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A simple and fast approach for predicting (1)H and (13)C chemical shifts: toward chemical shift-guided simulations of RNA.

ABSTRACT: We introduce a simple and fast approach for predicting RNA chemical shifts from interatomic distances that performs with an accuracy similar to existing predictors and enables the first chemical shift-restrained simulations of RNA to be carried out. Our analysis demonstrates that the applied restraints can effectively guide conformational sampling toward regions of space that are more consistent with chemical shifts than the initial coordinates used for the simulations. As such, our approach should be widely applicable in mapping the conformational landscape of RNAs via chemical shift-guided molecular dynamics simulations. The simplicity and demonstrated sensitivity to three-dimensional structure should also allow our method to be used in chemical shift-based RNA structure prediction, validation, and refinement.

SUBMITTER: Frank AT

PROVIDER: S-EPMC4207130 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

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A simple and fast approach for predicting (1)H and (13)C chemical shifts: toward chemical shift-guided simulations of RNA.

Frank Aaron T AT Law Sean M SM Brooks Charles L CL

The journal of physical chemistry. B 20141015 42

We introduce a simple and fast approach for predicting RNA chemical shifts from interatomic distances that performs with an accuracy similar to existing predictors and enables the first chemical shift-restrained simulations of RNA to be carried out. Our analysis demonstrates that the applied restraints can effectively guide conformational sampling toward regions of space that are more consistent with chemical shifts than the initial coordinates used for the simulations. As such, our approach sho ...[more]

PMID: 25255209

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