Ishita Mukerji

HU Binding to DNA: Evidence for Multiple Complex Formation and DNA Bending

HU, a nonspecific histone-like DNA binding protein, participates in a number of genomic events as an accessory protein and forms multiple complexes with DNA. The HU-DNA binding interaction was characterized by fluorescence, generated with the guanosine analogue 3-methyl-8-(2-deoxy-beta-D-ribofuranosyl)isoxanthopterin (3-MI) directly incorporated into DNA duplexes. The stoichiometry and equilibrium binding constants of complexes formed between HU and 13 and 34 bp DNA duplexes were determined using fluorescence anisotropy and analytical ultracentrifugation. These measurements reveal that three HU molecules bind to the 34 bp duplexes, while two HU molecules bind to the 13 bp duplex. The data are well described by an independent binding site model, and the association constants for the first binding event for both duplexes are similar (approximately 1 x 10(6) M(-1)), indicating that HU binding affinity is independent of duplex length. Further analysis of the binding curves in terms of a nonspecific binding model is indicative that HU binding to DNA exhibits little to no cooperativity. The fluorescence intensity also increases upon HU binding, consistent with decreased base stacking and increased solvent exposure of the 3-MI fluorescence probe. These results are suggestive of a local bending or unwinding of the DNA. On the basis of these results we propose a model in which bending of DNA accompanies HU binding. Up to five complex bands are observed in gel mobility shift assays of HU binding to the 34 bp duplexes. We suggest that protein-induced bending of the DNA leads to the observation of complexes in the gel, which have the same molecular weight but different relative mobilities.

Formation of amyloid fibrils in vitro from partially unfolded intermediates of human γC-crystallin.

PURPOSE Mature-onset cataract results from the formation of light-scattering aggregates of lens crystallins. Although oxidative or mutational damage may be a prerequisite, little is known of the initiation or nucleation of these aggregated states. In mice carrying mutations in gamma-crystallin genes, a truncated form of gamma-crystallin formed intranuclear filamentous inclusions within lens fiber cells. Previous studies have shown that bovine crystallins and human gammaD-crystallin form amyloid fibrils under denaturing conditions in vitro. The amyloid fibril formation of human gammaC-crystallin (HgammaC-Crys) induced by low pH, together with characterization of a partially unfolded intermediate in the process were investigated. METHODS HgammaC-Crys was expressed and purified from Escherichia coli. Partially unfolded intermediates were detected by tryptophan fluorescence spectroscopy and UV resonance Raman spectroscopy. The aggregation into amyloid fibrils was monitored by solution turbidity and fluorescence assay. The morphology of aggregates was characterized using transmission electron microscopy (TEM). Secondary structure of the peptides in their fibrillar state was characterized using Fourier transform infrared spectroscopy (FTIR). RESULTS The structure of HgammaC-Crys was perturbed at low pH. Partially unfolded intermediates were detected when solution pH was lowered to pH 3. At pH 3, HgammaC-Crys aggregated into amyloid fibrils. The kinetics and extent of the reaction was dependent on protein concentration, pH, and temperature. TEM images of aggregates revealed aggregation stages from short to long fibrils and from long fibrils to light-scattering fibril networks. FTIR spectroscopy confirmed the cross-beta character of the secondary structure of these fibrils. CONCLUSIONS HgammaC-Crys formed amyloid fibrils on incubation at low pH via a partially unfolded intermediate. This process could contribute to the early stages of the formation of light-scattering species in the eye lens.

Energy transfer dynamics of an isolated light harvesting complex of Photosystem I from spinach: time-resolved fluorescence measurements at 295 K and 77 K

Abstract Time-resolved fluorescence relaxation measurements have been performed at 295 K and 77 K on a preparation of the light-harvesting complex of Photosystem I (LHCI) containing about 100 chlorophylls (Chl) per complex. At both temperatures five exponential components were required to fit the data. The resulting determined lifetimes are 30 ps, 200 ps, 1.0 ns, 3.3 ns and 6.5 ns. Previous steady-state fluorescence measurements demonstrated that the emission at 735 nm increases dramatically upon cooling to 77 K. Time-resolved fluorescence measurements performed at 77 K reveal the presence of two risetimes for emission between 700 and 750 nm. These results are consistent with an efficient trap for electronic excitation existing at longer wavelengths than the absorption maximum of P700, the reaction center of Photosystem I (PS I). Excitation of Chl b results in a relative amplitude enhancement of decay components emitting between 720 and 750 nm. This confirms that Chl b is specifically associated with long wavelength emitters in Photosystem I.

Mapping of the Signal Peptide-Binding Domain of Escherichia coli SecA Using Förster Resonance Energy Transfer

Identification of the signal peptide-binding domain within SecA ATPase is an important goal for understanding the molecular basis of SecA preprotein recognition as well as elucidating the chemo-mechanical cycle of this nanomotor during protein translocation. In this study, Forster resonance energy transfer methodology was employed to map the location of the SecA signal peptide-binding domain using a collection of functional monocysteine SecA mutants and alkaline phosphatase signal peptides labeled with appropriate donor-acceptor fluorophores. Fluorescence anisotropy measurements yielded an equilibrium binding constant of 1.4 or 10.7 muM for the alkaline phosphatase signal peptide labeled at residue 22 or 2, respectively, with SecA, and a binding stoichiometry of one signal peptide bound per SecA monomer. Binding affinity measurements performed with a monomer-biased mutant indicate that the signal peptide binds equally well to SecA monomer or dimer. Distance measurements determined for 13 SecA mutants show that the SecA signal peptide-binding domain encompasses a portion of the preprotein cross-linking domain but also includes regions of nucleotide-binding domain 1 and particularly the helical scaffold domain. The identified region lies at a multidomain interface within the heart of SecA, surrounded by and potentially responsive to domains important for binding nucleotide, mature portions of the preprotein, and the SecYEG channel. Our FRET-mapped binding domain, in contrast to the domain identified by NMR spectroscopy, includes the two-helix finger that has been shown to interact with the preprotein during translocation and lies at the entrance to the protein-conducting channel in the recently determined SecA-SecYEG structure.

Spectroscopic and Molecular Dynamics Evidence for a Sequential Mechanism for the A-to-B Transition in DNA ☆

The A-to-B form transition has been examined in three DNA duplexes, d(CGCGAATTCGCG)(2), d(CGCGAATTGCGC), and d(CGCAAATTTCGC), using circular dichroism spectroscopy, ultraviolet resonance Raman (UVRR) spectroscopy, and molecular dynamics (MD) simulation. Circular dichroism spectra confirm that these molecules adopt the A form under conditions of reduced water activity. UVRR results, obtained under similar conditions, suggest that the transition involves a series of intermediate forms between A and B. Cooperative and distinct transitions were observed for the bases and the sugars. Independent MD simulations on d(CGCGAATTCGCG)(2) show a spontaneous change from the A to B form in aqueous solution and describe a kinetic model that agrees well with UVRR results. Based on these observations, we predict that the mechanism of the transition involves a series of A/B hybrid forms and is sequential in nature, similar to previous crystallographic studies of derivatized duplexes. A simulation in which waters were restrained in the major groove of B DNA shows a rapid, spontaneous change from B to A at reduced water activity. These results indicate that a quasiergodic sampling of the solvent distribution may be a problem in going from B to A at reduced water activity in the course of an MD simulation.

Fluoride substitution in the Mn cluster from Photosystem II: EPR and X-ray absorption spectroscopy studies

Abstract X-band electron paramagnetic resonance (EPR) and Mn K-edge X-ray fluorescence absorption were used to study the effects of fluoride inhibition on the Mn complex in Photosystem II. The tetrameric Mn complex, responsible for the light-induced oxidation of H2O to form molecular oxygen, is influenced by treatments in which the naturally occurring chloride salts are removed or replaced. Inhibition of the complex by fluoride is examined by parallel enzyme activity and EPR studies. It is found that, as a function of increasing fluoride concentration, the declining enzymatic activity is paralleled initially by an exchange of the S = 1 2 ‘multiline’ EPR signal for the S > 1 2 , ‘g = 4’ EPR signal in illuminated samples. High concentrations of fluoride induce a broad (≈ 200 G), featureless radical signal in samples which have not been illuminated; subsequent illumination of these samples also generates the g = 4 EPR signal. X-ray absorption studies (XAS) of fluoride-inhibited samples show subtle alterations of the conformation of the Mn complex that are consistent with the presence of two dissimilar pairs of Mn atoms. The halide studies are discussed in terms of structural models for the Mn complex.

Integration Host Factor (IHF) Dictates the Structure of Polyamine-DNA Condensates: Implications for the Role of IHF in the Compaction of Bacterial Chromatin

Integration host factor (IHF), a nucleoid-associated protein in bacterial cells, is implicated in a number of chromosomal functions including DNA compaction. IHF binds to all duplex DNA with micromolar affinity and at sequence-specific sites with much higher affinity. IHF is known to induce sharp bends in the helical axis of DNA in both modes of binding, but the role of IHF in controlling DNA condensation within bacterial cells has remained undetermined. Here we demonstrate that IHF influences the morphology of DNA condensed by polyamines in vitro. In the absence of IHF, spermidine and spermine condense DNA primarily into toroidal structures, whereas in the presence of IHF, polyamines condense DNA primarily into rodlike structures. Computer simulations of DNA condensation in the absence and presence of IHF binding lend support to our model in which DNA bending proteins, such as IHF and HU, promote the condensation of DNA into rodlike structures by providing the free energy necessary to bend DNA at the ends of linear bundles of condensed DNA. We propose that a common function of IHF and HU in bacterial cells is to facilitate DNA organization in the nucleoid by the introduction of sharp bends in chromosomal DNA.

Analysis of High-Affinity Binding of Protein Kinase R to Double-Stranded RNA

Protein kinase R (PKR) is an interferon-induced kinase that plays a pivotal role in the innate immunity response to viral infection. PKR is activated upon binding to double-stranded RNA (dsRNA). Our previous analysis of binding of PKR to dsRNAs ranging from 20 to 40 bp supports a dimerization model for activation in which 30 bp represents the minimal length required to bind two PKR monomers and activate PKR via autophosphorylation. These studies were complicated by the formation of protein-RNA aggregates, particularly at low salt concentrations using longer dsRNAs. Here, we have taken advantage of the enhanced sensitivity afforded using fluorescence-detected analytical ultracentrifugation to reduce the RNA concentrations from micromolar to nanomolar. Under these conditions, we are able to characterize high-affinity binding of PKR to longer dsRNAs in 75 mM NaCl. The PKR binding stoichiometries are increased at lower salt concentrations but remain lower than those previously obtained for the dsRNA binding domain. The dependence of the limiting PKR binding stoichiometries on dsRNA length does not conform to standard models for nonspecific binding and suggests that binding to longer sequences occurs via a different binding mode with a larger site size. Although dimerization plays a key role in the PKR activation mechanism, the ability of shorter dsRNAs to bind two PKR monomers is not sufficient to induce autophosphorylation. We propose that activation of PKR by longer RNAs is correlated with an alternative binding mode in which both of the dsRNA binding motifs contact the RNA, inducing PKR to dimerize via a direct interaction of the kinase domains.

UV resonance Raman spectroscopy and hydrogen bonding of the proline peptide bond

Abstract UV resonance Raman (UVRR) spectroscopy with 210 nm laser excitation enhances the ≈ 1460 cm −1 CN stretching vibration of the X-Pro peptide bond, which is designated as amide IIp. Studies of dipeptides reveal that the amide IIp frequency is insensitive to proline cis/trans isomerization and to pyrrolidine ring puckering, but is sensitive to hydrogen bonding of the X-Pro carbonyl group. A 9 cm −1 downshift in the amide IIp frequency of Gly-Pro when the pH is raised from 6.5 to 10.5 is shown to result from the loss of an intramolecular hydrogen bond from the terminal amino group, since this shift is absent when the N-terminus is blocked by a t-BOC group. Studies of solvent hydrogen bonding to N -acetylpyrrolidine (NAP), a convenient model of the X-Pro bond, showed a linear increase with solvent acceptor number for amide IIp and a concomitant decrease in the CO stretching vibration (amide Ip). The amide IIp band profile is reported for native and unfolded states of cytochrome c , myoglobin and lysozyme. Comparison with X-ray crystallographic coordinates indicates that the amide IIp frequency is ≈ 1460 cm −1 for strongly hydrogen bonded X-Pro carbonyl groups, but decreases to ≈ 1445 cm −1 in the absence of hydrogen bonding. The observed frequency is ≈ 1460 cm −1 for the unfolded proteins, reflecting strong hydrogen bonding from solvent molecules.

HU Binding to a DNA Four-Way Junction Probed by Förster Resonance Energy Transfer

The Escherichia coli protein HU is a non-sequence-specific DNA-binding protein that interacts with DNA primarily through electrostatic interactions. In addition to nonspecific binding to linear DNA, HU has been shown to bind with nanomolar affinity to discontinuous DNA substrates, such as repair and recombination intermediates. This work specifically examines the HU-four-way junction (4WJ) interaction using fluorescence spectroscopic methods. The conformation of the junction in the presence of different counterions was investigated by Förster resonance energy transfer (FRET) measurements, which revealed an ion-type conformational dependence, where Na(+) yields the most stacked conformation followed by K(+) and Mg(2+). HU binding induces a greater degree of stacking in the Na(+)-stabilized and Mg(2+)-stabilized junctions but not the K(+)-stabilized junction, which is attributed to differences in the size of the ionic radii and potential differences in ion binding sites. Interestingly, junction conformation modulates binding affinity, where HU exhibits the lowest affinity for the Mg(2+)-stabilized form (24 μM(-1)), which is the least stacked conformation. Protein binding to a mixed population of open and stacked forms of the junction leads to nearly complete formation of a protein-stabilized stacked-X junction. These results strongly support a model in which HU binds to and stabilizes the stacked-X conformation.