The day/night switch of the circadian clock of synechococcus elongatus and hydrogen bonds of dna and rna

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Title: The day/night switch of the circadian clock of synechococcus elongatus and hydrogen bonds of dna and rna
Author: Kim, Yong-Ick
Abstract: The circadian oscillator of the cyanobacterium Synechococcus elongatus is composed of only three proteins , KaiA , KaiB , and KaiC , which together with ATP can generate a self -sustained ~24 hour oscillation of KaiC phosphorylation for several days . KaiA induces KaiC to autophosphorylate whereas KaiB blocks the stimulation of KaiC by KaiA , which allows KaiC to autodephosphorylate . We propose and support a model in which the C -terminal loops of KaiC , the ?A -loops ? , are the master switch that determines overall KaiC activity . When the A -loops are in their buried state , KaiC is an autophosphatase . When the A -loops are exposed , however , KaiC is an autokinase . The data suggest that KaiA stabilizes the exposed state of the A -loops through direct binding . We also show evidence that if KaiA cannot stabilize the exposed state KaiC remains hypophosphorylated . We propose that KaiB inactivates KaiA by preventing it from stabilizing the exposed state of the A -loops . Thus , KaiA and KaiB likely act by shifting the dynamic equilibrium of the A -loops between exposed and buried states , which shifts the balance of autokinase and autophosphatase activities of KaiC . A -loop exposure likely moves the ATP closer to the sites of phosphorylation and we show evidence in support of how this movement may be accomplished . Density functional theory calculations of isolated Watson ?Crick A :U and A :T base pairs predict that adenine 13C2 trans -hydrogen bond deuterium isotope shifts due to isotopic substitution at the pyrimidine H3 , 2h ?13C2 , are sensitive to the hydrogen -bond distance between the N1 of adenine and the N3 of uracil or thymine , which supports the notion that 2h ?13C2 is sensitive to hydrogen -bond strength . Calculated 2h ?13C2 values at a given N1 ?N3 distance are the same for isolated A :U and A :T base pairs . Replacing uridine residues in RNA with 5 -methyl uridine and substituting deoxythymidines in DNA with deoxyuridines do not statistically shift empirical 2h ?13C2 values . Thus , we show experimentally and computationally that the C7 methyl group of thymine has no measurable affect on 2h ?13C2 values . Furthermore , 2h ?13C2 values of modified and unmodified RNA are more negative than those of modified and unmodified DNA , which supports our hypothesis that RNA hydrogen bonds are stronger than those of DNA . It is also shown here that 2h ?13C2 is context dependent and that this dependence is similar for RNA and DNA .
URI: http : / /hdl .handle .net /1969 .1 /ETD -TAMU -2319
Date: 2009-05-15

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The day/night switch of the circadian clock of synechococcus elongatus and hydrogen bonds of dna and rna. Available electronically from http : / /hdl .handle .net /1969 .1 /ETD -TAMU -2319 .

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