A new method for evaluating the specificity of indirect readout in protein-DNA recognition.

ABSTRACT: Proteins recognize a specific DNA sequence not only through direct contact (direct readout) with base pairs but also through sequence-dependent conformation and/or flexibility of DNA (indirect readout). However, it is difficult to assess the contribution of indirect readout to the sequence specificity. What is needed is a straightforward method for quantifying its contributions to specificity. Using Bayesian statistics, we derived the probability of a particular sequence for a given DNA structure from the trajectories of molecular dynamics (MD) simulations of DNAs containing all possible tetramer sequences. Then, we quantified the specificity of indirect readout based on the information entropy associated with the probability. We tested this method with known structures of protein-DNA comp

SUBMITTER: Yamasaki S 

PROVIDER: S-EPMC3458528 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature