title: Extracting enzyme processivity from kinetic assays.
abstract: A steady-state analysis for the catalytic turnover of molecules containing two substrate sites is presented. A broad class of Markovian dynamic models, motivated by the action of DNA modifying enzymes and the rich variety of translocation mechanisms associated with these systems (e.g., sliding, hopping, intersegmental transfer, etc.), is considered. The modeling suggests an elementary and general method of data analysis, which enables the extraction of the enzyme's processivity directly and unambiguously from experimental data. This analysis is not limited to the initial velocity regime. The predictions are validated both against detailed numerical models and by revisiting published experimental data for EcoRI endonuclease acting on DNA.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA.
authors.forename: Itay
authors.initials: I
authors.lastname: Barel
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA.
authors.forename: Norbert O
authors.initials: NO
authors.lastname: Reich
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA.
authors.forename: Frank L H
authors.initials: FL
authors.lastname: Brown
mesh_terms: D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D015246:Deoxyribonuclease EcoRI / Q000737:chemistry / Q000378:metabolism*; D007700:Kinetics; D008390:Markov Chains
chemical_list: D004247:DNA; D015246:Deoxyribonuclease EcoRI