Basic polypeptides as histone models: circular dichroism of complexes of model polypeptides with DNA.

Circular dichroism (CD) was used to study the complexes of DNA (in 0.15M NaCl) with two polypeptides considered as models of the histone molecules. CD spectra in the region of DNA absorption were studied with respect to the concentration used for annealing and to the molecular weight and composition of the DNA used. The properties of supernatants after centrifugation of aggregated complexes were examined. The effect of selectively bound antibiotics (actinomycin D and netropsin) on CD sprectra of complexes was investigated. The induced CD of proflavine molecules bound to DNA in the various complexes was also studied. It was concluded that changes in the CD spectra of DNA in complexes with the polypeptides are due to the formation of chiral superstructures, even if some conformational changes of DNA molecules themselves may also be decisive in some cases. The superstructure is affected by the composition of DNA, the role of (G + C) rich segments being particularly important.     

Basic polypeptides as histone models. Synthesis, conformation, and interaction with DNA of statistical copolymers (Lys x,Ala y)n.

Statistical copolymers (Lys^x,Ala^y)_n were synthesized by copolymerization of N-carboxyanhydrides of L -amino acids. The conformation of copolymers in aqueous solutions was investigated using circular dichroism (CD). Calculations based on the CD data showed that polymers (Lys^x,Ala^y)_n can exhibit a random conformation, an α-helix, and a β-structure in various ratios. CD spectra of complexes of copolymers with DNA prepared by gradual dialysis from a high ionic strength to 0.15 M NaCl can be correlated with the copolymer conformation in medium and high ionic strength. For copolymers forming an α-helix and β-structure, these spectra show resemblance with similar spectra of complexes of those histones that are able to exhibit ordered conformations.     

A circular dichroism study of charged polypeptides interaction with salts.

The effect of salts on the experimental circular dichroism spectra of polypeptides is presented using poly-L-lysine as the main model. Salt effects are analyzed into: (a) shielding at low (less than 0.5 M) concentrations of all salts; (b) binding to positively charged and some neutrally charged side-chains by certain anions (e.g., CCl3COO-, CF3C00-, ClO4-), with induction of helicity; (c) binding of these same anions, at high concentration, to the backbone leading toward random structure; (d) binding of high concentration of denaturing cations (La+3, Ca++, Li+) to the backbone, with La+3 and Ca++ leading to collapsed random structure (R) while Li+ tends to leave the polypeptide somewhat extended; (e) indirect interaction of salting-out salts (NaH2PO4, (NH4)2SO4, NH4F), at high concentration, leading toward complete alpha helicity, probably by competition with the polypeptide and the anion for available water. Effects of changing the temperature from 5 degrees to 50 degrees on the circular dishroism spectra of different polypeptide-salt solutions throughout the region from extended (LES) to alpha helical conformation are analyzed in terms of introduction of randomness (R) at high temperature. Applications to effects of salt on protein structures are considered.     

Vacuum ultraviolet circular dichroism as an indicator of helical handedness in nucleic acids.

Calculated circular dichroism spectra are presented for double-stranded polynucleotides of regular sequences in A-RNA, A-DNA, B-DNA, and Z-DNA conformations. Quantum mechanical matrix method calculations were carried out in the near and vacuum ultraviolet regions. In the near UV, the calculated spectra agreed qualitatively with the measured spectra. However in the far and vacuum UV, the calculated CD compared nearly quantitatively with the experimental spectra. The calculations show that the sign of the CD in the vacuum UV, in contrast to that in the near UV, can be correlated with the handedness of the helix.     

Structure of DNA complexes with chromosomal protein HMGB1 and histone H1 in the presence of manganese ions: 2. Vibrational circular dichroism spectroscopy

DNA complexes with nonhistone HMGB1 chromatin protein and histone H1 in the presence of manganese ions were studied using methods of absorption and circular dichroism spectroscopy in the infrared region. It was demonstrated that the method provides good results, even for solutions that contain large particles, which cause scattering in UV region. It was determined that manganese ions in the complex are able to coordinate not only to different chemical groups in DNA, but also to dicarboxylic acid residues of the HMGB1 protein, which stimulates DNA condensation and slightly weakens DNA-protein interactions in the complex.     

Condensation of DNA by the C-terminal domain of histone H1. A circular dichroism study

The condensation of DNA by the C-terminal domain of histone H1 has been studied by circular dichroism in physiological salt concentration (0.14 M NaF). As the intact H1 molecule, its C-terminal domain induces the so-called psi state of DNA that is characterized by a nonconservative circular dichroism spectrum which is currently attributed to ordered aggregation of the DNA molecules. On a molar basis, intact H1 and its C-terminal domain give spectra of similar intensity. Neither the globular domain of H1 nor an N-terminal fragment, that includes both the globular and N-terminal domains, has any effect on the conservative circular dichroism of DNA. From these results it is concluded that the condensation of DNA mediated by histone H1 is mainly due to its C-terminal domain. The effect of the salt concentration and the size of DNA molecules on the circular dichroism of the complexes are also examined.     

The circular dichroism of synthetic ribonucleic acids and the influence of uracil on conformation

We present CD spectra of four trinucleoside diphosphates, UpUpG, GpUpG, ApUpA, and ApUpG, of four single-stranded polymers, poly AC, poly GU, poly AU, and poly AdU, and of five double-stranded polymers, poly A:U, poly G:C, poly AU:AU, poly AdU:AdU, and poly GC:GC. The measured spectra are compared with empirical firstneighbor calculations. Our results, taken together with data from the literature, suggest that UpA and UpG sequences are relatively unstacked in a single-stranded RNA compared with these isolated dimers in solution. These sequences may influence the structure and function of natural RNAs. Our results on double-stranded RNAs indicate that the spectral changes which occur upon formation of a double helix are unique to the type of base pair involved and are relatively independent of sequence.     

Immunological and circular dichroism studies of maleylated f-1 (A) histone and complexes with DNA

Complexes of calf thymus f-1 (A) histone and homologous DNA were examined by circular dichroism. The maleylation of f-1 (A) produces a polypeptide with decreased ability to modify the circular dichroism spectrum of f-1 (A)-DNA complexes. By the introduction of two to three maleyl groups per f-1 (A) molecule, the alteration of the DNA CD spectrum is reduced by nearly half compared to that induced by the native nonmaleylated f-1 (A). Similarly maleylation reduces the serological reactivity of the histone, i.e., the reaction of the maleylated f-1 (A) with specific complement fixing f-1 (A) antibodies. On the other hand, moderate maleylation of f-1 (A) improves the cross-inhibition of the f-2b-anti-f-2b reaction by native f-1 (A) while extensively maleylated f-1 (A) is inert with respect to the same reaction. These results are interpreted in terms of possible conformational changes induced in f-1 (A) by maleylation, partially due to decreasing the histone net charge and perhaps as well as removal of specific site charges necessary for correct binding and interaction. Such an interpretation is consistent with the altered CD spectrum of maleylated f-1 (A) (i.e., a decreased and slightly red-shifted [θ]₁₉₈) and moreover explains why maleylation of two to three lysines per f-1 (A) molecule hinders simultaneously the very different DNA-histone and histone-complement fixing antibody interactions.     

Vibrational circular dichroism of A-, B-, and Z-form nucleic acids in the PO2-stretching region.

Vibrational circular dichroism (VCD) spectra were measured for H2O solutions of several natural and model DNAs (single and double strands, oligomers and polymers) in the B-form, poly(dG-dC)-poly(dG-dC) in the Z-form, and various duplex RNAs in an A-form over the PO2-stretching region. Only the symmetric PO2 stretch at approximately 1075 cm-1 yields a significant intensity VCD signal. Differences of the PO2-stretching VCD spectra found for these conformational types are consistent with the spectral changes seen in the base region, but no sequence dependence was seen in contrast to VCD for base modes. The B to Z transition is accompanied by an inversion of the PO2- VCD spectra, which is characteristic of the change in the helical sense of the nucleic acid backbone. A-RNAs give rise to the same sense of couplet VCD as do B-DNAs but have a somewhat different shape because of overlapping ribose modes. These PO2- VCD spectral characteristics have been successfully modeled using simple dipole coupling calculations. The invariability of the symmetric PO2- stretching mode VCD spectra to the base sequence as opposed to that found for the C = O stretching and base deformation modes is evidence that this mode will provide a stable indication of the DNA helical sense.     

Scanning microcalorimetry and circular dichroism study of melting of the natural polypeptides in the left-handed helical conformation

It has been shown that in aqueous solution histone H1 and H5 C-terminal fragments and peptide hormones -endorphin and ACTH adopt preferably the left-handed helical conformation of the poly-l-proline II type. Scanning microcalorimetry and circular dichroism have been used to show that the linear temperature dependence of CD maximum amplitude and partial heat capacity value are broken in the temperature interval between 50 and 60°C, after which [C] _p reaches the constant level. It was proposed to be due to noncooperative disordering of the conformation caused by the destruction of the polypeptide hydration shell.     

DNA methylation, histone H3 methylation, and histone H4 acetylation in the genome of a crustacean.

In this work, we used antibodies against histone H3 trimethylated at lysine 9 (H3K9m3); against histone H4 acetylated at lysines 5, 8, 12, and 16 (H4ac); and against DNA methylated at 5C cytosine (m5C) to study the presence and distribution of these markers in the genome of the isopod crustacean Asellus aquaticus. The use of these 3 antibodies to immunolabel spermatogonial metaphases yields reproducible patterns on the chromosomes of this crustacean. The X and Y chromosomes present an identical banding pattern with each of the antibodies. The heterochromatic telomeric regions and the centromeric regions are rich in H3K9m3, but depleted in m5C and H4ac. Thus, m5C does not seem to be required to stabilize the silence of these regions in this organism.     

Cooperative interaction of histone H1 with DNA.

The cooperative binding of histone H1 with DNA was studied using a fluorescently labelled histone H1. The titration data were analysed in terms of the large ligand model. The stoichiometric number, n = 65 +/- 10 bases/H1, was independent of NaCl concentration (0.02 - 0.35 M). The nucleation and the cooperative binding constants, K' and K, and the cooperativity parameter q were sensitive to salt concentration; K = 3.6 +/- 0.8 X 10(7) M-1 and q = 1.1 +/- 0.4 X 10(3) at 0.2 M NaCl. The dependence of K' on NaCl concentration revealed that 6 Na+ ions were released from DNA upon complex formation. An extrapolation of K' to 1M NaCl yielded a small value, K' = 5 +/- 2 M-1. Thus the binding of H1 is essentially electrostatic, being compatible with its independence of temperature. A calculation of K' based on the counterion release reproduced the salt concentration dependence of K'. Therefore, the binding of H1 is of an electrostatic territorial type. Thus, H1 may move along the DNA chain to a certain extent, when both salt concentration and the degree of saturation are sufficiently low. The condition is so restricted that the sliding would not play an important role in vivo. It was concluded from the DNA concentration independent binding isotherm that H1 can cooperatively bind onto a single DNA molecule. A simple power law dependence of the cooperativity parameter q upon NaCl concentration was found; q oc[NaCl]h with h = 0.72, though the physical basis of this dependence remains unknown.     

Effect of temperature on the circular dichroism spectra of polypeptides in the extended state

The circular dichroism (CD) spectra of poly-L -proline and of poly-L -glutamic acid and poly-L -lysine in their charged states have been studied as a function of temperature. The variation of CD spectra with temperature is inconsistent with the assignment of the spectrum of such charged polypetides to an unordered chain conformation, but does support our earlier assignment to a locally ordered structure—what we have called the extended helix conformation. These results also strengthen our previous assignment of the CD spectrum of an unordered chain, and indicate that three conformational states (α-helix, extended helix, and unordered) should be incorporated in our thinking about conformational transitions in polypeptides.