Modeling bacterial DNA replication initiation complex by molecular dynamics simulation

Biophysics Theoretical Biophysics PTB004

Chromosomal replication is a dynamic process that is initiated by DNA unwinding. To understand the DNA unwinding mechanism at replication initiation, we studied the formation of the structure of a DNA-protein complex at the replication origin. This is called the replication initiation complex. In the video, we modeled a part of the initiation complex by coarse-grained molecular dynamics simulation. In the video, DNA is shown in gray and DNA-bending protein (Integration Host Factor) is shown in black. The molecules that form a pentamer on the DNA are DnaA proteins. For visibility, we colored DnaA proteins in two alternating ways: blue (oligomerization domain) and light purple (DNA-binding domain); or green (oligomerization domain) and yellowish green (DNA-binding domain).

Gammaproteobacteria

Phylum
Proteobacteria
Class
Gammaproteobacteria