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A Klug

Publications and source records attributed to A Klug.

At least 55 records · Page 3Linked to original sources
PubMed1995

Protein motifs 5. Zinc fingers.

The term zinc finger was first used to describe a 30-residue, repeated sequence motif found in an unusually abundant Xenopus transcription factor. It was proposed that each motif is folded around a central zinc ion to form an independent minidomain and that adjacent zinc fingers are combined as modules to make up a DNA-binding domain with the modules "gripping" the DNA (hence the term finger). We now know that these proposals were correct and that these DNA-binding motifs are found in many eukaryotic DNA-binding proteins. More recently, crystal structures of three different complexes between zinc finger domains and their target DNA binding sites have revealed a remarkably simple mode of interaction with DNA. The simplicity of the zinc finger structure, and of its interaction with DNA, is a very striking feature of this protein domain. After the discovery of the zinc finger motif, patterns of potential zinc ligands have been found in several other proteins, some of which also bind to DNA. Structural studies of these domains have revealed how zinc can stabilize quite diverse protein architectures. In total, 10 such small zinc-binding domains have been studied structurally. These form a diverse collection, but each in turn has been termed a zinc finger motif-although clearly what they have in common is only their zinc-binding property, which stabilizes an apparently autonomously folded unit.

Amino Acid Sequence↗
PubMed1994

In vivo repression by a site-specific DNA-binding protein designed against an oncogenic sequence.

A DNA-binding peptide comprising three zinc-fingers has been engineered to bind specifically to a unique nine-base-pair region of a BCR-ABL fusion oncogene in preference to the parent genomic sequences. Binding to the target oncogene in chromosomal DNA is possible in transformed cells in culture, and results in blockage of transcription. Consequently, murine cells rendered independent of growth factors by the action of the oncogene revert to factor dependence upon transient transfection with a vector expressing the peptide.

Amino Acid Sequence↗
PubMed1994

Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage.

We have used two selection techniques to study sequence-specific DNA recognition by the zinc finger, a small, modular DNA-binding minidomain. We have chosen zinc fingers because they bind as independent modules and so can be linked together in a peptide designed to bind a predetermined DNA site. In this paper, we describe how a library of zinc fingers displayed on the surface of bacteriophage enables selection of fingers capable of binding to given DNA triplets. The amino acid sequences of selected fingers which bind the same triplet are compared to examine how sequence-specific DNA recognition occurs. Our results can be rationalized in terms of coded interactions between zinc fingers and DNA, involving base contacts from a few alpha-helical positions. In the paper following this one, we describe a complementary technique which confirms the identity of amino acids capable of DNA sequence discrimination from these positions.

Amino Acid Sequence↗
PubMed1994

Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions.

In the preceding paper [Choo, Y. & Klug, A. (1994) Proc. Natl. Acad. Sci. USA 91, 11163-11167], we showed how selections from a library of zinc fingers displayed on phage yielded fingers able to bind to a number of DNA triplets. Here, we describe a technique to deal efficiently with the converse problem--namely, the selection of a DNA binding site for a given zinc finger. This is done by screening against libraries of DNA triplet binding sites randomized in two positions but having one base fixed in the third position. The technique is applied here to determine the specificity of fingers previously selected by phage display. We find that some of these fingers are able to specify a unique base in each position of the cognate triplet. This is further illustrated by examples of fingers which can discriminate between closely related triplets as measured by their respective equilibrium dissociation constants. Comparing the amino acid sequences of fingers which specify a particular base in a triplet, we infer that in most instances, sequence-specific binding of zinc fingers to DNA can be achieved by using a small set of amino acid-nucleotide base contacts amenable to a code.

Amino Acid Sequence↗
PubMed1993

Co-chairman's remarks: protein designs for the specific recognition of DNA.

The selective expression of a gene is achieved through the interaction of protein transcription factors with characteristic nucleotide sequences located in the regulatory region of the gene, which is usually distinct from the coding region. These proteins contain domains which bind specifically to the DNA sites (or response elements). Some general principles in the design of these DNA-binding domains are described, followed by examples of the different structural classes discovered so far and how they recognise their binding sites.

Animals↗
PubMed1993

A role in DNA binding for the linker sequences of the first three zinc fingers of TFIIIA.

Zinc fingers of the TFIIIA type are connected by short linker sequences between the structural units. Structural investigations by 2D NMR in solution and by X-ray crystallographic analyses of complexes with DNA point to a passive role for the linkers. We have therefore investigated the influence of the linker sequence on DNA binding using as a model the first three fingers of the protein TFIIIA. Insertion of certain heterologous linkers abolishes binding, and replacement of individual amino acids can reduce binding by factors of up to twenty-four.

Amino Acid Sequence↗
PubMed1993

Zinc fingers.

Explore the source record for details and available documents.

Amino Acid Sequence↗
PubMed1992

Adjacent zinc-finger motifs in multiple zinc-finger peptides from SWI5 form structurally independent, flexibly linked domains.

Peptides containing either one, two or three of the three zinc-finger motifs from the yeast transcription factor SWI5 have been prepared by expression in Escherichia coli. The DNA binding characteristics of these peptides were investigated, and a two-dimensional nuclear magnetic resonance (n.m.r.) study undertaken to establish the three-dimensional structures of the two-finger peptide. The peptide containing fingers 1 and 2 binds sequence specifically to two thirds of the DNA binding site recognized either by intact SWI5 or by the isolated three-finger peptide, and hence has the correct tertiary fold for DNA recognition. These results also establish the polarity of DNA binding, since the N-terminal two fingers of SWI5 bind to the 5' end of the DNA binding site. Mild proteolysis of the three-finger peptide using trypsin results in a small number of discrete products, which is consistent with the presence of three structured mini-domains. Nearly complete n.m.r. signal assignments were obtained for two peptides containing finger 2 alone or fingers 1 + 2. Comparison of two-dimensional spectra of these peptides and others clearly shows that the NOE enhancements and chemical shifts characteristic of each finger are quite insensitive to the presence or absence of neighbouring fingers. This clearly indicates that adjacent zinc-finger domains are structurally independent in these peptides from SWI5. However, there must be some steric limitations on the possible relative orientations of the fingers, and to establish limits for these a set of structures for the peptide containing fingers 1 + 2 was calculated using the YASAP simulated annealing protocol in conjunction with n.m.r.-based constraints. A more detailed description of the three-dimensional structures of finger 1 and finger 2, and their relationship to other previously determined structures of single zinc-fingers, is given in the accompanying paper.

Amino Acid Sequence↗
PubMed1992

Solution structures of two zinc-finger domains from SWI5 obtained using two-dimensional 1H nuclear magnetic resonance spectroscopy. A zinc-finger structure with a third strand of beta-sheet.

This paper describes the detailed three-dimensional structures of two zinc-finger domains from the yeast transcription factor SWI5, calculated using the results of the n.m.r. experiments described in the accompanying paper. The structure of finger 2 is essentially similar to those previously obtained by others for isolated, synthetic single zinc-finger domains in solution, and for the three zinc-finger peptide Zif268 in its crystalline complex with DNA. The N-terminal half of the sequence forms a two-stranded, irregular beta-sheet containing both of the metal-binding cysteine residues, while the remainder of the structure forms a helix. Approximately the first half of this helix is alpha-helical, whereas the C-terminal portion, including the two metal-binding histidine residues, is 3(10) helical. Four invariant hydrophobic residues form a core to the structure. In contrast to all previously described structures of zinc-finger domains, finger 1 has an additional strand in the beta-sheet, formed by residues N-terminal to the formal start of the finger motif. This additional strand plays a role in stabilising the folded form of finger 1, since a two-finger peptide lacking the N-terminal residues showed folded structure in finger 2 but not in finger 1.

Amino Acid Sequence↗
PubMed1992

Comparison of X-ray structures of the nucleosome core particle in two different hydration states.

The X-ray structure of the nucleosome core particle was determined at 7 A resolution using crystals containing mixed-sequence DNA and 21% to 27% of 1,6-hexanediol (partially dehydrated crystals). The alcohol was added to the crystals after growth to overcome the non-isomorphism of the crystals and improve the quality of their X-ray diffraction. Here, we report the structure of the nucleosome core particle from these crystals in the absence of the alcohol 1,6-hexanediol at 9 A resolution. The structure, under conditions of nearly full hydration, has been solved by multiple isomorphous replacement methods employing multiple heavy-atom compounds identical to those used for the partially dehydrated structure. The electron density of particles in the two crystal structures is well-correlated throughout the maps and structural elements of the DNA superhelix and histone proteins are generally similar, e.g. the DNA bends sharply at positions +/- 1 and +/- 4 double-helical turns from the DNA center. These results rule out the occurrence of gross structural changes in the 7 A structure due to addition of alcohol. The parts of the nucleosome core particle structure, which are dissimilar between the two forms, can be attributed to differences in molecular packing induced by the addition of 1,6-hexanediol. In contrast to the structure seen in the partially dehydrated crystals, the fully hydrated crystals show a particle in which the H2A-H2B dimers are symmetrically related by the dyad axis found in the H3-H4 tetramer region. However, in the fully hydrated crystals, the first and last double-helical turns of DNA superhelix are not related by dyad symmetry, and one of these segments has reduced contact with the adjacent H2A-H2B dimer.

Fourier Analysis↗
PubMed1990

Sequence-specific [1H]NMR resonance assignments and secondary structure identification for 1- and 2-zinc finger constructs from SW15. A hydrophobic core involving four invariant residues.

Complete [1H]NMR resonance assignments are presented for the second of the three zinc fingers from SW15 as it appears in both 1- and 2-finger constructs. Signals from finger 2 are unaffected by the presence or absence of finger 1, showing that the protein has a modular construction. The structure of finger 2 comprises a helix running from N56 to Q67, and a region approximating to an anti-parallel beta-sheet running from Y42 to F53. These features combine to produce a hydrophobic core in the structure involving the invariant residues Y42, F53, L59 and H62.

Amino Acid Sequence↗
PubMed1990

Different configurational states of beta-amyloid and their distributions relative to plaques and tangles in Alzheimer disease.

Antibodies have been raised against synthetic peptides corresponding to different parts of the beta-amyloid sequence. These antibodies stain different kinds of amyloid distributions in the hippocampal formation in Alzheimer disease, suggesting the existence of different states of aggregation and/or folding of beta-amyloid molecules. An antibody directed against the middle region of beta-amyloid stained mostly amyloid plaques without cores, whereas an antibody directed against the carboxyl-terminal region of beta-amyloid stained only amyloid plaques with cores. An antiserum directed against the amino terminus of beta-amyloid stained numerous tangle-bearing cells and bodies, as well as the neuritic component of plaques and neuropil threads. These antibodies, in conjunction with anti-tau antibodies, were used to demonstrate a close spatial relationship between amyloid deposits and neurofibrillary tangles.

Alzheimer Disease↗
PubMed1990

Topographical relationship between beta-amyloid and tau protein epitopes in tangle-bearing cells in Alzheimer disease.

Double-labeling immunohistochemistry was used to investigate the topographical relationship between beta-amyloid and tau protein epitopes present in cells bearing neurofibrillary tangles found in the hippocampal formation of patients with Alzheimer disease. An antiserum raised against the amino terminus of beta-amyloid stained numerous tangle-bearing cells and other bodies ("extracellular tangles"), but double labeling showed that the beta-amyloid staining is invariably peripheral to that of the tau-positive tangle proper. This and other results suggest that the extracellular amyloid plaques and the intracellular neurofibrillary tangles are biochemically distinct but may result from related pathological events that originate at the level of the nerve cell and lead to its degeneration.

Alzheimer Disease↗
PubMed1990

Mode of interaction of the zinc finger protein TFIIIA with a 5S RNA gene of Xenopus.

The zinc finger protein TFIIIA, a positive transcription factor of the 5S RNA gene, binds to an internal control region of 50 nucleotides. Two modes of binding have been considered for the TFIIIA-DNA complex, one of which has been proposed on the basis of nuclease and chemical protection experiments and the other on model building. Since then, evidence has accumulated on the structures of individual components of the complex--for example, zinc finger polypeptides studied by NMR and a segment of the binding site analyzed by x-ray crystallography, but no high-resolution structural data on the TFIIIA-DNA complex itself are available. Probes used previously to study the TFIIIA-DNA complex do not react with every nucleotide of DNA, unlike hydroxyl radical, which cleaves DNA at every backbone position. We describe here the quantitative analysis of high-resolution hydroxyl radical footprints and suggest how the array of zinc fingers might interact with the double helix.

Animals↗
PubMed1990

Molecular analysis of neurofibrillary degeneration in Alzheimer's disease. An immunohistochemical study.

Antibodies directed against three regions of tau, ubiquitin, and B-amyloid were used in a histologic study of neurofibrillary degeneration in Alzheimer's disease to distinguish two populations of neurofibrillary tangles. Intracellular tangles were immunolabeled exclusively by two antibodies raised against antigens in the fuzzy coat of the paired helical filament (PHF). Extracellular tangles were distinguished by selective immunolabeling with a monoclonal antibody raised against antigens in the PHF core. This was associated with removal of the fuzzy coat and exposure of PHF-core epitopes. In the transition from intracellular to extracellular compartments in vivo, tangles appeared to undergo changes similar to protease digestion in vitro. The transition was associated with the appearance of amyloid immunoreactivity. These findings suggest that tangle degradation occurs in a series of distinct stages, including ubiquitination of some unknown molecule, a change in tau immunoreactivity, and partial proteolysis of tangle-bound tau in extracellular tangles.

Aged↗
PubMed1989

Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops.

The telomeric ends of eukaryotic chromosomes are composed of simple repeating sequences in which one DNA strand contains short tracts of guanine residues alternating with short tracts of A/T-rich sequences. The guanine-rich strand is always oriented in a 5'-3' direction towards the end of the chromosome and is extended to produce a 3' overhang of about two repeating units in species where the telomeric terminus is known. This overhang has been implicated in the formation of several unusual intra-and intermolecular DNA structures, although none of these structures has been characterized fully. We now report that oligonucleotides encoding Tetrahymena telomeres dimerize to form stable complexes in solution. This salt-dependent dimerization is mediated entirely by the 3'-terminal telomeric overhang (TT-GGGGTTGGGG) and produces complexes in which the N7 position of every guanine in the overhangs is chemically inaccessible. We therefore propose that telomeric DNA dimerizes by hydrogen bonding between two intramolecular hairpin loops, to form antiparallel quadruplexes containing cyclic guanine base tetrads. These novel hairpin dimers may be important in telomere association and recombination and could also provide a general mechanism for pairing two double helices in other recombinational processes.

Animals↗