We've updated our Privacy Policy to make it clearer how we use your personal data.

We use cookies to provide you with a better experience. You can read our Cookie Policy here.

Advertisement
Towards Computional Specificity Screening of DNA-Binding Proteins
News

Towards Computional Specificity Screening of DNA-Binding Proteins

Towards Computional Specificity Screening of DNA-Binding Proteins
News

Towards Computional Specificity Screening of DNA-Binding Proteins

Read time:
 

Want a FREE PDF version of This News Story?

Complete the form below and we will email you a PDF version of "Towards Computional Specificity Screening of DNA-Binding Proteins"

First Name*
Last Name*
Email Address*
Country*
Company Type*
Job Function*
Would you like to receive further email communication from Technology Networks?

Technology Networks Ltd. needs the contact information you provide to us to contact you about our products and services. You may unsubscribe from these communications at any time. For information on how to unsubscribe, as well as our privacy practices and commitment to protecting your privacy, check out our Privacy Policy

Abstract
DNA-binding proteins are key players in the regulation of gene expression and, hence, are essential for cell function. Chimeric proteins composed of DNA-binding domains and DNA modifying domains allow for precise genome manipulation. A key prerequisite is the specific recognition of a particular nucleotide sequence. Here, we quantitatively assess the binding affinity of DNA-binding proteins by molecular dynamics-based alchemical free energy simulations. A computational framework was developed to automatically set up in silico screening assays and estimate free energy differences using two independent procedures, based on equilibrium and non-equlibrium transformation pathways. The influence of simulation times on the accuracy of both procedures is presented. The binding specificity of a zinc-finger transcription factor to several sequences is calculated, and agreement with experimental data is shown. Finally we propose an in silico screening strategy aiming at the derivation of full specificity profiles for DNA-binding proteins.

The article is published online in Nucleic Acids Research and is free to access.

Advertisement