Biomedical subjects

T Pan

Publications and source records attributed to T Pan.

At least 91 records · Page 5Linked to original sources

PubMed1996

Domain structure of the ribozyme from eubacterial ribonuclease P.

Large RNAs can be composed of discrete domains that fold independently. One such "folding domain" has been identified previously in the ribozyme from Bacillus subtilis ribonuclease P (denoted P RNA). This domain contains roughly one-third of all residues. Folding of an RNA construct consisting of the remaining two-thirds of B. subtilis P RNA was examined by Fe(II)-EDTA hydroxyl radical protection. This molecule folds into the proper higher-order structure under identical conditions as the full-length P RNA, suggesting the presence of a second folding domain in B. subtilis P RNA. Folding analysis of the Escherichia coli P RNA by hydroxyl radical protection shows that this P RNA is completely folded at 5-6 mM Mg2+. In order to analyze the structural organization of folding domains in E. coli P RNA, constructs were designed based on the domain structure of B. subtilis P RNA. Fe(II)-EDTA protection indicates that E. coli P RNA also contains two folding domains. Despite the significant differences at the secondary structure level, both P RNAs appear to converge structurally at the folding domain level. The pre-tRNA substrate, localized in previous studies, may bind across the folding domains with the acceptor stem/3'CCA contacting the domain including the active site and the T stem-loop contacting the other. Because all eubacterial P RNAs share considerable homology in secondary structure to either B. subtilis or E. coli P RNA, these results suggest that this domain structure may be applicable for most, if not all, eubacterial P RNAs. Identification of folding domains should be valuable in dissecting structure-function relationship of large RNAs.

Bacillus subtilis↗

PubMed1996

Effects of continuous infusion fentanyl citrate on cerebrovascular and systemic prostanoids in postsurgical newborn piglets.

BACKGROUND: Newborns admitted to the intensive care unit undergo multiple painful procedures. Fentanyl citrate (FC) is one of the most commonly used drugs for pain relief in the newborn. Although it has been reported that one of the biological effects of fentanyl is hemodynamic stability, the response of systemic and/or cerebrovascular prostanoids to FC infusions have not been studied. METHODS: To examine the effects of continuous intravenous (IV) infusion of FC on systemic and cerebrovascular prostanoid concentrations, two groups of spontaneously breathing newborn piglets (1-3 days old) were studied. The study group (n = 6) and the control group (n = 8) were respectively given a loading dose of 30 micrograms/kg IV over 15 minutes, immediately followed by a continuous IV infusion of 10 micrograms/kg/hr for 6 hours, or a placebo (PB) solution of 5% dextrose in a similar fashion. Cerebrospinal fluid (0.5 mL) from cisterna magna puncture and blood samples (1.0 mL) from the sagittal sinus vein and carotid artery were collected serially before and after FC or PB infusion for drug and PG determinations. FC was measured by high pressure liquid chromatography (HPLC), and the prostanoids were measured using enzyme immunoassay (EIA) kits. RESULTS: FC infusion induced marked elevations in 6-ketoPGF1 alpha (300%, p < 0.001) and TXB2 (150%, p < 0.001) at 30 minutes, and remained elevated up to 2 hours of infusion. In addition, systemic 6-ketoPGF1 alpha increased by 180% (p < 0.001) and PGE2 concentrations fell dramatically at 30 minutes (87%, p < 0.001) and did not return to normal levels during the infusion time (83% to 81%, p < 0.001 to p < 0.01). CSF 6-ketoPGF1 alpha and TXB2 levels increased by 152% and 80%, respectively (p < 0.001), but PGE2 decreased by 76% (p < 0.001), at 6 hours of infusion. An inverse relationship existed between FC, and sagittal sinus PGE2 levels (r = 0.46, p < 0.03) and systemic PGE2 levels (r = 0.602, p < 0.02). CONCLUSION: The data suggest FC is rapidly transported across the blood brain barrier and the effects on cerebrovascular prostanoids, particularly PGE2 is rapid and prolonged. PGE2 appears to be the primary responsive prostanoid. The magnitude of the response, as evidenced by the early and sharp reductions in systemic and cerebrovascular concentrations, suggest vasoconstriction, with possible adverse effects on organ blood flow and metabolic activity. However, further studies are required to evaluate the effects on organ blood flow and metabolism.

Analgesics, Opioid↗

PubMed1995

Probing of tertiary interactions in RNA: 2'-hydroxyl-base contacts between the RNase P RNA and pre-tRNA.

A general method has been developed to analyze all 2' hydroxyl groups involved in tertiary interactions in RNA in a single experiment. This method involves comparing the activity of populations of circularly permuted RNAs that contain or lack potential hydrogen-bond donors at each position. The 2' hydroxyls of the pre-tRNA substrate identified as potential hydrogen bond donors in intermolecular interactions with the ribozyme from eubacterial RNase P (P RNA) are located in the T stem and T loop, acceptor stem, and 3' CCA regions. To locate the hydrogen-bond acceptors for one of those 2' hydroxyls in the P RNA, a phylogenetically conserved adenosine was mutated to a guanosine. When this mutant P RNA was used, increased cleavage activity of a single circularly permuted substrate within the population was observed. The cleavage efficiency (kcat/Km) of a singly 2'-deoxy-substituted substrate at this position in the T stem was also determined. For the wild-type P RNA, the catalytic efficiency was significantly decreased compared with that of the all-ribo substrate, consistent with the notion that this 2' hydroxyl plays an important role. For the P RNA mutant, no additional effect was found upon 2'-deoxy substitution. We propose that this particular 2' hydroxyl in the pre-tRNA interacts specifically with this adenosine in the P RNA. This method should be useful in examining the role of 2' hydroxyl groups in other RNA-RNA and RNA-protein complexes.

Adenosine↗

PubMed1995

Novel RNA substrates for the ribozyme from Bacillus subtilis ribonuclease P identified by in vitro selection.

Novel RNA substrates for the ribozyme from Bacillus subtilis ribonuclease P (P RNA) have been obtained by in vitro selection. The selection method involves cleavage of a circular RNA library by the P RNA, isolation of the linear cleavage product, and regeneration of circular RNA to allow amplification and multiple cycles of selection. The use of circular RNA ensures that potential substrates can be selected without restricted location of the cleavage site. Such a selection method has been used previously to isolate RNA motifs that undergo autolytic cleavage with Pb2+ [Pan, T., & Uhlenbeck, O. (1992) Biochemistry 31, 3887-3895]. The circular RNA pool after eight cycles of selection was cleaved by the B. subtilis P RNA as efficiently as a pre-tRNA(Phe) substrate, estimated to be more than 10 orders of magnitude better than the unselected RNA library. Kinetic analysis of individual variants showed that the kcat/KM of the selected RNA was up to 4-fold higher than that of the pre-tRNA(Phe). When cleavage was carried out with Escherichia coli P RNA, the selected RNA was 10-60-fold less reactive than the reaction of the pre-tRNA(Phe). Two distinct classes of variants are selected, both of which appear to differ significantly from the known P RNA substrates. Terminal truncation experiments suggest that a large number of nucleotides in the class I variants can be deleted without affecting the cleavage activity. The resulting minimal class I substrates contain a short stem-loop with no other apparent helical structures. The class II substrates are cleaved within a putative helical stem that is formed entirely by the primer sequences.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed1995

Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P.

Folding of the ribozyme from Bacillus subtilis ribonuclease P (denoted P RNA) has been examined by Fe(II)-EDTA protection and bimolecular association. Fe(II)-EDTA results show that, in the presence of Mg2+, P RNA is folded into a core structure which includes most of the phylogenetically conserved nucleotides. Folding is cooperative and is complete at 5-6 mM Mg2+ with the [Mg2+]1/2 at 2-3 mM. The Hill constant indicates that this folding transition requires binding of at least three additional Mg2+ ions. Two RNA molecules consisting of nucleotides 62-239 [p(62-239)] and 240-401 + 1-61 [p(240-61)] of the B. subtilis P RNA have been constructed. These RNAs can in principle form the catalytically active structure primarily, if not solely, through tertiary interactions. Although either molecule by itself is inactive, the bimolecular complex is as active as the circularly permuted P RNAs from which it is derived. The binding constant of the complex can be as low as 0.1 microM and is strongly dependent on Mg2+ and K+ concentrations. Association of these molecules also induces a Mg2+ dependent cleavage at nucleotide 103 in p(62-239). p(62-239) gives a Fe(II)-EDTA protection pattern very similar to the wild-type P RNA at identical Mg2+ concentrations. However, Fe(II)-EDTA protection in p(240-61) is completely lost, even though it contains many nucleotides that are conserved among all P RNAs. These results suggest that, like other RNAs, P RNA contains domains that can fold in the absence of the rest of the molecule. The implications of these results are discussed in the context of the P RNA structure and catalysis.

Bacillus subtilis↗

PubMed1995

9-cis-retinoic acid is more effective than all-trans-retinoic acid in upregulating expression of the alpha-fetoprotein gene.

In McA-RH 8994 rat hepatoma cells, all-trans-retinoic acid (t-RA) induces expression of the alpha-fetoprotein (AFP) and albumin genes and results in a phenotype similar to differentiated fetal hepatocytes. The present study elucidated the mechanism involved in AFP gene regulation mediated by retinoic acid. Northern blot analyses demonstrated that 9-cis-retinoic acid (c-RA), a ligand for retinoid x receptors (RXRs), also induced expression of the AFP gene in McA-RH 8994 cells. The induction was time- and dose-dependent. Northern blots and transfection assays using the 7.3 kb full-length regulatory region of the AFP gene demonstrated that c-RA was more effective than t-RA in regulating expression of the AFP gene. At 10(-7) M, c-RA increased AFP mRNA 5-fold and chloramphenicol acetyltransferase (CAT) activity 2.5-fold. In contrast, t-RA at a concentration of 10(-7) M exerted no significant effect; 10(-6) to 10(-5) M t-RA was needed to affect AFP gene expression. These data suggested that activation of RXRs is essential for the regulation of the AFP gene. Co-transfection experiments revealed that over-expression of RXR alpha in McA-RH 8994 cells further enhanced the CAT activity induced by c-RA. In addition, c-RA did not alter the half-life of AFP mRNA. Thus, RXR alpha may play a crucial role in transcriptional regulation of the AFP gene and in controlling hepatocyte phenotype.

Animals↗

PubMed1994

Selection of circularly permuted ribozymes from Bacillus subtilis RNAse P by substrate binding.

The effect of a single break in the phosphodiester backbone of Bacillus subtilis RNAse P RNA (P RNA) was examined using circular permutation analysis (CPA). This method reveals that many of the phosphodiester bonds in this catalytic RNA can be broken with little or no effect on substrate binding. Phosphate positions that show strong effects are located mostly in regions conserved among all RNAse P RNAs, or they are in regions known to interact directly with the pre-tRNA substrate. Two circularly permuted isomers of P RNA were constructed and analyzed in detail. The KM for both circularly permuted isomers is nearly identical to that of the wild-type P RNA. Since the KM of the P RNA is essentially the same as the binding constant to the substrate, this finding confirms the CPA results. The implications of backbone breakage are discussed with respect to folding and catalysis of the RNAse P RNA.

Bacillus subtilis↗

PubMed1994

In vitro selection of small RNAs that bind to Escherichia coli phenylalanyl-tRNA synthetase.

Small RNAs were selected from a highly degenerate library on the basis of their ability to bind tightly to Escherichia coli phenylalanyl-tRNA synthetase (FRS). The 63 nucleotide library consisted of the acceptor stem and portions of the D and T stems of E. coli tRNA(Phe) flanking a 32 nucleotide randomized region. Because FRS binding relies on a correctly folded tRNA substrate, the selected variants from this library were expected to resemble tRNA(Phe) structure. After seven cycles of selection, the RNA library bound to FRS with similar affinity to that of the E. coli tRNA(Phe), but did not show detectable aminoacylation. Fourteen FRS-specific isolates were sequenced and found to contain an anticodon stem-loop including the anticodon triplet of tRNA(Phe). The tight-binding RNAs fell into two classes depending on the location of this step-loop within the sequence. The acceptor stem defined by the non-randomized sequence was also found to be essential for binding. Mutation of two residues within a common hexanucleotide sequence present in one of the classes reduced binding to FRS. Taken together, these results suggest that in order to bind RNAs tightly, FRS requires the simultaneous interaction of the anticodon stem-loop and acceptor stem, and additional sequences needed for proper folding. This approach should assist in the detection of motifs that resemble tRNA, but are too dissimilar to be identified by sequence comparison.

Base Sequence↗

PubMed1994

Properties of an in vitro selected Pb2+ cleavage motif.

The addition of Pb2+ to a small RNA molecule consisting of an asymmetric internal loop of six nucleotides results in site-specific cleavage followed by hydrolysis of the 2',3'-cyclic phosphate intermediate [Pan, T., & Uhlenbeck, O.C. (1992) Nature 358, 560-563]. Here we show that the reaction is highly specific for Pb2+ and the cleavage rate increases exponentially with pH from 5.5 to 7.0, both in the presence and in the absence of Mg2+. This suggests that the reaction mechanism involves Pb2+ hydroxide acting as a base. Several sequence variants of the RNA are found to be equally active in both steps of the reaction, suggesting that they fold into a similar structure.

Cations, Divalent↗

PubMed1994

Structure and function of retinal ganglion cells innervating the cat's geniculate wing: an in vitro study.

We have examined in vitro the morphology and visual response properties of retinal ganglion cells innervating a component of the cat's lateral geniculate nucleus known as the geniculate wing (or retinorecipient zone of the pulvinar). Ganglion cells were first labeled in situ by retrograde transport of fluorescent microspheres from the geniculate wing. Labeled cells were injected intracellular with Lucifer yellow and biocytin in the isolated retina and visualized immunohistochemically. With one exception, stained cells appeared to belong to a single morphological class that corresponded closely to the epsilon cell of earlier descriptions (Leventhal et al., 1980; Rodieck and Watanabe, 1986). They had somas comparable in size to those of beta cells and large, sparse dendritic trees that ramified in the inner (ON) sublayer of the inner plexiform layer. Dendritic fields increased in size with eccentricity, but only within the central retina, and were among the largest so far reported for cat ganglion cells, exceeding those of alpha cells at most eccentricities. Dendritic profiles were typically elliptical with long axes pointing toward the area centralis. Axons were about as thick as those of beta cells and thicker than those of other varieties of non-alpha, non-beta ganglion cells. We recorded extracellularly from microsphere-labeled wing-projecting ganglion cells in a superfused, flattened eyecup preparation. All such cells exhibited sustained responses to standing contrast and had very large, concentric receptive fields with ON-centers and OFF-surrounds. Their response to gratings showed that they have relatively poor spatial resolution and a moderate amount of nonlinearity of spatial summation. These cells thus have many physiological response properties in common with ganglion cells previously termed "on-center tonic W-cells," "on-center sluggish sustained cells," and "Q-cells." These findings indicate that ganglion cells innervating the cat's geniculate wing form a structurally and functionally homogeneous class. Their large dendritic and receptive fields and low-pass spatial frequency tuning suggest that fine spatial resolution is not required for the execution of their functional role(s).

Animals↗

PubMed1993

Using circular permutation analysis to redefine the R17 coat protein binding site.

The bacteriophage R17 coat protein binding site consists of an RNA hairpin with a single purine nucleotide bulge in the helical stem. Circular permutation analysis (CPA) was used to examine binding effects caused by a single break in the phosphodiester backbone. This method revealed that breakage of all but one phosphodiester bond within a well-defined binding site substantially reduced the binding affinity. This is probably due to destabilization of the hairpin structure upon breaking the ribose phosphates at these positions. One circularly permuted isomer with the 5' and 3' ends at the bulged nucleotide bound with wild-type affinity. However, extending the 5' end of this CP isomer greatly reduces binding, making it unlikely that this circularly permuted binding site will be active when embedded in a larger RNA. CPA also locates the 5' and 3' boundaries of protein binding sites on the RNA. The 5' boundary of the R17 coat protein site as defined by CPA was two nucleotides shorter (nucleotides -15 to +2) than the previously determined site (-17 to +2). The smaller binding site was verified by terminal truncation experiments. A minimal-binding fragment (-14 to +2) was synthesized and was found to bind tightly to the coat protein. The site size determined by 3-ethyl-1-nitrosourea-modification interference was larger at the 5' end (-16 to +1), probably due, however, to steric effects of ethylation of phosphate oxygens. Thus, the apparent site size of a protein binding site is dependent upon the method used.

Bacteriophages↗

PubMed1993

Circularly permuted DNA, RNA and proteins--a review.

Circular permutation represents a form of macromolecular isomerization when the normal termini are covalently linked and new termini introduced by breaking the backbone elsewhere. Here, we describe implications of circular permutation on the folding and function of biologically relevant macromolecules. A method permitting the analysis of the folding of all circularly permuted isomers of RNA is presented that has been successfully applied for a tRNA and the binding site of the coliphage R17 coat protein.

Animals↗

PubMed1993

Replacement of RNA hairpins by in vitro selected tetranucleotides.

An in vitro selection method based on the autolytic cleavage of yeast tRNA(Phe) by Pb2+ was applied to obtain tRNA derivatives with the anticodon hairpin replaced by four single-stranded nucleotides. Based on the rates of the site-specific cleavage by Pb2+ and the presence of a specific UV-induced crosslink, certain tetranucleotide sequences allow proper folding of the rest of the tRNA molecule, whereas others do not. One such successful tetramer sequence was also used to replace the acceptor stem of yeast tRNA(Phe) and the anticodon hairpin of E.coli tRNA(Phe) without disrupting folding. These experiments suggest that certain tetramers may be able to replace structurally nonessential hairpins in any RNA.

Base Sequence↗

PubMed1993

A study of homologous chromosomes using a morphometric approach.

A previous study of 100 karyotyped metaphase cells has demonstrated the utility of a graphic arts tool in deriving chromosome measurements for relative length determination. In the present study we utilize this same approach to address the question: "What are the average differences in relative lengths between apparently normal homologous chromosomes?" Normal standards derived from this study will be useful for testing specific hypotheses involving heteromorphic differences between homologs. No such data on normal controls could readily be found in either An International System for Human Cytogenetic Nomenclature (1985) or elsewhere.

Chromosomes↗

PubMed1992

A small metalloribozyme with a two-step mechanism.

An RNA molecule consisting of an asymmetric internal loop of six nucleotides can be rapidly and specifically cleaved by Pb2+ in the presence of Mg2+. The 5' cleavage product terminates with a 3' phosphomonoester generated from a 2',3'-cyclic phosphodiester reaction intermediate. This two-step reaction mechanism resembles that of many protein ribonucleases but has not previously been observed for reactions catalysed by RNA.

Base Sequence↗

PubMed1992

In vitro selection of RNAs that undergo autolytic cleavage with Pb2+.

An in vitro selection method has been developed to obtain RNA molecules that specifically undergo autolytic cleavage reactions by Pb2+ ion. The method utilizes a circular RNA intermediate which is regenerated following the cleavage reaction to allow amplification and multiple cycles of selection. Pb2+ is known to catalyze a specific cleavage reaction between U17 and G18 of yeast tRNA(Phe). Starting from pools of RNA molecules which have a random distribution of sequences at nine or ten selected positions in the sequence of yeast tRNA(Phe), we have isolated many RNA molecules that undergo rapid and specific self-cleavage with Pb2+ at a variety of different sites. Terminal truncation experiments suggest that most of these self-cleaving RNA molecules do not fold like tRNA. However, two of the variants are cleaved rapidly with Pb2+ at U17 even though they lack the highly conserved nucleotides G18 and G19. Both specific mutations and terminal truncation experiments suggest that the D and T loops of these two variants interact in a manner similar to that of tRNA(Phe) despite the absence of the G18U55 and G19C56 tertiary interactions. A model for an alternate tertiary interaction involving a U17U55 pair is presented. This model may be relevant to the structure of about 100 mitochondrial tRNAs that also lack G18 and G19. The selection method presented here can be directly applied to isolate catalytic RNAs that undergo cleavage in the presence of other metal ions, modified nucleotides, or sequence-specific nucleases.

Base Composition↗

PubMed1991

Folding of circularly permuted transfer RNAs.

All of the ribose-phosphate linkages in yeast tRNA(Phe) that could be cleaved without affecting the folding of the molecule have been determined in a single experiment. Circular permutation analysis subjects circular tRNA molecules to limited alkaline hydrolysis in order to generate one random break per molecule. Correctly folded tRNAs were identified by lead cleavage at neutral pH, a well-characterized reaction that requires proper folding of tRNA(Phe). Surprisingly, most of the circularly permuted tRNA molecules folded correctly. This result suggests that the tRNA folding motif could occur internally within other RNA sequences, and a computer search of Genbank entries has identified many examples of such motifs.

Base Sequence↗

PubMed1991

Structure of the binuclear metal-binding site in the GAL4 transcription factor.

The GAL4 transcription factor from yeast contains within its N-terminal DNA-binding domain an amino acid sequence containing six cysteine residues, C11-X2-C14-X6-C21-X6-C28-X2-C31-X6-C38. The six Cys residues will form a binuclear metal cluster with either Zn(II) or Cd(II) in which two of the -S- donors are bridging ligands between the two metal ions. Binding of Zn(II) or Cd(II) to the GAL4 DNA-binding domain is essential to induce the conformation of GAL4 required for the protein to recognize the specific DNA sequence, UASG, to which GAL4 binds. Evidence for the presence of the binuclear cluster has come from 113Cd NMR and 2D 1H-113Cd heteronuclear NMR studies of the cloned DNA-binding domain of GAL4 consisting of the N-terminal 62 residues, GAL4(62*) [Pan and Coleman (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 2077]. Cd(II) binding to the GAL4 DNA is highly cooperative, thus the Cd2Cys6 cluster is always formed. On the other hand, Zn(II) forms well-defined Zn1 and Zn2 complexes with the DNA-binding domain of GAL4, both of which bind specifically to the UASG DNA sequence. The structural details of the Cd2-, Zn2-, and Zn1GAL4(62*) proteins have been determined by a variety of heteronuclear and 2D NMR techniques. When Cd(II) is exchanged for Zn(II), the cluster appears to expand to accommodate the larger Cd(II) ion as suggested by changes of 2 to 4 Hz in the 3JHN alpha coupling constants for the amino acid residues which form the polypeptide loops enclosing the cluster, residues 10-40. These changes suggest alterations in the backbone phi torsional angles of from 20 degrees to 30 degrees. A metal-ligand structure derived from the 1H-113Cd heteronuclear NMR as well as the polypeptide backbone connectivity around the cluster as determined from short-range 1H-1H NOE's is presented. The metal ions also determine the major folding of GAL4(62*), since the chemical shift dispersion in the entire NH-alpha CH fingerprint region of the 1H-1H COSY spectrum collapses on removal of the metal ion. Two short segments of the GAL4(62*) polypeptide (residues 14-19 and 30-36 in the cluster forms, 12-19 and 30-36 in the Zn1 species) show significant dNN(i,i + 1) NOE's. These short segments of polypeptide chain are the only ones that could be helical in the GAL4(62*).(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗