Modeling DNA-binding of Escherichia coli sigma70 exhibits a characteristic energy landscape around strong promoters.

ABSTRACT: We present a computational model of DNA-binding by sigma70 in Escherichia coli which allows us to extract the functional characteristics of the wider promoter environment. Our model is based on a measure for the binding energy of sigma70 to the DNA, which is derived from promoter strength data and used to build up a non-standard weight matrix. Opposed to conventional approaches, we apply the matrix to the environment of 3765 known promoters and consider the average matrix scores to extract the common features. In addition to the expected minimum of the average binding energy at the exact promoter site, we detect two minima shortly upstream and downstream of the promoter. These are likely to occur due to correlation between the two binding sites of sigma70. Moreover, we observe a characteri

SUBMITTER: Weindl J 

PROVIDER: S-EPMC2175306 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature