Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuations

Jeffrey R. Moffitt, Yann R. Chemla, Carlos Bustamante

Research output: Contribution to journalArticle

Abstract

The time it takes an enzyme to complete its reaction is a stochastic quantity governed by thermal fluctuations. With the advent of high-resolution methods of single-molecule manipulation and detection, it is now possible to observe directly this natural variation in the enzymatic cycle completion time and extract kinetic information from the statistics of its fluctuations. To this end, the inverse of the squared coefficient of variation, which we term n min, is a useful measure of fluctuations because it places a strict lower limit on the numberof kinetic states in the enzymatic mechanism. Here we show that there is a single general expression for the substrate dependence of nmin for a wide range of kinetic models. This expression is governed by three kinetic parameters, which we term NL, NS, and α. These parameters have simple geometric interpretations and provide clear constraints on possible kinetic mechanisms. As a demonstration of this analysis, we fit the fluctuations in the dwell times of the packaging motor of the bacteriophage φ29, revealing additional features of the nucleotide loading process in this motor. Because a diverse set of kinetic models display the same substrate dependence for their fluctuations, the expression for this general dependence may prove of use in the characterization and study of the dynamics of a wide range of enzymes.

Original languageEnglish (US)
Pages (from-to)15739-15744
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume107
Issue number36
DOIs
StatePublished - Sep 7 2010

Keywords

  • Enzyme dynamics
  • Molecular motors
  • Single molecule
  • Statistical kinetics

ASJC Scopus subject areas

  • General

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