Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCIG Base Pairs

Yildirim, Ilyas; Stern, Harry; Šponer,  Jiří; Špačková, Naděžda; Turner, Douglas

Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCIG Base Pairs

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Authors	YILDIRIM Ilyas STERN Harry ŠPONER Jiří ŠPAČKOVÁ Naděžda TURNER Douglas
Year of publication	2009
Type	Article in Periodical
Magazine / Source	Journal of Chemical Theory and Computation
MU Faculty or unit	Faculty of Science
Citation
Field	Biophysics
Keywords	base pairs; NMR; amber force field
Description	Guanine-adenine (GA) base pairs play important roles in determining the structure, dynamics, and stability of RNA. Calculations reported here test the thermodynamic integration (TI) approach with the amber99 force field by comparing computational predictions of free energy differences with the free energy differences expected on the basis of NMR determined structures of the RNA motifs.
Related projects:	Biomolecular centre