We wish to submit a new manuscript entitled “Principle of K+/Na+selectivity in the active site of Group II intron at various stages ofself-splicing pathway” for consideration by the journal “Journal of Molecular Graphics and Modelling”. We confirm that this work is original and has not beenpublished elsewhere nor is it currently under consideration for publicationelsewhere.Group II introns are large ribozymes which can catalyticallysplice and religate itself without the help of any other proteins. Recent x-raystructures of the group II intron at different stages of splicing has revealedthe intricate architecture of the catalytic pocket within its core, which containsa heteronuclear metal ion center (two Mg2+ and two K+),that plays a crucial role for its function. It has also been established that thecatalytic 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 energycalculations of K+ vs Na+ binding to group II introns atdifferent stages of splicing. Despite structural and biochemical studies, theorigin of K+ vs Na+ recognition by group II introns isunknown. The study quantitatively estimated the energetic basis, that enables groupII introns for selectively binding K+ with respect to Na+in its active site. The study has provided the link between energetics and 3Dstructure. The paper should be of interest to readers in the areas of RNA-ionrecognition using computational approach. Please address all correspondence concerning this manuscriptto me at ” psatpati@iitg.
ernet.in”.Thank you for your consideration of thismanuscript.