Literature DB >> 17994718

Kinetic analysis of sequential multistep reactions.

Yajun Zhou1, Xiaowei Zhuang.   

Abstract

Many processes in biology and chemistry involve multistep reactions or transitions. The kinetic data associated with these reactions are manifested by superpositions of exponential decays that are often difficult to dissect. Two major challenges have hampered the kinetic analysis of multistep chemical reactions: (1) reliable and unbiased determination of the number of reaction steps, and (2) stable reconstruction of the distribution of kinetic rate constants. Here, we introduce two numerically stable integral transformations to solve these two challenges. The first transformation enables us to deduce the number of rate-limiting steps from kinetic measurements, even when each step has arbitrarily distributed rate constants. The second transformation allows us to reconstruct the distribution of rate constants in the multistep reaction using the phase function approach, without fitting the data. We demonstrate the stability of the two integral transformations by both analytic proofs and numerical tests. These new methods will help provide robust and unbiased kinetic analysis for many complex chemical and biochemical reactions.

Mesh:

Year:  2007        PMID: 17994718      PMCID: PMC2646179          DOI: 10.1021/jp073708+

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  27 in total

1.  Chi-sequence recognition and DNA translocation by single RecBCD helicase/nuclease molecules.

Authors:  K M Dohoney; J Gelles
Journal:  Nature       Date:  2001-01-18       Impact factor: 49.962

2.  Applying hidden Markov models to the analysis of single ion channel activity.

Authors:  L Venkataramanan; F J Sigworth
Journal:  Biophys J       Date:  2002-04       Impact factor: 4.033

3.  Kinesin walks hand-over-hand.

Authors:  Ahmet Yildiz; Michio Tomishige; Ronald D Vale; Paul R Selvin
Journal:  Science       Date:  2003-12-18       Impact factor: 47.728

4.  Statistical kinetics of macromolecular dynamics.

Authors:  Joshua W Shaevitz; Steven M Block; Mark J Schnitzer
Journal:  Biophys J       Date:  2005-07-22       Impact factor: 4.033

5.  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

6.  Robust reconstruction of the rate constant distribution using the phase function method.

Authors:  Yajun Zhou; Xiaowei Zhuang
Journal:  Biophys J       Date:  2006-09-15       Impact factor: 4.033

7.  Stochastic protein expression in individual cells at the single molecule level.

Authors:  Long Cai; Nir Friedman; X Sunney Xie
Journal:  Nature       Date:  2006-03-16       Impact factor: 49.962

8.  Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting".

Authors:  Shixin Liu; Gregory Bokinsky; Nils G Walter; Xiaowei Zhuang
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-11       Impact factor: 11.205

9.  Analyzing the distribution of decay constants in pulse-fluorimetry using the maximum entropy method.

Authors:  A K Livesey; J C Brochon
Journal:  Biophys J       Date:  1987-11       Impact factor: 4.033

10.  Currents carried by sodium and potassium ions through the membrane of the giant axon of Loligo.

Authors:  A L HODGKIN; A F HUXLEY
Journal:  J Physiol       Date:  1952-04       Impact factor: 5.182

View more
  10 in total

1.  Analysis of kinetic intermediates in single-particle dwell-time distributions.

Authors:  Daniel L Floyd; Stephen C Harrison; Antoine M van Oijen
Journal:  Biophys J       Date:  2010-07-21       Impact factor: 4.033

2.  Age-dependent stochastic models for understanding population fluctuations in continuously cultured cells.

Authors:  Evgeny B Stukalin; Ivie Aifuwa; Jin Seob Kim; Denis Wirtz; Sean X Sun
Journal:  J R Soc Interface       Date:  2013-06-12       Impact factor: 4.118

3.  G-quadruplexes significantly stimulate Pif1 helicase-catalyzed duplex DNA unwinding.

Authors:  Xiao-Lei Duan; Na-Nv Liu; Yan-Tao Yang; Hai-Hong Li; Ming Li; Shuo-Xing Dou; Xu-Guang Xi
Journal:  J Biol Chem       Date:  2015-01-27       Impact factor: 5.157

4.  Extracting conformational memory from single-molecule kinetic data.

Authors:  Steve Pressé; Julian Lee; Ken A Dill
Journal:  J Phys Chem B       Date:  2013-01-09       Impact factor: 2.991

5.  Stochastic modelling of biochemical systems of multi-step reactions using a simplified two-variable model.

Authors:  Qianqian Wu; Kate Smith-Miles; Tianshou Zhou; Tianhai Tian
Journal:  BMC Syst Biol       Date:  2013-10-23

6.  A Multi-stage Representation of Cell Proliferation as a Markov Process.

Authors:  Christian A Yates; Matthew J Ford; Richard L Mort
Journal:  Bull Math Biol       Date:  2017-10-13       Impact factor: 1.758

7.  Analyzing dwell times with the Generalized Method of Moments.

Authors:  Sadie Piatt; Allen C Price
Journal:  PLoS One       Date:  2019-01-08       Impact factor: 3.240

8.  Inferring quantity and qualities of superimposed reaction rates from single molecule survival time distributions.

Authors:  Matthias Reisser; Johannes Hettich; Timo Kuhn; Achim P Popp; Andreas Große-Berkenbusch; J Christof M Gebhardt
Journal:  Sci Rep       Date:  2020-02-04       Impact factor: 4.379

9.  Dimensionality-reduction techniques for complex mass spectrometric datasets: application to laboratory atmospheric organic oxidation experiments.

Authors:  Abigail R Koss; Manjula R Canagaratna; Alexander Zaytsev; Jordan E Krechmer; Martin Breitenlechner; Kevin J Nihill; Christopher Y Lim; James C Rowe; Joseph R Roscioli; Frank N Keutsch; Jesse H Kroll
Journal:  Atmos Chem Phys       Date:  2020-01-27       Impact factor: 6.133

10.  Enzyme-Mediated Directional Transport of a Small-Molecule Walker With Chemically Identical Feet.

Authors:  Christopher J Martin; Alan T L Lee; Ralph W Adams; David A Leigh
Journal:  J Am Chem Soc       Date:  2017-08-15       Impact factor: 15.419

  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.