title: Directional dependent dynamics of protein molecules on DNA.
abstract: We demonstrate that a protein molecule of interest undergoing the one-dimensional Brownian dynamics along DNA can exhibit a directional dependent net transport either toward or away from its target site depending on the distribution of the initial positions of the other classes of protein molecules present on the same DNA. Directionality arises as a consequence of the confinement of the search space and dynamic reflections by other protein molecules present on the same DNA chain. Energy cost for such directionality comes from the free energy spent on setting the initial positions of the other protein molecules. In the mechanism of action of cis-acting elements on the initiation of transcription, such free-energy inputs are derived from the site-specific binding affinities of the inflowing transcriptional factors toward their cis-acting elements. If the initial distribution of other protein molecules is a random one, then the protein molecule of interest exhibits a net transport away from its target site. This directionality originates from unequal natures of enhancing and retarding effects of the randomly distributed other classes of protein molecules. The protein molecule of interest overcomes the retarding effects of the other classes of protein molecules in a dynamical manner by increasing the number of dissociation-association events when it is far away from its target site and then by switching back to the sliding dynamics due to increase in the enhancing effects as it moves closer to its target site.
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Madras (IITM), Chennai, Tamil Nadu 600 036, India. rmurugan@gmail.com
authors.forename: Rajamanickam
authors.initials: R
authors.lastname: Murugan
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004247:DNA / Q000378:metabolism*; D008958:Models, Molecular; D011506:Proteins / Q000378:metabolism*
chemical_list: D011506:Proteins; D004247:DNA