Correlation analysis of enzymatic reaction of a single protein molecule

DOI10.1214/12-AOAS541MaRDI QIDQ714353zbMATHOpenAlexWikidataFDO

Authors Chao Du, S. C. Kou

Publication date 21 October 2012

Published in The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1209.6210

zbMATH Keywords

single-molecule experimentcontinuous time Markov chainautocorrelationsfluorescence intensityMichaelis-Menten modelstochastic network modelturnover time

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42) Biophysics (92C05) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

Abstract: New advances in nano sciences open the door for scientists to study biological processes on a microscopic molecule-by-molecule basis. Recent single-molecule biophysical experiments on enzyme systems, in particular, reveal that enzyme molecules behave fundamentally differently from what classical model predicts. A stochastic network model was previously proposed to explain the experimental discovery. This paper conducts detailed theoretical and data analyses of the stochastic network model, focusing on the correlation structure of the successive reaction times of a single enzyme molecule. We investigate the correlation of experimental fluorescence intensity and the correlation of enzymatic reaction times, and examine the role of substrate concentration in enzymatic reactions. Our study shows that the stochastic network model is capable of explaining the experimental data in depth.

Recommendations

• Stochastic networks in nanoscale biophysics
• Stochastic modeling in nanoscale biophysics: subdiffusion within proteins
• A selective view of stochastic inference and modeling problems in nanoscale biophysics
• Single-substrate enzyme kinetics: the quasi-steady-state approximation and beyond
• Reverse-engineering of biochemical reaction networks from spatio-temporal correlations of fluorescence fluctuations

Cites work

• scientific article; zbMATH DE number 192975 (Why is no real title available?)
• A selective view of stochastic inference and modeling problems in nanoscale biophysics
• Bayesian Analysis of Single-Molecule Experimental Data
• Matrix Analysis
• On the validity of the steady state assumption of enzyme kinetics
• Stochastic modeling in nanoscale biophysics: subdiffusion within proteins
• Stochastic networks in nanoscale biophysics

Cited in

(6)

• The lack of long-range correlations is a necessary condition for a functional biologically active protein
• Stochastic modeling in nanoscale biophysics: subdiffusion within proteins
• Superiority of single covalent modification in specificity: from deterministic to stochastic viewpoint
• A selective view of stochastic inference and modeling problems in nanoscale biophysics
• Statistical methodology in single-molecule experiments
• Stochastic networks in nanoscale biophysics

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