Conformational entropy of the RNA phosphate backbone and its contribution to the folding free energy.

ABSTRACT: While major contributors to the free energy of RNA tertiary structures such as basepairing, base-stacking, and charge and counterion interactions have been studied extensively, little is known about the intrinsic free energy of the backbone. To assess the magnitude of the entropic strains along the phosphate backbone and their impact on the folding free energy, we have formulated a mathematical treatment for computing the volume of the main-chain torsion-angle conformation space between every pair of nucleobases along any sequence to compute the corresponding backbone entropy. To validate this method, we have compared the computed conformational entropies against a statistical free energy analysis of structures in the crystallographic database from several-thousand backbone conformations b

SUBMITTER: Mak CH 

PROVIDER: S-EPMC3976523 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature