the Nucleus but does not Bind DNA In Vitro.

After Ctr1-mediated cell uptake, copper (Cu) is transported by the cytoplasmic Cu chaperone Atox1 to P1B type ATPases ATP7A and ATP7B in the Golgi network, for incorporation into Cudependent enzymes. Atox1 is a small 68-residue protein that binds Cu in a conserved CXXC motif; it delivers Cu to target domains in ATP7A/B via direct protein-protein interactions. Specific transcription factors regulating expression of the human Cu transport proteins have not been reported although Atox1 was recently suggested to have dual functionality such that it, in addition to its cytoplasmic chaperone function, acts as a transcription factor in the nucleus. To examine this hypothesis, here we investigated the localization of Atox1 in HeLa cells using fluorescence imaging in combination with in vitro binding experiments to fluorescently labeled DNA duplexes harboring the proposed promotor sequence. We found that whereas Atox1 is present in the nucleus in HeLa cells, it does not bind to DNA in vitro. It appears that Atox1 mediates transcriptional regulation via additional (unknown) proteins

Specific DNA sequences allosterically enhance protein–protein interaction in a transcription factor through modulation of protein dynamics: implications for specificity of gene regulation

Most genes are regulated by multiple transcription factors, often assembling into multi-protein complexes in the gene regulatory region. Understanding of the molecular origin of specificity of gene regulatory complex formation in the context of the whole genome is currently inadequate. A phage transcription factor λ-CI forms repressive multi-protein complexes by binding to multiple binding sites in the genome to regulate the lifecycle of the phage. The protein–protein interaction between two DNA-bound λ-CI molecules is stronger when they are bound to the correct pair of binding sites, suggesting allosteric transmission of recognition of correct DNA sequences to the protein–protein interaction interface. Exploration of conformation and dynamics by time-resolved fluorescence anisotropy decay and molecular dynamics suggests a change in protein dynamics to be a crucial factor in mediating allostery. A lattice-based model suggests that DNA-sequence induced allosteric effects could be crucial underlying factors in differentially stabilizing the correct site-specific gene regulatory complexes. We conclude that transcription factors have evolved multiple mechanisms to augment the specificity of DNA–protein interactions in order to achieve an extraordinarily high degree of spatial and temporal specificities of gene regulatory complexes, and DNA-sequence induced allostery plays an important role in the formation of sequence-specific gene regulatory complexes

Recognition of Different DNA Sequences by a DNA-Binding Protein Alters Protein Dynamics Differentially

k-Repressor–operator sites interaction, particularly OR1 and OR2, is a key component of the k-genetic switch. FRET from the dansyl bound to the C-terminal domain of the protein, to the intercalated EtBr in the operator DNA indicates that the structure of the protein is more compact in the OR2 complex than in the OR1 complex. Fluorescence anisotropy reveals enhanced flexibility of the C-terminal domain of the repressor at fast timescales after complex formation with OR1. In contrast, OR2 bound repressor shows no significant enhancement of protein dynamics at these timescales. These differences are shown to be important for correct protein–protein interactions. Altered protein dynamics upon specific DNA sequence recognition may play important roles in assembly of regulatory proteins at the correct positions