title: Energetic and structural considerations for the mechanism of protein sliding along DNA in the nonspecific BamHI-DNA complex.
abstract: The molecular mechanism by which DNA-binding proteins find their specific binding sites is still unclear. To gain insights into structural and energetic elements of this mechanism, we used the crystal structure of the nonspecific BamHI-DNA complex as a template to study the dominant electrostatic interaction in the nonspecific association of protein with DNA, and the possible sliding pathways that could be sustained by such an interaction. Based on calculations using the nonlinear Poisson-Boltzmann method and Brownian dynamics, a model is proposed for the initial nonspecific binding of BamHI to B-form DNA that differs from that seen in the crystal structure of the nonspecific complex. The model is electrostatically favorable, and the salt dependence as well as other thermodynamic parameters calculated for this model are in good agreement with experimental results. Several residues in BamHI are identified for their important contribution to the energy in the nonspecific binding model, and specific mutagenesis experiments are proposed to test the model on this basis. We show that a favorable sliding pathway of the protein along DNA is helical.
authors.affiliation: Department of Physiology and Biophysics, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, NY 10029, USA.
authors.forename: Jian
authors.initials: J
authors.lastname: Sun
authors.forename: Hector
authors.initials: H
authors.lastname: Viadiu
authors.forename: Aneel K
authors.initials: AK
authors.lastname: Aggarwal
authors.forename: Harel
authors.initials: H
authors.lastname: Weinstein
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D015245:Deoxyribonuclease BamHI / Q000737:chemistry*; D004735:Energy Transfer; D004789:Enzyme Activation; D004795:Enzyme Stability; D046911:Macromolecular Substances; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D055672:Static Electricity
chemical_list: D004268:DNA-Binding Proteins; D046911:Macromolecular Substances; D004247:DNA; D015245:Deoxyribonuclease BamHI