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We wish to submit a new manuscript entitled “Principle of K+/Na+
selectivity in the active site of Group II intron at various stages of
self-splicing pathway” for consideration by the journal “Journal of Molecular Graphics and Modelling”.

We confirm that this work is original and has not been
published elsewhere nor is it currently under consideration for publication
elsewhere.

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Group II introns are large ribozymes which can catalytically
splice and religate itself without the help of any other proteins. Recent x-ray
structures of the group II intron at different stages of splicing has revealed
the intricate architecture of the catalytic pocket within its core, which contains
a heteronuclear metal ion center (two Mg2+ and two K+),
that plays a crucial role for its function. It has also been established that the
catalytic activity of group II introns is very selective for monovalent ion K+
and buffer containing only Na+ could fully destroy the activity.

In this paper, we report molecular dynamics free energy
calculations of K+ vs Na+ binding to group II introns at
different stages of splicing. Despite structural and biochemical studies, the
origin of K+ vs Na+ recognition by group II introns is
unknown. The study quantitatively estimated the energetic basis, that enables group
II introns for selectively binding K+ with respect to Na+
in its active site. The study has provided the link between energetics and 3D
structure. The paper should be of interest to readers in the areas of RNA-ion
recognition using computational approach. 

Please address all correspondence concerning this manuscript
to me at ” [email protected]
“.

Thank you for your consideration of this
manuscript. 

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