Literature DB >> 24616494

Role of substrate unbinding in Michaelis-Menten enzymatic reactions.

Shlomi Reuveni1, Michael Urbakh, Joseph Klafter.   

Abstract

The Michaelis-Menten equation provides a hundred-year-old prediction by which any increase in the rate of substrate unbinding will decrease the rate of enzymatic turnover. Surprisingly, this prediction was never tested experimentally nor was it scrutinized using modern theoretical tools. Here we show that unbinding may also speed up enzymatic turnover--turning a spotlight to the fact that its actual role in enzymatic catalysis remains to be determined experimentally. Analytically constructing the unbinding phase space, we identify four distinct categories of unbinding: inhibitory, excitatory, superexcitatory, and restorative. A transition in which the effect of unbinding changes from inhibitory to excitatory as substrate concentrations increase, and an overlooked tradeoff between the speed and efficiency of enzymatic reactions, are naturally unveiled as a result. The theory presented herein motivates, and allows the interpretation of, groundbreaking experiments in which existing single-molecule manipulation techniques will be adapted for the purpose of measuring enzymatic turnover under a controlled variation of unbinding rates. As we hereby show, these experiments will not only shed first light on the role of unbinding but will also allow one to determine the time distribution required for the completion of the catalytic step in isolation from the rest of the enzymatic turnover cycle.

Keywords:  enzyme kinetics; renewal theory; single enzyme

Mesh:

Substances:

Year:  2014        PMID: 24616494      PMCID: PMC3970482          DOI: 10.1073/pnas.1318122111

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  41 in total

1.  Electrochemical Surface Science This manuscript is based on the Bonhoeffer-Eucken-Scheibe lectures of the Deutsche Bunsengesellschaft, given by the author at Erlangen, Berlin, and Leipzig in 1999/2000.

Authors:  Dieter M. Kolb
Journal:  Angew Chem Int Ed Engl       Date:  2001-04-01       Impact factor: 15.336

2.  Zero-mode waveguides for single-molecule analysis at high concentrations.

Authors:  M J Levene; J Korlach; S W Turner; M Foquet; H G Craighead; W W Webb
Journal:  Science       Date:  2003-01-31       Impact factor: 47.728

3.  Mechanistic constraints from the substrate concentration dependence of enzymatic fluctuations.

Authors:  Jeffrey R Moffitt; Yann R Chemla; Carlos Bustamante
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-20       Impact factor: 11.205

4.  Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited.

Authors:  Brian P English; Wei Min; Antoine M van Oijen; Kang Taek Lee; Guobin Luo; Hongye Sun; Binny J Cherayil; S C Kou; X Sunney Xie
Journal:  Nat Chem Biol       Date:  2005-12-25       Impact factor: 15.040

5.  Manipulating single enzymes by an external harmonic force.

Authors:  Michael A Lomholt; Michael Urbakh; Ralf Metzler; Joseph Klafter
Journal:  Phys Rev Lett       Date:  2007-04-19       Impact factor: 9.161

6.  The energy landscapes and motions of proteins.

Authors:  H Frauenfelder; S G Sligar; P G Wolynes
Journal:  Science       Date:  1991-12-13       Impact factor: 47.728

7.  Universality of Poisson indicator and Fano factor of transport event statistics in ion channels and enzyme kinetics.

Authors:  Srabanti Chaudhury; Jianshu Cao; Nikolai A Sinitsyn
Journal:  J Phys Chem B       Date:  2013-01-07       Impact factor: 2.991

Review 8.  Extracting signal from noise: kinetic mechanisms from a Michaelis-Menten-like expression for enzymatic fluctuations.

Authors:  Jeffrey R Moffitt; Carlos Bustamante
Journal:  FEBS J       Date:  2013-10-25       Impact factor: 5.542

9.  Effects of macromolecular crowding on genetic networks.

Authors:  Marco J Morelli; Rosalind J Allen; Pieter Rein ten Wolde
Journal:  Biophys J       Date:  2011-12-20       Impact factor: 4.033

10.  Single-molecule imaging of an in vitro-evolved RNA aptamer reveals homogeneous ligand binding kinetics.

Authors:  Mark P Elenko; Jack W Szostak; Antoine M van Oijen
Journal:  J Am Chem Soc       Date:  2009-07-29       Impact factor: 15.419

View more
  11 in total

1.  Path statistics, memory, and coarse-graining of continuous-time random walks on networks.

Authors:  Michael Manhart; Willow Kion-Crosby; Alexandre V Morozov
Journal:  J Chem Phys       Date:  2015-12-07       Impact factor: 3.488

2.  Dependence of the Enzymatic Velocity on the Substrate Dissociation Rate.

Authors:  Alexander M Berezhkovskii; Attila Szabo; T Rotbart; M Urbakh; Anatoly B Kolomeisky
Journal:  J Phys Chem B       Date:  2016-12-01       Impact factor: 2.991

3.  Equilibrium Studies of Iron (III) Complexes with Either Pyrazine, Quinoxaline, or Phenazine and Their Catecholase Activity in Methanol.

Authors:  José J N Segoviano-Garfias; Gabriela A Zanor; Fidel Ávila-Ramos; Egla Yareth Bivián-Castro
Journal:  Molecules       Date:  2022-05-19       Impact factor: 4.927

4.  Statistical Mechanics of Allosteric Enzymes.

Authors:  Tal Einav; Linas Mazutis; Rob Phillips
Journal:  J Phys Chem B       Date:  2016-04-29       Impact factor: 2.991

5.  Contribution of time delays to p53 oscillation in DNA damage response.

Authors:  Conghua Wang; Haihong Liu; Jin Zhou
Journal:  IET Syst Biol       Date:  2019-08       Impact factor: 1.615

6.  Aerenchyma, gas diffusion, and catalase activity in Typha domingensis: a complementary model for radial oxygen loss.

Authors:  Vinícius P Duarte; Marcio P Pereira; Felipe F Corrêa; Evaristo M de Castro; Fabricio J Pereira
Journal:  Protoplasma       Date:  2021-01-06       Impact factor: 3.356

7.  A Semi-Deterministic Random Walk with Resetting.

Authors:  Javier Villarroel; Miquel Montero; Juan Antonio Vega
Journal:  Entropy (Basel)       Date:  2021-06-28       Impact factor: 2.524

8.  Frequency-preference response in covalent modification cycles under substrate sequestration conditions.

Authors:  Juliana Reves Szemere; Horacio G Rotstein; Alejandra C Ventura
Journal:  NPJ Syst Biol Appl       Date:  2021-08-17

9.  Variance-corrected Michaelis-Menten equation predicts transient rates of single-enzyme reactions and response times in bacterial gene-regulation.

Authors:  Otto Pulkkinen; Ralf Metzler
Journal:  Sci Rep       Date:  2015-12-04       Impact factor: 4.379

10.  Single-molecule theory of enzymatic inhibition.

Authors:  Tal Robin; Shlomi Reuveni; Michael Urbakh
Journal:  Nat Commun       Date:  2018-02-22       Impact factor: 14.919

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.