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Human telomeric repeat binding factor 2 (hTRF2) is a protein that plays an important role in capping human telomeres to protect them from DNA damage repair systems. The ineffectiveness of hTRF2 may be linked to aging and cancer. We report the use of PLIMSTEX (protein-ligand interactions by mass spectrometry, titration, and H/D exchange) and selective acetylation of lysine residues to study the interaction of the DNA-binding domain and double-stranded telomeric DNA (repeats of TTAGGG). By increasing the resolution of PLIMSTEX to the peptide level, we localized the changes in deuterium uptake of hTRF2 as a function of varying amounts of a model oligodeoxynucleotide. From these experiments, we determined the affinity constant for binding to DNA, which is within a factor of 3 of the previously reported value. Amide H/D exchange revealed portions of the protein that have contacts with the phosphate backbone of DNA, whereas acetylation disclosed the decrease in solvent accessibility of regions containing Lys 447 and 488, which must be involved in interactions with the DNA major and minor grooves. These complementary approaches of amide H/D exchange and selective side chain modification can be employed effectively to pinpoint and quantify protein-ligand, in particular protein-DNA, interactions.

It has been suggested that the hexasome, in which one of the H2A/H2B dimers is depleted from the canonical nucleosome core particle (NCP), is an essential intermediate during NCP assembly and disassembly, but little structural evidence of this exists. In this study, reconstituted products in a conventional NCP preparation were analyzed by native electrospray ionization mass spectrometry, and it was found that the hexasome, which migrated in a manner almost identical to that of the octasome NCP in native polyacrylamide gel electrophoresis, was produced simultaneously with the octasome NCP. This result might contribute to understanding the assembly and disassembly mechanism of NCPs.

Cytochrome bo is a four-subunit quinol oxidase in the aerobic respiratory chain of Escherichia coli and functions as a redox-coupled proton pump. Subunit I binds all the redox metal centers, low-spin heme b, high-spin heme o, and CuB, whose axial ligands have been identified to be six invariant histidines. This work explored the possible roles of the aromatic amino acid residues conserved in the putative transmembrane helices (or at the boundary of the membrane) of subunit I. Sixteen aromatic amino acid residues were individually substituted by Leu, except for Tyr61 and Trp282 by Phe and Phe415 by Trp. Leu substitutions of Trp280 and Tyr288 in helix VI, Trp331 in loop VII-VIII, and Phe348 in helix VIII reduced the catalytic activity, whereas all other mutations did not affect the in vivo activity. Spectroscopic analyses of the purified mutant enzymes revealed that the defects were attributable to perturbations of the binuclear center. On the basis of these findings and recent crystallographic studies on cytochrome c oxidases, we discuss the possible roles of the conserved aromatic amino acid residues in subunit I of the heme-copper terminal oxidases.

The DNA-binding domain of the c-myb protooncogene product consists of three homologous tandem repeats of 51-52 amino acids (denoted as R1, R2, and R3 from the N-terminal side). In order to analyze conformational and thermodynamic characteristics of the homologous repeats, we have examined the DNA-binding domain by circular dichroism (CD) and differential scanning calorimetry (DSC). The CD spectra for the three individual repeats are significantly different in the fine profiles, indicating subtle differences in their conformations. The melting analyses for the fragments show that the thermal stability of each fragment is different from one another, with the following order of stability: R1(Tm = 61 degrees C) approximately greater than R3(57 degrees C) >> R2(43 degrees C), where R2 is much less stable than the other repeats. The denaturing process for the whole DNA-binding domain, measured by DSC, is characterized by a very broad transition ranging from 30 to 80 degrees C. The denaturation curve can be fit well by a three-state transition with one intermediate state. The transition temperature for the native-to-intermediate transition coincides with the melting temperature of R2, indicating that the intermediate state corresponds to the unfolding of unstable R2. The CD spectrum of the whole domain is almost identical to the sum of the individual spectra. Thus, these results suggest that the individual repeats in the whole DNA-binding domain behave independently in terms of conformation and stability. The addition of DNA to the DNA-binding fragment drastically changed the melting profile, in which the broad transition curve was replaced by a sharp peak at 58 degrees C.(ABSTRACT TRUNCATED AT 250 WORDS)

We have investigated the internal motions of DNA in a nucleosome core particle and chromatin by measuring the nanosecond fluorescence depolarization of intercalated ethidium. Assuming that the observed anisotrophy decay originates from the torsional motion of DNA, we have analyzed the dynamics of DNA in a nucleosome core particle and in chromatin in detail. The results suggest that DNA in a nucleosome core particle has a torsional rigidity similar to that of DNA in solution and that even at the point of the ionic bonds between DNA and a histone octamer the torsional motion of DNA is not completely inhibited. On the other hand, the dynamics of linker DNA in chromatin were found to reflect the overall structural state of the chromatin: the motion of linker DNA was suppressed as the structure of chromatin turned from an extended state to a condensed one. This indicates that, in solenoidal chromatin, nucleosome movements in chromatin are largely suppressed. Furthermore, the result may suggest that the torsional rigidity of linker DNA is increased as it is forced to bend in solenoidal chromatin.

Internal motion of the DNA in chicken erythrocyte chromatin fibers was studied by measurement of the fluorescence anisotropy decay of ethidium intercalated in the linker region. A comparison of the decay curves of the dye in chicken erythrocyte chromatin with those of calf thymus chromatin [Ashikawa, I., Kinosita, K., Jr., Ikegami, A., Nishimura, Y., Tsuboi, M., Watanabe, K., Iso, K., & Nakano, T. (1983) Biochemistry 22, 6018-6026] revealed greater suppression of nucleosome movement in chicken erythrocyte chromatin. Furthermore, the transition of this chromatin to the compact (solenoidal) structure occurred at lower solvent concentrations of Na+ or Mg2+ than those for calf thymus chromatin. These results demonstrated increased stability of the higher order structure (the solenoid) of chicken erythrocyte chromatin, which may be related to the reduction of nuclear activity in the chicken erythrocyte cell. In addition to intact chicken erythrocyte chromatin, we studied the structural transitions of H1-depleted and H1,H5-depleted chromatins. The result indicated that histone H5 of this chromatin stabilizes the higher order structure in the presence of magnesium (or divalent) cation and did not induce the transition in the solution containing only sodium cation.