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Biomedical subjects

D Rhodes

Publications and source records attributed to D Rhodes.

At least 73 records · Page 4Linked to original sources
PubMed1996

The solution structure of the first zinc finger domain of SWI5: a novel structural extension to a common fold.

BACKGROUND: The 2Cys-2His (C2-H2) zinc finger is a protein domain commonly used for sequence-specific DNA recognition. The zinc fingers of the yeast transcription factors SWI5 and ACE2 share strong sequence homology, which extends into a region N-terminal to the first finger, suggesting that the DNA-binding domains of these two proteins include additional structural elements. RESULTS: Structural analysis of the zinc fingers of SWI5 reveals that a 15 residue region N-terminal to the finger motifs forms part of the structure of the first finger domain, adding a beta strand and a helix not previously observed in other zinc finger structures. Sequence analysis suggests that other zinc finger proteins may also have this structure. Biochemical studies show that this additional structure increases DNA-binding affinity. CONCLUSIONS: The structural analysis presented reveals a novel zinc finger structure in which additional structural elements have been added to the C2-H2 zinc finger fold. This additional structure may enhance stability and has implications for DNA recognition by extending the potential DNA-binding surface of a single zinc finger domain.

Amino Acid Sequence↗
PubMed1996

Towards an understanding of protein-DNA recognition.

Understanding how proteins recognize DNA in a sequence-specific manner is central to our understanding of the regulation of transcription and other cellular processes. In this article we review the principles of DNA recognition that have emerged from the large number of high-resolution crystal structures determined over the last 10 years. The DNA-binding domains of transcription factors exhibit surprisingly diverse protein architectures, yet all achieve a precise complementarity of shape facilitating specific chemical recognition of their particular DNA targets. Although general rules for recognition can be derived, the complex nature of the recognition mechanism precludes a simple recognition code. In particular, it has become evident that the structure and flexibility of DNA and contacts mediated by water molecules contribute to the recognition process. Nevertheless, based on known structures it has proven possible to design proteins with novel recognition specificities. Despite this considerable practical success, the thermodynamic and kinetic properties of protein/DNA recognition remain poorly understood.

Amino Acid Sequence↗
PubMed1996

The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA.

Telomeres, the nucleoprotein complexes at the ends of eukaryotic chromosomes, are essential for chromosome stability. In the yeast S. cerevisiae, telomeric DNA is bound in a sequence-specific manner by RAP1, a multifunctional protein also involved in transcriptional regulation. Here we report the crystal structure of the DNA-binding domain of RAP1 in complex with telomeric DNA site at 2.25 A resolution. The protein contains two similar domains that bind DNA in a tandem orientation, recognizing a tandemly repeated DNA sequence. The domains are structurally related to the homeodomain and the proto-oncogene Myb, but show novel features in their DNA-binding mode. A structured linker between the domains and a long C-terminal tail contribute to the binding specificity. This structure provides insight into the recognition of the conserved telomeric DNA sequences by a protein.

Amino Acid Sequence↗
PubMed1996

Detecting Discrimination: Analyzing Racial Disparities in Public Contracting

In City of Richmond v. J. A. Croson Co. (1989), the Supreme Court established strict scrutiny as the standard applicable to affirmative action programs which set aside quotas of public contracts for minority-owned businesses, and Aderand v. Pena (1995) extended the strict scrutiny standard to federal programs. Although the requirements of these decisions clearly require multivariate statistical analysis, most "disparity studies" have used a univariate comparison between the expected and the observed shares of contracts going to minority-owned firms. We examine four statistical methods-ordinary least square multiple regression, logit and tobit models, and a multivariate procedure for comparing expected and observed outcomes. Because no data are presently available at the level of specificity required by Croson, we constructed synthetic data sets to represent typical variations among large U.S. cities. Applying the statistical methods to each data set allows evaluation of the extent to which each method is able to both remove spurious and detect valid estimates of racial disparity when relevant control variables are added. Findings: (a) All four models removed apparent disparities which, although significant in univariate analysis, were known to be spurious. (b) Tobit and logit models, whose underlying assumptions better fit the nature of public contracting data, provided more accurate and more sensitive estimates than OLS regression. (c) Comparison of expected and observed outcomes within categories of control variables yielded results very similar to logit and tobit models and, because of the nature of the comparison specified in Croson, produced slightly more sensitive probability estimates.

Journal Article↗
PubMed1996

Betaine aldehyde dehydrogenase in sorghum.

The ability to synthesize and accumulate glycine betaine is wide-spread among angiosperms and is thought to contribute to salt and drought tolerance. In plants glycine betaine is synthesized by the two-step oxidation of choline via the intermediate betaine aldehyde, catalyzed by choline monooxygenase and betaine aldehyde dehydrogenase (BADH). Two sorghum (Sorghum bicolor) cDNA clones, BADH1 and BADH15, putatively encoding betaine aldehyde dehydrogenase were isolated and characterized. BADH1 is a truncated cDNA of 1391 bp. BADH15 is a full-length cDNA clone, 1812 bp in length, predicted to encode a protein of 53.6 kD. The predicted amino acid sequences of BADH1 and BADH15 share significant homology with other plant BADHs. The effects of water deficit on BADH mRNA expression, leaf water relations, and glycine betaine accumulation were investigated in leaves of preflowering sorghum plants. BADH1 and BADH15 mRNA were both induced by water deficit and their expression coincided with the observed glycine betaine accumulation. During the course of 17 d, the leaf water potential in stressed sorghum plants reached -2.3 MPa. In response to water deficit, glycine betaine levels increased 26-fold and proline levels increased 108-fold. In severely stressed plants, proline accounted for > 60% of the total free amino acid pool. Accumulation of these compatible solutes significantly contributed to osmotic potential and allowed a maximal osmotic adjustment of 0.405 MPa.

Aldehyde Oxidoreductases↗
PubMed1995

The oestrogen receptor recognizes an imperfectly palindromic response element through an alternative side-chain conformation.

BACKGROUND: Structural studies of protein-DNA complexes have tended to give the impression that DNA recognition requires a unique molecular interface. However, many proteins recognize DNA targets that differ from what is thought to be their ideal target sequence. The steroid hormone receptors illustrate this problem in recognition rather well, since consensus DNA targets are rare. RESULTS: Here we describe the structure, at 2.6 A resolution, of a complex between a dimer of the DNA-binding domain from the human oestrogen receptor (ERDBD) and a non-consensus DNA target site in which there is a single base substitution in one half of the palindromic binding site. This substitution results in a 10-fold increase in the dissociation constant of the ERDBD-DNA complex. Comparison of this structure with a structure containing a consensus DNA-binding site determined previously, shows that recognition of the non-consensus sequence is achieved by the rearrangement of a lysine side chain so as to make an alternative base contact. CONCLUSIONS: This study suggests that proteins adapt to recognize different DNA sequences by rearranging side chains at the protein-DNA interface so as to form alternative patterns of intermolecular contacts.

Amino Acid Sequence↗
PubMed1995

Telomere structure and function.

Telomeres, the termini of linear eukaryotic chromosomes, contain specific DNA sequences that are widely conserved. These sequences not only recruit telomere-specific proteins, but also give telomeric DNA the ability to fold into four-stranded DNA structures. Recent structural studies have shown that the repertoire of quadruplexes formed by the G-rich strand is larger than had been envisaged. Even more surprising is a novel four-stranded structure formed by the C-rich strand, called the i-tetraplex. Genetic and biochemical analyses have been used to identify proteins involved in telomeric DNA packaging and organization. The possibility that four-stranded structures may play a role in telomere function has been strengthened by the discovery that telomeric proteins can bind to and promote the formation of G-quadruplexes.

Base Sequence↗
PubMed1995

A practical approach to the evaluation and treatment of erectile dysfunction. A private practitioner's viewpoint.

There are many changes occurring in the delivery of health care that are economically impacting our urology practices. Certainly, the days of being primarily prostate and TURP doctors are over. Incorporating an impotence component in our practices is an effective method of filling the void left by treating BPH. Treating impotence will not require any significant additional equipment or staff. Not only are there opportunities within our own practices, there are thousands of men suffering from impotence in our communities who need our help and our expertise. Finally, using the two-visit technique, most men can be evaluated and begin a treatment program that will result in a successful resolution to their sexual problem in a cost-effective fashion.

Communication↗
PubMed1994

Promotion of parallel DNA quadruplexes by a yeast telomere binding protein: a circular dichroism study.

Repressor-activator protein 1 (RAP1) has an essential role in the maintenance of yeast telomeres. Yeast telomeric DNA consists of simple repeated G-rich sequences that are bound by RAP1. We have found that RAP1, in addition to its known binding activity for double-stranded DNA, interacts with the G-rich strand containing guanine base (G)-tetrads. We show here using circular dichroism spectroscopy that RAP1 promotes the formation of one particular type of DNA quadruplex, parallel G4-DNA. Furthermore, RAP1 is able to bind to both preformed parallel and antiparallel DNA quadruplexes. These results have implications for the possible use of DNA quadruplexes in telomere-telomere association in vivo.

Animals↗
PubMed1994

The yeast telomere-binding protein RAP1 binds to and promotes the formation of DNA quadruplexes in telomeric DNA.

The protein RAP1 is essential for the maintenance of the telomeres of Saccharomyces cerevisiae and binds in vitro to multiple sites found within the TG1-3 telomeric repeats. We show here that, in addition to its known binding activity for double-stranded DNA, RAP1 binds sequence-specifically to the GT-strands. This indicates that RAP1 is the protein that binds to the telomeric terminal GT-tails. Furthermore, we have found that RAP1 binds to and promotes the formation of G-tetrads, i.e. DNA quadruplexes, in GT-strand oligonucleotides at nanomolar concentrations. The formation of DNA quadruplexes appears to involve the intermolecular association of GT-strands. The minimal DNA-binding domain of RAP1 (DBD) binds only to double-stranded DNA, so that the novel DNA-binding activity we have found involves regions of the protein located outside of the DBD. The finding that a telomeric protein promotes the formation of G-tetrads argues for the use of DNA quadruplexes in telomere association.

Base Sequence↗
PubMed1994

Effects of inhibition of return on voluntary and visually guided saccades.

Four experiments examined the effects of inhibition of return on endogenously generated and visually guided saccades. In Experiments 1-3, subjects responded to a peripheral target by making either a prosaccade (toward the target) or an antisaccade (toward the field opposite the target). Prior to the appearance of the target, one of the two equiprobable target locations was activated by presenting a peripheral precue (Experiments 1 and 2), or by executing an endogenous saccade in response to a central precue (Experiment 3). In Experiment 1, the eyes remained fixed when the cue appeared; in Experiment 2 subjects made a saccade to the peripheral cue, and returned their eyes to the centre before the target appeared. In both experiments, saccade latencies were longer for targets appearing at the precued location for both prosaccade and antisaccade tasks. In Experiment 3, saccade latencies were longer for targets appearing at the precued location only in the prosaccade task; no effect of the precue was obtained in the antisaccade task. These results suggest that endogenously generated saccades activate both an inhibition of target detection and a motor alternation bias. Experiment 4 showed that inhibition of return generated by a peripheral precue increased the latency for a subsequent endogenous saccade (from a central, arrow target) toward the precued location. Inhibition of return may affect perceptual processing and also produce a motor alternation bias dependent upon whether it is activated exogenously or endogenously.

Attention↗
PubMed1994

Extracellular matrix constituents affect superficial gastric epithelial cell adhesion.

The interfoveolar and upper gastric pit cells become necrotic and slough off after superficial luminal injury to the gastric mucosa. The subsequent rapid epithelial restitution of the wound is dependent on an intact basal lamina upon which viable mucous cells migrate. Several lines of evidence suggest that migrating mucous cells recognize specific moieties in the basal lamina which would then affect restitution and the ability of the gastric mucosa to be repaired. Therefore, this study examined the effect of three individual protein constituents of the extracellular matrix, laminin, fibronectin and type IV collagen as well as a synthetic basal lamina, Matrigel, on adherence of mucous cells isolated from guinea-pig stomach to these substrates in culture. After 3 h, approximately 40% of the cells adhered to Matrigel, 25% to both collagen IV and fibronectin, but only about 10% to laminin and 3% to uncoated plastic substrates. Disruption of protein synthesis by pre-incubation with cyclohexamide significantly reduced adherence to Matrigel and collagen IV but not laminin, fibronectin or plastic substrates. These results suggest that gastric mucous cells have multiple receptors for extracellular matrix proteins (ligands) which influence the adherence and probably the migration of these cells. Furthermore, some of these receptors are synthesized in response to moieties in the substrate itself.

Animals↗
PubMed1993

The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition.

The Cys2-His2 zinc-finger is the most widely occurring DNA-binding motif. The first structure of a zinc-finger/DNA complex revealed a fairly simple mechanism for DNA recognition suggesting that the zinc-finger might represent a candidate template for designing proteins to recognize DNA. Residues at three key positions in an alpha-helical 'reading head' play a dominant role in base-recognition and have been targets for mutagenesis experiments aimed at deriving a recognition code. Here we report the structure of a two zinc-finger DNA-binding domain from the protein Tramtrack complexed with DNA. The amino-terminal zinc-finger and its interaction with DNA illustrate several novel features. These include the use of a serine residue, which is semi-conserved and located outside the three key positions, to make a base contact. Its role in base-recognition correlates with a large, local, protein-induced deformation of the DNA helix at a flexible A-T-A sequence and may give insight into previous mutagenesis experiments. It is apparent from this structure that zinc-finger/DNA recognition is more complex than was originally perceived.

Amino Acid Sequence↗
PubMed1993

DNA recognition by the oestrogen receptor: from solution to the crystal.

BACKGROUND: The steroid/nuclear hormone receptors are a large family of conserved ligand-activated transcription factors that regulate gene expression through binding to response elements upstream of their target genes. Most members of this family bind to DNA as homodimers or heterodimers and recognize the sequence, spacing and orientation of the two half-sites of their response elements. The recognition and discrimination of the sequence and arrangements of these half-sites are mediated primarily by a highly conserved DNA-binding domain. RESULTS: Here we describe the DNA-binding properties of the isolated DNA-binding domain of the oestrogen receptor, the ERDBD, and its refined NMR structure. This domain is monomeric in solution, but two molecules bind cooperatively to specific DNA sequences; this cooperativity determines the arrangement of half-sites that is recognized by the ERDBD. The 10 carboxy-terminal residues and a region of 15 residues within the domain are disordered in the solution structure, yet are important for DNA binding. CONCLUSION: The cooperative nature of ERDBD binding to DNA is important. The previously-determined X-ray structure of the ERDBD dimer bound to DNA shows that the 15 internal residues disordered in solution make contact both with DNA and with the corresponding region of the other monomer. These results suggest that these residues become ordered during the process of binding to DNA, forming the dimer interface and thus contributing to the cooperative interaction between monomers.

Amino Acid Sequence↗
PubMed1993

The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements.

The nuclear hormone receptors are a superfamily of ligand-activated DNA-binding transcription factors. We have determined the crystal structure (at 2.4 A) of the fully specific complex between the DNA-binding domain from the estrogen receptor and DNA. The protein binds as a symmetrical dimer to its palindromic binding site consisting of two 6 bp consensus half sites with three intervening base pairs. This structure reveals how the protein recognizes its own half site sequence rather than that of the related glucocorticoid receptor, which differs by only two base pairs. Since all nuclear hormone receptors recognize one or the other of these two consensus half site sequences, this recognition mechanism applies generally to the whole receptor family.

Amino Acid Sequence↗
PubMed1993

Distortion of the DNA double helix by RAP1 at silencers and multiple telomeric binding sites.

Repressor Activator Protein 1 (RAP1) is an essential nuclear protein of the yeast Saccharomyces cerevisiae that recognizes a 13 base-pair (bp) consensus sequence found in numerous upstream activating sequences, at the silencers of transcriptionally repressed mating-type genes, and in telomeric tracts, called (C1-3 A) repeats. RAP1 has been shown to influence transcriptional activation, transcriptional repression, telomere length, circular plasmid segregation and meiotic recombination in vivo. We have studied the structure of the protein-DNA complex reconstituted in vitro with highly purified RAP1, by using DNase I and chemical footprinting. Both full-length RAP1 and its minimal DNA-binding domain of roughly 30 kDa, induce a distortion within the 13 bp recognition site, as demonstrated by reactivity to KMnO4 primarily at nucleotides 8 and 10 in the binding consensus Rc/AAYCCRYNCAYY. Dimethylsulphate reactivity shows that RAP1 binding does not create unpaired regions at its binding site, although the DNA may be locally underwound or aberrantly base-paired at the permanganate reactive nucleotides. In addition to the permanganate-sensitive distortion, the full-length RAP1, but not its DNA-binding domain, induces a bend in DNA 5' of the recognition sequence, altering the electrophoretic mobility of the protein-DNA complex. The KMnO4-reactivity has allowed a precise mapping of RAP1 molecules on telomeric DNA, revealing RAP1 sites as frequently as one per 18 bp of telomeric DNA, or potentially 20 RAP1 molecules bound per average telomeric tract of 370 bp. This suggests that RAP1 plays a major role in organizing yeast telomeres, and is consistent with recently published immunofluorescence studies showing a major fraction of RAP1 at the ends of meiotic chromosomes.

Amino Acid Sequence↗