Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.

ABSTRACT:

Background

Specific binding of proteins to DNA is one of the most common ways gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a simple recognition code, therefore the prediction of DNA target sequences is not straightforward. DNA-protein interactions can be studied using computational methods which can complement the current experimental methods and offer some advantages. In the present work we use physical effective potentials to evaluate the DNA-protein binding affinities for the lambda repressor-DNA complex for which structural and thermodynamic experimental data are available.

Results

The binding free energy of two molecules can be expressed as the sum of an

SUBMITTER: Moroni E 

PROVIDER: S-EPMC2194778 | biostudies-literature | 2007 Sep

REPOSITORIES: biostudies-literature