A comprehensive computational model of facilitated diffusion in prokaryotes

• DOI: 10.1093/bioinformatics/bts178
• Publication Date: 2012-04-08T08:06:13Z
• Authors: Nicolae Radu Zabet; Boris Adryan
• Keywords: Transcriptional Activation; 0301 basic medicine; 610; QH426 Genetics; DNA; Original Papers; Facilitated Diffusion; 620; 03 medical and health sciences; QC Physics; Models, Chemical; Escherichia coli; Lac Repressors; Thermodynamics; Computer Simulation

Abstract Motivation: Gene activity is mediated by site-specific transcription factors (TFs). Their binding to defined regions in the genome determines the rate at which their target genes are transcribed. Results: We present a comprehensive computational model of the search process of TF for their genomic target site(s). The computational model considers: the DNA sequence, various TF species and the interaction of the individual molecules with the DNA or between themselves. We also demonstrate a systematic approach how to parametrize the system using available experimental data. Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.