Tektins as structural determinants in basal bodies

Tektins, present as three equimolar 47-55 kDa protein components, form highly insoluble protofilaments that are integral to the junctional region of outer doublet microtubules in cilia and flagella. To identify and quantify tektins in other compound microtubules such as centrioles or basal bodies, a rabbit antiserum was raised against tektin filaments isolated from Spisula solidissima (surf clam) sperm flagellar outer doublets and affinity-purified with nitrocellulose blot strips of tektins resolved by SDS- or SDS-urea-PAGE. These antibodies recognized analogous tektins in axonemes of organisms ranging from ctenophores to higher vertebrates. Quantitative immunoblotting established that outer doublet tektins occur in a 1:17 weight ratio to tubulin. Cilia and basal apparatuses were prepared from scallop gill epithelial cells; cilia and deciliated cells were prepared from rabbit trachea. Tektins were detected by immunoblotting in basal body-enriched preparations while tektins were localized to individual basal bodies by immunofluorescence. Supported by greater fluorescence in basal bodies than in adjacent axonemes in tracheal cells, analysis of basal apparatuses demonstrated both a proportionately greater ratio of tektin to tubulin (approximately 1:13) and two distinct solubility classes of tektins, consistent with tektins comprising the B-C junction of triplets in addition to the A-B junction as in doublets.     

Dispositional and structural determinants of volunteerism.

The dispositional and structural correlates of volunteerism were examined in a panel study. AIDS service organization volunteers answered questions about affect toward the organization, organizational commitment, motives for volunteering, and a prosocial personality orientation. These measures were used to predict 4 volunteer-related behaviors. Length of service was weakly correlated with the 3 other volunteer behaviors. Altruistic motives and prosocial personality characteristics predicted several of the volunteer behaviors. Initial levels of volunteer activity and organizational commitment also predicted final levels of volunteer activity, but these effects were mediated through intermediate levels of volunteer activities. The findings are discussed within the context of the volunteer process model and role identity models of volunteerism. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Structural determinants of progesterone hydroxylation by cytochrome P450 2B5: the role of nonsubstrate recognition site residues

The enzymic interconversion of Escherichia coli isocitrate dehydrogenase (ICDH) between the catalytically active and inactive forms is mediated through the activities of ICDH-kinase/phosphatase in response to changes in the metabolic environment. In this study, the use of mutant strains devoid of isocitrate lyase (aceA:: Tn10) and pyruvate dehydrogenase activities revealed that the signal which triggers the reversible inactivation of ICDH in vivo is not directly related to acetate itself, but rather to the need to maintain high intracellular levels of isocitrate and free co-enzyme A. The use of these mutants also revealed, rather unexpectedly, that acetate grown cells contain more ICDH protein than those grown with other carbon sources and that the catalytic activity of ICDH kinase/phosphatase is in excess of cellular demands. Furthermore, this study also revealed the presence of a 50-kDa (+/- 2 kDa) acetate-specific polypeptide, the identity of which has yet to be established.     

Importance of residues carboxyl terminal relative to the cleavage site in substrates of mitochondrial processing peptidase for their specific recognition and cleavage

We previously identified distal and proximal arginine residues in the N-terminal portion and an aromatic amino acid at position 1 (P1' site3) relative to the cleavage site as important recognition signals in substrates of mitochondrial processing peptidase [Niidome, T., Kitada, S., Shimokata, K., Ogishima, T., and Ito, A. (1994) J. Biol. Chem. 269, 24714-24722; Ogishima, T., Niidome, T., Shimokata, K., Kitada, S., and Ito, A. (1995) ibid. 270, 30322-30326]. To further elucidate the elements required for the specific recognition and cleavage by the enzyme, we synthesized synthetic peptides that possessed only the distal and proximal arginine residues and phenylalanine at the P1' site in a poly alanine sequence, and analyzed the processing reaction toward them. They were not cleaved by the peptidase although they inhibited the peptidase activity. However, when serine was introduced into the C-terminal portions of the sequence, processing was observed. The efficiency of the resultant peptides improved as the number of serine residues was increased. A peptide with serine or histidine at P2' and threonine at P3' was processed most efficiently. These results indicate that the processing reaction catalyzed by the peptidase depends not only on the N-terminal portion but also on the C-terminal portion from the cleavage site in the substrates.     

Minimal molecular determinants of substrates for recognition by the intestinal peptide transporter

Proton-dependent electrogenic transporters for di- and tripeptides have been identified in bacteria, fungi, plants, and mammalian cells. They all show sequence-independent transport of all possible di- and tripeptides as well as of a variety of peptidomimetics. We used the mammalian intestinal peptide transporter PEPT1 as a model to define the molecular basis for its multisubstrate specificity. By employing computational analysis of possible substrate conformations in combination with transport assays using transgenic yeast cells and Xenopus laevis oocytes expressing PEPT1, the minimal structural requirements for substrate binding and transport were determined. Based on a series of medium chain fatty acids bearing an amino group as a head group (omega-amino fatty acids, omega-AFA), we show that electrogenic transport by PEPT1 requires as a minimum the two ionized head groups separated by at least four methylene groups. Consequently, a > 500 pm < 630 pm distance between the two charged centers (carboxylic carbon and amino nitrogen) is sufficient for substrate recognition and transport. Removal of either the amino group or the carboxyl group in omega-AFA maintained the affinity of the compound for interaction with the transporter but abolished the capability for electrogenic transport. Additional groups in the omega-AFA backbone that provide more hydrogen bonding sites appear to increase substrate affinity but are not essential. The information provided here does (a) explain the capability of the peptide carrier for sequence-independent transport of thousands of different substrates and (b) set the molecular basis for a rational drug design to increase the absorption of peptide-based drugs mediated by PEPT1.     

High resolution footprinting of a type I methyltransferase reveals a large structural distortion within the DNA recognition site

The type I DNA methyltransferase M.EcoR124I is a multi-subunit enzyme that binds to the sequence GAAN6RTCG, transferring a methyl group from S-adenosyl methionine to a specific adenine on each DNA strand. We have investigated the protein-DNA interactions in the complex by DNase I and hydroxyl radical footprinting. The DNase I footprint is unusually large: the protein protects the DNA on both strands for at least two complete turns of the helix, indicating that the enzyme completely encloses the DNA in the complex. The higher resolution hydroxyl radical probe shows a smaller, but still extensive, 18 bp footprint encompassing the recognition site. Within this region, however, there is a remarkably hyper-reactive site on each strand. The two sites of enhanced cleavage are co-incident with the two adenines that are the target bases for methylation, showing that the DNA is both accessible and highly distorted at these sites. The hydroxyl radical footprint is unaffected by the presence of the cofactor S-adenosyl methionine, showing that the distorted DNA structure induced by M.EcoR124I is formed during the initial DNA binding reaction and not as a transient intermediate in the reaction pathway.     

Fine structural specificity differences of trimethoprim allergenic determinants

BACKGROUND: Adverse reactions, including immediate hypersensitivity, to the widely used antibacterial agent trimethoprim occur quite frequently. In recent years some progress has been made in developing an immunoassay to aid diagnosis of type 1 allergic reactions to trimethoprim and to define the basis of IgE antibody recognition of the drug. OBJECTIVES: The molecular basis of IgE binding to trimethoprim was examined more closely with a view to defining the fine structural recognition differences between patient's sera. Utilization of such information may lead to immunoassays that are more specific and sensitive and of greater diagnostic value. METHODS: Immunoassays for specific IgE antibodies and quantitative hapten inhibition studies with trimethoprim and selected structural analogues were employed, together with sera from eight subjects clearly defined clinically as allergic to trimethoprim. RESULTS: Three different allergenic determinant structures have been identified on the trimethoprim molecule. Identification of the 3,4-dimethoxybenzyl group as a determinant was achieved on the basis of inhibitory activities of diaveridine, 3,4-dimethoxyphenylethylamine, 3,4-dimethoxybenzoic acid and 3,4,5-trimethoxycinnamic acid. Evidence that the opposite end of the trimethoprim molecule was not being recognized was obtained from results with some pyrimidine derivatives, each of which showed no activity. Identification of the second determinant, the 2,4-diamino-5-(3',4'-dimethoxybenzyl) pyrimidine group, rested mainly on the superior inhibitory potency of diaveridine, which differs from trimethoprim by just one methoxy group. With sera from some trimethoprim-allergic subjects, only trimethoprim was active, suggesting that the entire molecule was a third IgE-binding determinant structure. CONCLUSION: As with other drug allergenic determinants defined so far, heterogeneity of trimethoprim IgE-binding determinants exists, and fine structural differences between determinants may be as small as a single methoxy group. Identification of the 2,4-diamino-5-(3',4'-dimethoxybenzyl) pyrimidine group as an allergenic determinant increases the number of known trimethoprim determinants to three, and suggests that the number and heterogeneity of determinants will be a reflection of the number of allergic subjects studied.     

A structural explanation for the recognition of tyrosine-based endocytotic signals

Many cell surface proteins are marked for endocytosis by a cytoplasmic sequence motif, tyrosine-X-X-(hydrophobic residue), that is recognized by the mu2 subunit of AP2 adaptors. Crystal structures of the internalization signal binding domain of mu2 complexed with the internalization signal peptides of epidermal growth factor receptor and the trans-Golgi network protein TGN38 have been determined at 2.7 angstrom resolution. The signal peptides adopted an extended conformation rather than the expected tight turn. Specificity was conferred by hydrophobic pockets that bind the tyrosine and leucine in the peptide. In the crystal, the protein forms dimers that could increase the strength and specificity of binding to dimeric receptors.     

Study on site specific cleavage of RNA

The precursor of an RNA molecule from bacteriophage T4 infected Escherichia coli cell (p2Sp1 RNA) has the ability to cleave itself. It has been found that the site specific RNA cleavage reaction occurred at the pyridine-adenosine sequence in the presence of a monovalent cation and a non-ionic detergent. In order to investigate the mechanism of this cleavage reaction, we designed a RNA oligonucleotide (UUUAUU) and this RNA was cleavage activity at the U-A sequence.     

An atypical homeodomain in SATB1 promotes specific recognition of the key structural element in a matrix attachment region

SATB1 is a cell type-specific nuclear matrix attachment region (MAR) DNA-binding protein, predominantly expressed in thymocytes. We identified an atypical homeodomain and two Cut-like repeats in SATB1, in addition to the known MAR-binding domain. The isolated MAR-binding domain recognizes a certain DNA sequence context within MARs that is highly potentiated for base unpairing. Unlike the MAR-binding domain, the homeodomain when isolated binds poorly and with low specificity to DNA. However, the combined action of the MAR-binding domain and the homeodomain allows SATB1 to specifically recognize the core unwinding element within the base-unpairing region. The core unwinding element is critical for MAR structure, since point mutations within this core abolish the unwinding propensity of the MAR. The contribution of the homeodomain is abolished by alanine substitutions of arginine 3 and arginine 5 in the N-terminal arm of the homeodomain. Site-directed mutagenesis of the core unwinding element in the 3' MAR of the immunoglobulin heavy chain gene enhancer revealed the sequence 5'-(C/A)TAATA-3' to be essential for the increase in affinity mediated by the homeodomain. SATB1 may regulate T-cell development and function at the level of higher order chromatin structure through the critical DNA structural elements within MARs.     

Functional requirements for specific ligand recognition by a biotin-binding RNA pseudoknot

Ligand-binding RNAs and DNAs (aptamers) isolated by in vitro selection from random sequence pools provide convenient model systems for understanding the basic relationships between RNA structure and function. We describe a series of experiments that define the functional requirements for an RNA motif that specifies high-affinity binding to the carboxylation cofactor biotin. A simple pseudoknot containing an adenosine-rich loop accounts for binding in all independently derived aptamers selected to bind biotin, suggesting that it alone represents a global optimum for recognition of this particular nonaromatic, electrostatically neutral ligand. In contrast to virtually all previously identified aptamers, unpaired nucleotides make up a small fraction of the binding motif. Instead, the identity of 14 nucleotides involved in base pairing is highly conserved among functional clones and their substitution by nonidentical base pairs significantly reduces or eliminates binding. Chemical probing is consistent with the predicted pseudoknot motif and indicates that relatively little change in structure accompanies ligand binding, a strong contrast with results for other aptamers. Competition experiments suggest that the aptamer recognizes all parts of the biotin ligand, including its thiophane ring and fatty acid tail. Two alternative modes of binding are suggested by a three-dimensional model of the pseudoknot, both of which entail significant interactions with base-paired nucleotides.     

Idiodynamic sets as determinants of children's false recognition errors.

Reports 2 experiments in which the object-referent and dimension-referent response sets identified from the word association data of children were used to investigate the basis for false recognition errors by kindergartners and by 2nd and 6th grade Ss (n = 32 each). Word association data from these Ss were consistent with previous findings, validating the developmental changes in the dominant dimensions of associative organization. The false recognition data involving object-referent associations paralleled the word association data, but the results for dimension-referent associations did not. Instead, kindergartners made more errors to dimension-referent than to object-referent associates, and there was a significant decrease in the number of errors to both types of associates with increasing age. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Characterization of a specific binding site for angiotensin II in chicken liver

We have characterized a specific binding site for angiotensin II (AngII) in chicken liver membranes. Pseudo-equilibrium studies at 22 degrees C for 30 min have shown that this binding site recognizes AngII with a high affinity (pKD of 8.13 +/- 0.21). The binding sites are saturable and relatively abundant (maximal binding capacity varies from 0.318 to 0.88 pmol/mg of protein). Nonequilibrium kinetic analyses at 22 degrees C revealed a calculated kinetic pKD of 8.77 +/- 0.20. The binding site is pharmacologically distinct from the classic AngII receptors AT1 and AT2. Competitive binding studies with chicken liver membranes demonstrated the following rank order of effectiveness: AngII (human; Asp-Arg-Val-Tyr-Ile-His-Pro-Phe) > AngI(Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-His-Leu) > AngIII(Arg-Val-Tyr-Ile-His-Pro-Phe) > AngIV (Val-Tyr-Ile-His-Pro-Phe) > Ang(1-7) (Asp-Arg-Val-Tyr-Ile-His-Pro) > PD123319 (1-[4(dimethylamino)3-methylphenyl] methyl-5-(diphenylacetyl)-4,5,6,7-tetrahydro-1H-imidazo [4,5-c]pyridine-6-carboxylic acid) > DuP753 (2-n-butyl-4-chloro-5 hydroxymethyl-1-[(2'-1H-tetrazol-5-yl)biphenyl-4-yl)methyl] imidazole. This atypical AngII binding site (chicken AT) was sensitive to increasing concentrations of DTT and Mn2+. The structure-activity relationship on position 1 of AngII showed that the primary N-terminal amine was essential for binding affinity ([Asp1]AngII > [Suc1]AngII > or = [Sar1]AngII), but modifications of the side chain in position 1 had less influence on the affinity ([Gly1]AngII > [Cys1]AngII approximately [aminoisobutyryl1]AngII approximately [Ser1]AngII > > > [Sar1]AngII). The presence of substantial quantities of this binding site in chicken liver membranes suggests the possibility that the chicken AT may play an important, yet unrecognized, role in the renin-angiotensin system.     

Translation eukaryotic initiation factor 4G recognizes a specific structural element within the internal ribosome entry site of encephalomyocarditis virus RNA

A complex of eukaryotic initiation factors (eIFs) 4A, 4E, and 4G (collectively termed eIF4F) plays a key role in recruiting mRNAs to ribosomes during translation initiation. The site of ribosomal entry onto most mRNAs is determined by interaction of the 5'-terminal cap with eIF4E; eIFs 4A and 4G may facilitate ribosomal entry by modifying mRNA structure near the cap and by interacting with ribosome-associated factors. eIF4G recruits uncapped encephalomyocarditis virus (EMCV) mRNA to ribosomes without the involvement of eIF4E by binding directly to the approximately 450-nucleotide long EMCV internal ribosome entry site (IRES). We have used chemical and enzymatic probing to map the eIF4G binding site to a structural element within the J-K domain of the EMCV IRES that consists of an oligo(A) loop at the junction of three helices. The oligo(A) loop itself is not sufficient to form stable complexes with eIF4G since alteration of its structural context abolished its interaction with eIF4G. Addition of wild type or trans-dominant mutant forms of eIF4A to binary IRES.eIF4G complexes did not further alter the pattern of chemical/enzymatic modification of the IRES.     

Semantic and visual determinants of face recognition in a prosopagnosic patient

Prosopagnosia is the neuropathological inability to recognize familiar people by their faces. It can occur in isolation or can coincide with recognition deficits for other nonface objects. Often, patients whose prosopagnosia is accompanied by object recognition difficulties have more trouble identifying certain categories of objects relative to others. In previous research, we demonstrated that objects that shared multiple visual features and were semantically close posed severe recognition difficulties for a patient with temporal lobe damage. We now demonstrate that this patient's face recognition is constrained by these same parameters. The prosopagnosic patient ELM had difficulties pairing faces to names when the faces shared visual features and the names were semantically related (e.g., Tonya Harding, Nancy Kerrigan, and Josee Chouinard -three ice skaters). He made tenfold fewer errors when the exact same faces were associated with semantically unrelated people (e.g., singer Celine Dion, actress Betty Grable, and First Lady Hillary Clinton). We conclude that prosopagnosia and co-occurring category-specific recognition problems both stem from difficulties disambiguating the stored representations of objects that share multiple visual features and refer to semantically close identities or concepts.     

Amsacrine-promoted DNA cleavage site determinants for the two human DNA topoisomerase II isoforms alpha and beta

Site-specific DNA cleavage by topoisomerase II (EC 5.99.1.3) is induced by many antitumour drugs. Although human cells express two genetically distinct topoisomerase II isoforms, thus far the role and determinants of drug-induced DNA cleavage have been examined only for alpha. Here we report the first high-resolution study of amsacrine (mAMSA) induced DNA breakage by human topoisomerase II beta (overexpressed and purified from yeast) and a direct comparison with the recombinant alpha isoform. DNA cleavage in plasmid pBR322 and SV40 DNA was induced by alpha or beta in the absence or presence of the antitumour agent mAMSA, and sites were mapped using sequencing gel methodology. Low-resolution studies indicated that recombinant human alpha promoted DNA breakage at sites akin to those of beta, although some sites were only cleaved by one enzyme and different intensities were observed at some sites. However, statistical analysis of 70 drug-induced sites for beta and 70 sites for alpha revealed that both isoforms share the same base preferences at 13 positions relative to the enzyme cleavage site, including a very strong preference for A at +1. The result for recombinant alpha isoform is in agreement with previous studies using alpha purified from human cell lines. Thus, alpha and beta proteins apparently form similar ternary complexes with mAMSA and DNA. Previous studies have emphasized the importance of DNA topoisomerase II alpha; the results presented here demonstrate that beta is an in vitro target with similar site determinants, strongly suggesting that beta should also be considered a target of mAMSA in vivo.     

Common and specific determinants for fibroblast growth factors in the ectodomain of the receptor kinase complex

The assembly and activation of oligomeric complexes of FGF, the transmembrane receptor kinase (FGFR), and heparan sulfate transmit intracellular signals regulating growth and function of cells. An understanding of the structural relationships between the three subunits and their redundancy and specificity is essential for understanding the ubiquitous FGF signaling system in health and disease. Previously, we reported that a primary heparin or heparan sulfate binding site resides in a distinct sequence in immunoglobulin (Ig)-like module II of the three modules of FGFR. Here we report that in the absence of flanking sequences, isolated Ig module II of FGFR1 supports the binding of FGF-1, FGF-2, and FGF-7 in respective order of affinity. None of the three FGFs detectably bind Ig module I or the IIIb and IIIc splice variants of Ig module III in the absence of flanking sequences. Ig module I and the C-terminus of Ig module III are dispensable for high-affinity binding of FGF-1, FGF-2, and FGF-7. Alterations in highly conserved Ig module II in the heparin binding domain and substitution of individual sequence domains spanning the entire sequence of Ig module II with those from Ig module I obliterated FGF binding. Addition of a specific number of FGFR sequences to the C-terminus of Ig module II resulted in a gain in affinity for FGF-7. Several site-specific alterations in the C-terminus of full-length FGFR1IIIc, an isoform that otherwise absolutely rejects FGF-7, resulted in gain of FGF-7 binding. These results suggest that a complex of Ig module II and heparan sulfate is the base common active core of the FGFR ectodomain and that flanking structural domains modify FGF affinity and determine specificity.