Antisense interaction between r and a

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Revision as of 16:33, 2 October 2015 by Marcbiarnesc (talk | contribs) (Parameters)
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[NOTE TO MARC: Can you also check the parameter for this reaction? I found those papers cited below. Also, is the reaction reversible or irreversible? In Chatterjee they have modelled it as reversible. If it is, we are missing one parameter, because I only could find that one below.]

The full length mRNA of scbR (r) binds to the full length mRNA of scbA (a) and form a complex which prevents further translation of both mRNAs.

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Chemical equation

a + r \rightleftharpoons r-a

Rate equation

Failed to parse (Cannot store math image on filesystem.): r= K_{ar}\cdot [r]\cdot [a]-K_{-ar} \cdot [a-r]

Parameters

The parameter of this reaction is the dissociation constant for binding of scbR mRNA to scbA mRNA (Failed to parse (Cannot store math image on filesystem.): K_{ra} ).

Name Value Units Origin Remarks
K_{ar} Failed to parse (Cannot store math image on filesystem.): 0.06-0.18 [1] [2] [3] Failed to parse (Cannot store math image on filesystem.): nM^{-1} \cdot min^{-1}
Failed to parse (Cannot store math image on filesystem.): K_{-ar}

Parameters with uncertainty

The most plausible parameter value for the K_{ar} is decided to be  ?? and the confidence interval  ?? . This means that the mode of the PDF is 5 and the range where 95% of the values are found is between ?? and ??.

The probability distributions for the two parameters, adjusted accordingly in order to reflect the above values, are the following:


The location and scale parameters of the distribution are:

Parameter μ σ
K_{ar} ?? ??

References

  1. Shokeen S, Johnson CM, Greenfield TJ, Manias DA, Dunny GM, Weaver KE. Structural analysis of the Anti-Q-Qs interaction: RNA-mediated regulation of E. faecalis plasmid pCF10 conjugation. Plasmid. 2010;64(1):26-35.
  2. Brantl S. Regulatory mechanisms employed by cis-encoded antisense RNAs. Cell regulation (RNA special issue). 2007; 10: 102–109.
  3. Eguchi Y, Itoh T, Tomizawa J (1991) Antisense Rna. Annual Review of Biochemistry 60: 631–652.