Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding.

ABSTRACT: Protein-DNA binding is a fundamental component of gene regulatory processes, but it is still not completely understood how proteins recognize their target sites in the genome. Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-groove geometry using positively charged amino acids (shape readout). The underlying mechanism of DNA shape readout involves the correlation between minor-groove width and electrostatic potential (EP). To probe this biophysical effect directly, rather than using minor-groove width as an indirect measure for shape readout, we developed a methodology, DNAphi, for predicting EP in the minor groove and confirmed the direct role of EP in protein-DNA binding using massive sequencing data. The DNAphi method uses a sliding-window approach t

SUBMITTER: Chiu TP 

PROVIDER: S-EPMC5716191 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature