Construction of an annotated corpus to support biomedical information extraction

Background  

Information Extraction (IE) is a component of text mining that facilitates knowledge discovery by automatically locating instances of interesting biomedical events from huge document collections. As events are usually centred on verbs and nominalised verbs, understanding the syntactic and semantic behaviour of these words is highly important. Corpora annotated with information concerning this behaviour can constitute a valuable resource in the training of IE components and resources.     

ATP mediated receptor interconversion as a model of estrogen action: isolation of the factor which converts the non-estrogen binding form of the receptor to the lower affinity binding form

Two steroid binding states of an estrogen receptor each with different equilibrium constants (Kd values) Rx (Kd = 0.06 nM) and Ry (Kd = 0.8 nM) have been identified and characterized in the hen and estrogen-stimulated chick oviduct. A third non-estrogen binding form of the receptor, designated Rnb, has also been identified. These three forms of the receptor are interconvertible and appear to have a common molecular weight of approx. 66,000 under denaturing conditions. Hydroxytamoxifen binds preferentially and with high affinity to Rx (Kd 0.03 nM) and the conversion of Rx to Ry which is mediated by gamma phosphoryl group of ATP is also inhibitable by hydroxytamoxifen. Thus receptor interconversion, which may have general application to hormone action, potentially explains agonist/antagonist activity. The conversion of the non-estrogen binding form of the receptor (Rnb) to the lower affinity receptor (Ry) in chick oviduct cytosol is catalyzed by a reaction requiring the loss of the terminal phosphoryl moiety from ATP. There is a specific requirement for Mg2+. We now describe that ammonium sulfate fractionation of the cytosol allows the separation of the receptor entities from the "activating factor" (Fy) that catalyzes the conversion of Rnb to Ry. In the presence of gamma [32P]-ATP at 30 degrees C the purified non-steroid binding form of the receptor is phosphorylated. Phosphoamino acid analysis using Partisil-10 SAX anion exchange resin demonstrates that a serine is phosphorylated; and quantitation of the phosphorylation is indicative of one phosphoserine/receptor molecule. Treatment of the receptor with the partially purified activating factor to induce estradiol binding causes a dramatic reduction in phosphorylation.     

Receptor interconversion model of hormone action. II. Nucleotide-mediated conversion of estrogen receptors from nonsteroid binding to the lower affinity binding state

Two steroid binding states of an estrogen receptor each with different equilibrium constants (Kd values) Rx (Kd = 0.06 nM) and Ry (Kd = 0.8 nM) have been identified and characterized in the hen and estrogen-stimulated chick oviduct. A third nonestrogen binding form of the receptor, designated Rnb, is now described which exists in short-term estrogen withdrawn chick oviduct cytosol. A model is presented in which the receptor can be interconverted between the three states. The interconversion is monitored by Scatchard analysis, sucrose density gradient analysis, and affinity labeling using [3H]tamoxifen aziridine followed by receptor purification with estrogen receptor monoclonal antibody affinity chromatography and sodium dodecyl sulfate-gel electrophoresis. The results are consistent with each state existing in different conformations having a common molecular weight of approximately 66,000. This paper defines the conditions and nucleotide requirements for the Rnb to Ry conversion. The conversion to the steroid binding form is induced by ATP, ADP, and GTP. Cyclic nucleotides are ineffective. There is a specific requirement for Mg2+; neither Ca2+ nor Mn2+ will substitute. Nonhydrolyzable nucleotide analogues were tested for their relative efficiency to convert Rnb to Ry. Conversion occurred with alpha,beta-methylene adenosine triphosphate, but beta,gamma-methylene adenosine triphosphate and alpha,beta-methylene adenosine diphosphate were inert. Thus, activation of Rnb to form Ry appears to be catalyzed by an event requiring the loss of the terminal phosphoryl moiety from either ATP or ADP. Receptor derived from conversion of Rnb to Ry has the same physical properties as native Ry. Activation of Rnb is to Ry specifically; no increase in the Rx form of estrogen receptor was ever observed. The accompanying paper similarly describes the Rx to Ry conversion. Since these data also explain observations made with glucocorticoid and with epidermal growth factor receptors, it is speculated that the receptor interconversion model may have general application to hormone action.