Simulation of the kinetics of a sphere attached to a fluctuating polymer: Implications for target search by DNA-binding proteins.
We simulate the dynamics of a sphere, bound with a certain probability onto the beads of a harmonic bead-spring polymer in a confined geometry. The sphere hops from ith to the spatially closest i+/-kth bead. There is a crossover between kinetics dominated by different mechanisms with increasing binding probability. We relate these observations to the context of a biologically important problem of target location by DNA-binding proteins within a genome.
S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Calcutta 700091, India. jaydeb@boson.bose.res.in
J
J
Chakrabarti
S
S
Roy
D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D004563:Electrochemistry / Q000379:methods*; D007700:Kinetics; D008863:Microspheres; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D011108:Polymers / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation
D004268:DNA-Binding Proteins; D011108:Polymers; D004247:DNA