Methods in statistical kinetics

Methods in Enzymology
Jeffrey R MoffittCarlos Bustamante

Abstract

A variety of recent advances in single-molecule methods are now making possible the routine measurement of the distinct catalytic trajectories of individual enzymes. Unlike their bulk counterparts, these measurements directly reveal the fluctuations inherent to enzymatic dynamics, and statistical measures of these fluctuations promise to greatly constrain possible kinetic mechanisms. In this chapter, we discuss a variety of advances, ranging from theoretical to practical, in the new and growing field of statistical kinetics. In particular, we formalize the connection between the hidden fluctuations in the kinetic states that compose a full kinetic cycle and the measured fluctuations in the time to complete this cycle. We then discuss the characterization of fluctuations in a fashion that permits kinetic constraints to be easily extracted. When there are multiple observable enzymatic outcomes, we provide the proper way to sort events so as not to bias the final statistics, and we show that these classifications provide a first level of constraint on possible kinetic mechanisms. Finally, we discuss the basic substrate dependence of an important function of the statistical moments. The new kinetic parameters of this expression, ak...Continue Reading

Citations

Aug 16, 2011·Nature Structural & Molecular Biology·Bason E ClancySteven M Block
Aug 24, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey R MoffittCarlos Bustamante
May 11, 2013·Nucleic Acids Research·Amin Haghighat JahromiMaria Spies
Jul 23, 2013·PLoS Computational Biology·Joshua I GlaserKonrad P Kording
Feb 11, 2012·The Journal of Chemical Physics·Éva Dóka, Gábor Lente
Apr 4, 2014·Molecular Biology of the Cell·Chelsey Chandler Ruppersburg, H Criss Hartzell
Jun 10, 2015·Proceedings of the National Academy of Sciences of the United States of America·Michael J GreenbergE Michael Ostap
Jul 3, 2016·Proceedings of the National Academy of Sciences of the United States of America·William Y C HuangJay T Groves
Jun 28, 2019·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Nils G Walter
Aug 16, 2013·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Ajeet K Sharma, Debashish Chowdhury
Apr 3, 2019·Cold Spring Harbor Perspectives in Biology·Ameya P JalihalNils G Walter
Feb 26, 2019·Proceedings of the National Academy of Sciences of the United States of America·Keith J MickolajczykWilliam O Hancock
Feb 7, 2015·The Journal of Biological Chemistry·Geng-Yuan ChenWilliam O Hancock
Nov 8, 2011·Angewandte Chemie·Armin Hoffmann, Michael T Woodside
Nov 14, 2015·Physical Review Letters·Andre C Barato, Udo Seifert
Sep 9, 2018·Proceedings of the National Academy of Sciences of the United States of America·Felix WongJeremy Gunawardena
Apr 8, 2019·The Journal of Chemical Physics·Andrea Sabatino, Diego Frezzato
Dec 20, 2020·Biophysical Journal·Keith J MickolajczykTarun M Kapoor
Jan 18, 2014·Chemical Reviews·Marco BrucaleBruno Samorì
Jun 17, 2015·The Journal of Physical Chemistry. B·Ashutosh KumarArti Dua
Nov 7, 2021·Proceedings of the National Academy of Sciences of the United States of America·William Y C HuangJay T Groves

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