ATP-dependent translocation of proteins along single-stranded DNA: Models and methods of analysis of pre-steady state kinetics

Christopher J. Fischer, Timothy M. Lohman

Research output: Contribution to journalArticlepeer-review

58 Scopus citations

Abstract

Processive DNA helicases are able to translocate along single-stranded DNA (ssDNA) with biased directionality in a nucleoside triphosphate-dependent reaction, although translocation is not generally sufficient for helicase activity. An understanding of the mechanism of protein translocation along ssDNA requires pre-steady state transient kinetic experiments. Although ensemble experimental approaches have been developed recently for the study of translocation of proteins along DNA, quantitative analysis of the complete time-courses from these experiments, which is needed to obtain quantitative estimates of translocation kinetic parameters (rate constants, processivity, step sizes and ATP coupling) has been lacking. We discuss three ensemble transient kinetic experiments that can be used to study protein translocation along ssDNA, along with the advantages and limitations of each approach. We further describe methods to analyze the complete kinetic time-courses obtained from such experiments performed with a series of ssDNA lengths under "single-round" conditions (i.e. in the absence of re-binding of dissociated protein to DNA). These analysis methods utilize a sequential "n-step" model for protein translocation along ssDNA and enable quantitative determinations of the rate constant, processivity and step size for translocation through global non-linear least-squares fitting of the full time-courses.

Original languageEnglish
Pages (from-to)1265-1286
Number of pages22
JournalJournal of Molecular Biology
Volume344
Issue number5
DOIs
StatePublished - Dec 10 2004

Keywords

  • DNA translocation
  • helicase
  • motor protein
  • single turnover kinetics

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