Book of Abstracts: Albany 2009
June 16-20 2009
© Adenine Press (2008)
The Role of Conformational Flexibility in Proteins' Search for their Recognition Sites
Many DNA-binding proteins (DBPs) undergo a conformational transition upon binding to cognate sites. In some cases this transition is accomplished by folding of a natively unfolded region. What is the role of this conformational transition?
The recently proposed "fly-casting" mechanism suggests that this conformational transition facilitates binding by increasing the cross-section of the binding reaction due to the proteins partial unfolding. Here we propose an alternative mechanism--kinetic pre-selection--which allows rapid translocation along DNA while ensuring that protein that are near their target sites recognize it before they dissociate from DNA.
DBPs are believed to reach their target sites by alternating between 3D diffusion in solution and 1D diffusion along DNA. We seek to understand the importance of conformational flexibility in the context of the entire search process--from induction into the nucleus or nucleoid up to the final binding event on a target site. We previously found that if a DBP-DNA complex is limited to a single conformation, the protein can either slide efficiently, on a smooth, largely sequence-independent energy landscape, or bind tightly, on a rugged, highly sequence-dependent landscape, but not both. We suggested that distinct conformations of the complex could allow access to both landscapes.
Here we use simulations of the 3D/1D search process by a DBP that undergoes spontaneous conformational transition between a partially unstructured search conformation that allows rapid sliding and a folded recognition conformation in which it binds DNA tightly. We demonstrate (i) that there is an optimal rate of the conformational transition; and (ii) that partial destabilization of the recognition conformation is necessary for the mechanism to work. We examine the role of coupling between folding and binding, find conditions for such coupling to take place, and show how it facilitates the 3D/1D search process by increasing the probability of folding on the correct site (kinetic pre-selection). We find that this preselection of target sites allows proteins with experimentally estimated folding rates to recognize their target sites before translocating away and dissociating from DNA.
We demonstrate that kinetic pre-selection mechanism is consistent with available NMR and single-molecule measurements and provides a much more significant acceleration (~100 fold) that the earlier proposed fly-casting (~1.5-2 fold).