Immunofluorescent study of chromatin proteins in cultured fibroblasts

Antibodies against chromatin from 3T6 mouse fibroblasts and WI-38 human diploid fibroblasts were prepared by immunization of rabbits. Immunofluorescent studies showed species-specificity of these antichromatin antibodies. Furthermore, using anti-3T6 chromatin antibodies against 3T6 cells and anti-WI-38 chromatin antibodies against WI-38 cells, we observed, by immuno-fluorescent techniques, granular fluorescence in the diffusely stained nucleus and diffuse fluorescence in the cytoplasm. These results raise the possibility of the presence of a cytoplasmic pool of chromatin proteins.     

Immunofluorescent staining of keratin fibers in cultured cells.

Antibody prepared against a group of keratins purified from human stratum corneum was used to identify cells containing keratins by immunofluorescence. In sectioned tissue and in culture, keratinocytes of skin and other stratified squamous epithelia-whether human, rabbit of mouse-stained strongly, indicating homologous amino acid sequences in the keratins of these species. In all cases, the antibody revealed a dense cytoplasmic network of discrete fibers probably consisting of aggregated (tono-) filaments. The pattern of staining was not affected by cytochalasin B or colcemid. No keratins were detected in cultured cells of mesenchymal origin (3T3, NIL, BHK, human diploid fibroblasts) or in connective tissues, indicating that the 100 A filaments of fibroblasts are not related to the keratins. Keratinocytes at all stages of differentiation, including basal cells, stained brightly and therefore contained abundant keratins.     

Structural study of homeodomain protein-DNA complexes using a homology modeling approach

The homeodomain is a conserved protein motif that binds to DNA and plays a central role in gene regulation. We use homeodomain as a model system to study the specific interactions between protein and DNA in a complex. Following the fundamental concept of homology modeling, we have developed an algorithm for predicting structures of both protein and DNA using the known structure of a similar complex as the template. The accuracies of the algorithm in predicting the complex structures are evaluated when two of the homeodomain protein-DNA complexes with known structures (antennapedia and MATalpha2) are selected as test systems. This algorithm allows structural studies of homeodomain binds to DNA with different sequences.     

Immunofluorescent study of DNA polymerase alpha in rat cells and tissues

An indirect immunofluorescent test based on globulin preparation from a highly specific antiserum against rat liver DNA polymerase alpha was used to direct the enzyme in sections of various tissues of the rat. The immunofluorescent staining was found in cells of the thymus and the wall of intestine crypt, in sparse cells of the intestinal muscular layer, and in cells of the embryo skin epithelium. In sections of liver the intensity of staining and the number of stained cells increased significantly during regeneration. The immunoglobulins did not interact with the cytoplasm and nuclei of skeletal muscle myotubes, with the epithelial cells at the top of intestinal villi, and with erythrocytes. The intracellular localization of the fluorescence observed was of two general types: 1) staining in the region of the nuclear envelope and/or in the cytoplasm; 2) an additional intranuclear staining. The staining of the first type is characteristic of the cells of intact liver and of leyomyocytes. It was also observed in the proliferating cells of thymus and crypt wall, and in cultured myogenic L6 cells. Cells of the embryo skin epithelium, the satellite cells in the skeletal muscle, and about one half of the regenerating liver cells appeared to have the second type of staining. These data serve an indication of possible histotypical differences in in the intracellular localization of DNA polymerase alpha in proliferating cells. It is proposed that the presence of DNA polymerase in resting cells is in association with their ability to respond to the mitogenic stimulus.     

Analysis of the effectiveness of sodium chloride in dissociating non-histone chromatin proteins of cultured hepatoma cells

We examined the ability of NaCl (at 0.15 to 3 M) to release non-histone proteins from chromatin of cultured rat hepatoma cells. The percentage of the non-histones released increased with increasing NaCl concentrations up to 0.75 M; 1 and 3 M NaCl were not significantly more effective. A maximum of 50% of the non-histone protein was recovered free of DNA. The release of non-histones from sheared and unsheared chromatin was similar. The electrophoretic patterns of the non-histone proteins released by NaCl resembled that of the non-histones released by sodium dodecyl sulfate, which indicates that many of the detectable components were at least partially released by NaCl. Some non-histones (especially low molecular weight polypeptides) were fully released by NaCl and other proteins were relatively resistant to NaCl release. Higher recoveries of NaCl-dissociated non-histones were obtained with sucrose gradient centrifugation than with centrifugation in the absence of sucrose.     

Immunofluorescent and immunogold replica studies of desmin distribution in cultured normal and cardiomyopathic hamster heart cells.

The architecture of desmin intermediate filament arrangements in cultured cardiomyocytes from heart of normal and cardiomyopathic hamsters was studied by immunofluorescent light microscopy and immunogold replica electron microscopy. Both polyclonal and monoclonal antidesmin antibodies were used in a biotin-streptavidin system. Immunofluorescent staining of normal and cardiomyopathic myocytes for desmin at 5 days in culture exhibited filamentous staining patterns with polyclonal antidesmin and a coarse punctate staining pattern with the monoclonal antibody. At 9 days in culture, most normal myocytes showed filamentous staining with the polyclonal antibody; many of the stained filaments were associated with Z lines. With the monoclonal antidesmin, these same cells exhibited a very fine 'spotty' staining pattern. These results suggest that the arrangements and immunoreactivities of intermediate filaments change during normal cardiac myocyte development. In cardiomyopathic cells, this pattern of rearrangement and immunoreactivity appears to be delayed or possibly nonexistent. The three-dimensional electron-microscopic observation of immunogold localization of desmin achieved by a deep-etching replica technique is made on both normal and cardiomyopathic cultured heart cells. Abnormalities of desmin filament arrangements in cardiomyopathic cells are confirmed.     

Immunofluorescent localization of cyclic nucleotide-dependent protein kinases on the mitotic apparatus of cultured cells

Cyclic nucleotides and cyclic nucleotide-dependent protein kinases have been implicated in the regulation of cell motility and division, processes that depend on the cell cytoskeleton. To determine whether cyclic nucleotides or their kinases are physically associated with the cytoskeleton during cell division, fluorescently labeled antibodies directed against cyclic AMP, cyclic GMP, and the cyclic nucleotide- dpendent protein kinases were used to localize these molecules in mitotic PtK1 cells. Both the cyclic GMP-dependent protein kinase and the type II regulatory subunit of the cyclic AMP-dependent protein kinase were localized on the mitotic spindle. Throughout mitosis, their distribution closely resembled that of tubulin. Antibodies to cyclic AMP, cyclic GMP, and the type I regulatory and catalytic subunits of the cyclic AMP-dependent protein kinase did not label the mitotic apparatus. The association between specific components of the cyclic neucleotide system and the mitotic spindle suggests that cyclic nucleotide-dependent phosphorylation of spindle proteins, such as those of microtubules, may play a fundamental role in the regulation of spindle assembly and chromosome motion.     

Aromatic-aromatic interactions in structures of proteins and protein-DNA complexes: a study based on orientation and distance

Interactions between the aromatic amino acid residues have a significant influence on the protein structures and protein-DNA complexes. These interactions individually provide little stability to the structure; however, together they contribute significantly to the conformational stability of the protein structure. In this study, we focus on the four aromatic amino acid residues and their interactions with one another and their individual interactions with the four nucleotide bases. These are analyzed in order to determine the extent to which their orientation and the number of interactions contribute to the protein and protein-DNA complex structures.     

An overview of the structures of protein-DNA complexes

On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different structural/functional groups, which are further classified into 54 structural families. Here we present this classification and review the functions, structures and binding interactions of these protein-DNA complexes.     

Endocytosed non-histone proteins translocate in part to the nucleus in lymphocytes

[3H]Non-histone proteins ([3H]NHP), dissolved in the culture medium, are endocytosed by lymphocytes and equilibrate rapidly between the cytoplasm and the nucleus. During incubation, the proteins are gradually degraded in the lysosomes. The lysosomotropic agents conA, NaF, eserine and atropine have two parallel effects on resting lymphocytes, after they have endocytosed [3H]NHP: inhibition of degradation and increased translocation of [3H]NHP from the cytoplasm to the nucleus. This indicates that lysosomal degradation and translocation of [3H]NHP to the nucleus are linked and suggests that this translocation may be the result of inhibited lysosomal degradation of the [3H]NHP. The behaviour of endocytosed [3H]NHP appears similar to that of endogenous [3H]NHP in cells prelabeled with [3H]leucine, when subjected to the same lysosomotropic agents, reported previously (Polet, H, Exp cell res 148 (1983) 345). This observation may provide a model to study the mechanism(s) controlling nucleo-cytoplasmic traffic of NHP.     

Association of protein-DNA recognition complexes: electrostatic and nonelectrostatic effects

In this study the electrostatic and nonelectrostatic contributions to the binding free energy of a number of different protein-DNA recognition complexes are investigated. To determine the electrostatic effects in the protein-DNA association the Poisson-Boltzmann approach was applied. Overall the salt-dependent electrostatic free energy opposed binding in all protein-DNA complexes except one, and the salt-independent electrostatic contribution favored binding in more than half of the complexes. Further the salt-dependent electrostatic free energy increased with higher ionic concentrations and therefore complex association is stronger opposed at higher ionic concentrations. The hydrophobic effect in the protein-DNA complexes was determined from the buried accessible surface area and the surface tension. A majority of the complexes showed more polar than nonpolar buried accessible surface area. Interestingly the buried DNA-accessible surface area was preferentially hydrophilic, only in one complex a slightly more hydrophobic buried accessible surface area was observed. A quite sophisticated balance between several different free energy components seems to be responsible for determining the free energy of binding in protein-DNA systems.     

Recent advances in FRET: distance determination in protein-DNA complexes

Fluorescence resonance energy transfer (FRET) provides information on the distance between a donor and an acceptor dye in the range 10 to 100 A. Knowledge of the exact positions of some dyes with respect to nucleic acids now enables us to translate these data into precise structural information using molecular modeling. Advances in the preparation of dye-labeled nucleic acid molecules and in new techniques, such as the measurement of FRET in polyacrylamide gels or in vivo, will lead to an increasingly important role of FRET in structural and molecular biology.     

Bi-functional cross-linking reagents efficiently capture protein-DNA complexes in Drosophila embryos

Chromatin immunoprecipitation (ChIP) is widely used for mapping DNA-protein interactions across eukaryotic genomes in cells, tissues or even whole organisms. Critical to this procedure is the efficient cross-linking of chromatin-associated proteins to DNA sequences that are in close proximity. Since the mid-nineties formaldehyde fixation has been the method of choice. However, some protein-DNA complexes cannot be successfully captured for ChIP using formaldehyde. One such formaldehyde refractory complex is the developmentally regulated insulator factor, Elba. Here we describe a new embryo fixation procedure using the bi-functional cross-linking reagents DSG (disuccinimidyl glutarate) and DSP (dithiobis[succinimidyl propionate). We show that unlike standard formaldehyde fixation protocols, it is possible to capture Elba association with insulator elements in 2–5 h embryos using this new cross-linking procedure. We show that this new cross-linking procedure can also be applied to localize nuclear proteins that are amenable to ChIP using standard formaldehyde cross-linking protocols, and that in the cases tested the enrichment was generally superior to that achieved using formaldehyde cross-linking.     

Hydrogen bonds in protein-DNA complexes: where geometry meets plasticity

Recognition of a DNA sequence by a protein is achieved by interface-coupled chemical and shape complementation. This complementation between the two molecules is clearly directional and is determined by the specific chemical contacts including mainly hydrogen bonds. Directionality is an instrumental property of hydrogen bonding as it influences molecular conformations, which also affects DNA-protein recognition. The prominent elements in the recognition of a particular DNA sequence by a protein are the hydrogen-bond donors and acceptors of the base pairs into the grooves of the DNA that must interact with complementary moieties of the protein partner. Protein side chains make most of the crucial contacts through bidentate and complex hydrogen-bonding interactions with DNA base edges hence conferring remarkable specificity.