1
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Kundu P, Saha S, Gangopadhyay G. A minimal kinetic model for the interpretation of complex catalysis in single enzyme molecules. Phys Chem Chem Phys 2023; 26:463-476. [PMID: 38078459 DOI: 10.1039/d3cp01720f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Multi-exponential waiting-time distribution and randomness parameter greater than unity ascribe dynamic disorder in single-enzyme catalysis corroborated to the interplay of transforming conformers [English et al., Nat. Chem. Biol., 2006, 2, 87]. The associated multi-state model of enzymatic turnovers with statically heterogeneous catalytic rates misdescribes the non-linear uprising of the randomness parameter from unity in relation to the attributes of the fall-offs of the waiting-time distribution at different substrate concentrations. To resolve this crucial issue, we first employ a comprehensive stochastic reaction scenario and further rationalize and work out the minimal indispensable dynamic-disorder model that ensures the foregoing relationship upon comparison with the data. We elucidate that specific disregard for the transition rate coefficients in the multi-state model on account of the especially slow conformational transitions is the underlying reason for not achieving interrelation between the observables.
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Affiliation(s)
- Prasanta Kundu
- S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Soma Saha
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata 700073, India.
| | - Gautam Gangopadhyay
- S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
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2
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Das M, Ray DS. Critical and scaling behavior of delayed bifurcations in nonlinear systems with dynamic disorder. J CHEM SCI 2023. [DOI: 10.1007/s12039-023-02148-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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3
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Singh D, Punia B, Chaudhury S. Theoretical Tools to Quantify Stochastic Fluctuations in Single-Molecule Catalysis by Enzymes and Nanoparticles. ACS OMEGA 2022; 7:47587-47600. [PMID: 36591158 PMCID: PMC9798497 DOI: 10.1021/acsomega.2c06316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/02/2022] [Indexed: 06/11/2023]
Abstract
Single-molecule microscopic techniques allow the counting of successive turnover events and the study of the time-dependent fluctuations of the catalytic activities of individual enzymes and different sites on a single heterogeneous nanocatalyst. It is important to establish theoretical methods to obtain the statistical measurements of such stochastic fluctuations that provide insight into the catalytic mechanism. In this review, we discuss a few theoretical frameworks for evaluating the first passage time distribution functions using a self-consistent pathway approach and chemical master equations, to establish a connection with experimental observables. The measurable probability distribution functions and their moments depend on the molecular details of the reaction and provide a way to quantify the molecular mechanisms of the reaction process. The statistical measurements of these fluctuations should provide insight into the enzymatic mechanism.
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Affiliation(s)
- Divya Singh
- School
of Chemistry, Tel Aviv University, Tel Aviv6997801, Israel
| | - Bhawakshi Punia
- Department
of Chemistry, Indian Institute of Science
Education and Research, Dr. Homi Bhabha Road, Pune411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department
of Chemistry, Indian Institute of Science
Education and Research, Dr. Homi Bhabha Road, Pune411008, Maharashtra, India
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4
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An S, Patel P, Liu C, Skodje RT. Computational Aspects of Single-Molecule Kinetics for Coupled Catalytic Cycles: A Spectral Analysis. J Phys Chem A 2022; 126:3783-3796. [PMID: 35658508 DOI: 10.1021/acs.jpca.2c02153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catalysis from single active sites is analyzed using methods developed from single-molecule kinetics. Using a stochastic Markov-state description, the observable properties of general catalytic networks of reactions are expressed using an eigenvalue decomposition of the transition matrix for the Markov process. By the use of a sensitivity analysis, the necessary eigenvalues and eigenvectors are related to the energies of controlling barriers and wells located along the reaction routes. A generalization of the energetic span theory allows the eigenvalues to be computed from several activation energies corresponding to distinct barrier-well pairings. The formalism is demonstrated for model problems and for a physically realistic mechanism for an alkene hydrogenation reaction on a single-atom catalyst. The spectral analysis permits a hierarchy of timescales to be identified from the single-molecule signal, which correspond to specific relaxation modes in the network.
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Affiliation(s)
- Suming An
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Prajay Patel
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60639, United States
| | - Cong Liu
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60639, United States
| | - Rex T Skodje
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
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5
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Lim H, Jung Y. Reaction-path statistical mechanics of enzymatic kinetics. J Chem Phys 2022; 156:134108. [PMID: 35395879 DOI: 10.1063/5.0075831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We introduce a reaction-path statistical mechanics formalism based on the principle of large deviations to quantify the kinetics of single-molecule enzymatic reaction processes under the Michaelis-Menten mechanism, which exemplifies an out-of-equilibrium process in the living system. Our theoretical approach begins with the principle of equal a priori probabilities and defines the reaction path entropy to construct a new nonequilibrium ensemble as a collection of possible chemical reaction paths. As a result, we evaluate a variety of path-based partition functions and free energies by using the formalism of statistical mechanics. They allow us to calculate the timescales of a given enzymatic reaction, even in the absence of an explicit boundary condition that is necessary for the equilibrium ensemble. We also consider the large deviation theory under a closed-boundary condition of the fixed observation time to quantify the enzyme-substrate unbinding rates. The result demonstrates the presence of a phase-separation-like, bimodal behavior in unbinding events at a finite timescale, and the behavior vanishes as its rate function converges to a single phase in the long-time limit.
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Affiliation(s)
- Hyuntae Lim
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - YounJoon Jung
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
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6
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Kim K, Song S, Sung J. Non‐steady‐state enzyme reaction dynamics. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kyungwoo Kim
- Department of Chemistry and Institute of Innovative Functional Imaging Chung‐Ang University Seoul South Korea
| | - Sanggeun Song
- Department of Chemistry and Institute of Innovative Functional Imaging Chung‐Ang University Seoul South Korea
| | - Jaeyoung Sung
- Department of Chemistry and Institute of Innovative Functional Imaging Chung‐Ang University Seoul South Korea
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7
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Kang J, Park SJ, Kim JH, Chen P, Sung J. Stochastic Kinetics of Nanocatalytic Systems. PHYSICAL REVIEW LETTERS 2021; 126:126001. [PMID: 33834800 DOI: 10.1103/physrevlett.126.126001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/18/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
Catalytic reaction events occurring on the surface of a nanoparticle constitute a complex stochastic process. Although advances in modern single-molecule experiments enable direct measurements of individual catalytic turnover events occurring on a segment of a single nanoparticle, we do not yet know how to measure the number of catalytic sites in each segment or how the catalytic turnover counting statistics and the catalytic turnover time distribution are related to the microscopic dynamics of catalytic reactions. Here, we address these issues by presenting a stochastic kinetics for nanoparticle catalytic systems. We propose a new experimental measure of the number of catalytic sites in terms of the mean and variance of the catalytic event count. By considering three types of nanocatalytic systems, we investigate how the mean, the variance, and the distribution of the catalytic turnover time depend on the catalytic reaction dynamics, the heterogeneity of catalytic activity, and communication among catalytic sites. This work enables accurate quantitative analyses of single-molecule experiments for nanocatalytic systems and enzymes with multiple catalytic sites.
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Affiliation(s)
- Jingyu Kang
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
| | - Seong Jun Park
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
| | - Ji-Hyun Kim
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Jaeyoung Sung
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
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8
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Song S, Yang GS, Park SJ, Hong S, Kim JH, Sung J. Frequency spectrum of chemical fluctuation: A probe of reaction mechanism and dynamics. PLoS Comput Biol 2019; 15:e1007356. [PMID: 31525182 PMCID: PMC6762214 DOI: 10.1371/journal.pcbi.1007356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/26/2019] [Accepted: 08/22/2019] [Indexed: 11/18/2022] Open
Abstract
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically, and the frequency spectrum of this chemical fluctuation carries valuable information about the dynamics of the reactions creating these biomolecules. Recent advances in single-cell techniques enable direct monitoring of the time-traces of the protein number in each cell; however, it is not yet clear how the stochastic dynamics of these time-traces is related to the reaction mechanism and dynamics. Here, we derive a rigorous relation between the frequency-spectrum of the product number fluctuation and the reaction mechanism and dynamics, starting from a generalized master equation. This relation enables us to analyze the time-traces of the protein number and extract information about dynamics of mRNA number and transcriptional regulation, which cannot be directly observed by current experimental techniques. We demonstrate our frequency spectrum analysis of protein number fluctuation, using the gene network model of luciferase expression under the control of the Bmal 1a promoter in mouse fibroblast cells. We also discuss how the dynamic heterogeneity of transcription and translation rates affects the frequency-spectra of the mRNA and protein number.
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Affiliation(s)
- Sanggeun Song
- Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, Korea
- Department of Chemistry, Chung-Ang University, Seoul, Korea
| | - Gil-Suk Yang
- Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, Korea
- Department of Chemistry, Chung-Ang University, Seoul, Korea
| | - Seong Jun Park
- Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, Korea
- Department of Chemistry, Chung-Ang University, Seoul, Korea
| | - Sungguan Hong
- Department of Chemistry, Chung-Ang University, Seoul, Korea
- * E-mail: (SH); (JHK); (JS)
| | - Ji-Hyun Kim
- Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, Korea
- * E-mail: (SH); (JHK); (JS)
| | - Jaeyoung Sung
- Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, Korea
- Department of Chemistry, Chung-Ang University, Seoul, Korea
- * E-mail: (SH); (JHK); (JS)
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9
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Kang J, Park SJ, Kim J, Sung J. Effects of Non‐Poisson Transcription Dynamics on Mean mRNA Number Dynamics in Living Cells. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jingyu Kang
- Creative Research Initiative Center for Chemical Dynamics in Living CellsChung‐Ang University Seoul 06974 South Korea
- Department of ChemistryChung‐Ang University Seoul 06974 South Korea
| | - Seong Jun Park
- Creative Research Initiative Center for Chemical Dynamics in Living CellsChung‐Ang University Seoul 06974 South Korea
- Department of ChemistryChung‐Ang University Seoul 06974 South Korea
| | - Ji‐Hyun Kim
- Creative Research Initiative Center for Chemical Dynamics in Living CellsChung‐Ang University Seoul 06974 South Korea
| | - Jaeyoung Sung
- Creative Research Initiative Center for Chemical Dynamics in Living CellsChung‐Ang University Seoul 06974 South Korea
- Department of ChemistryChung‐Ang University Seoul 06974 South Korea
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10
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Shin K, Song S, Song YH, Hahn S, Kim JH, Lee G, Jeong IC, Sung J, Lee KT. Anomalous Dynamics of in Vivo Cargo Delivery by Motor Protein Multiplexes. J Phys Chem Lett 2019; 10:3071-3079. [PMID: 31117686 DOI: 10.1021/acs.jpclett.9b01106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Vesicle transport conducted by motor protein multiplexes (MPMs), which is ubiquitous among eukaryotes, shows anomalous and stochastic dynamics qualitatively different from the dynamics of thermal motion and artificial active matter; the relationship between in vivo vesicle-delivery dynamics and the underlying physicochemical processes is not yet quantitatively understood. Addressing this issue, we perform accurate tracking of individual vesicles, containing upconverting nanoparticles, transported by kinesin-dynein-multiplexes along axonal microtubules. The mean-square-displacement of vesicles along the microtubule exhibits unusual dynamic phase transitions that are seemingly inconsistent with the scaling behavior of the mean-first-passage time over the travel length. These paradoxical results and the vesicle displacement distribution are quantitatively explained and predicted by a multimode MPM model, developed in the current work, where ATP-hydrolysis-coupled motion of MPM has both unidirectional and bidirectional modes.
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Affiliation(s)
- Kyujin Shin
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology (GIST) , Gwangju 61005 , Korea
| | - Sanggeun Song
- Creative Research Initiative Center for Chemical Dynamics in Living Cells , Chung-Ang University , Seoul 06974 , Korea
- Department of Chemistry , Chung-Ang University , Seoul 06974 , Korea
- National Institute of Innovative Functional Imaging , Chung-Ang University , Seoul 06974 , Korea
| | - Yo Han Song
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology (GIST) , Gwangju 61005 , Korea
| | - Seungsoo Hahn
- Creative Research Initiative Center for Chemical Dynamics in Living Cells , Chung-Ang University , Seoul 06974 , Korea
- Da Vinci College of General Education , Chung-Ang University , Seoul 06974 , Korea
| | - Ji-Hyun Kim
- Creative Research Initiative Center for Chemical Dynamics in Living Cells , Chung-Ang University , Seoul 06974 , Korea
| | - Gibok Lee
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology (GIST) , Gwangju 61005 , Korea
| | - In-Chun Jeong
- Creative Research Initiative Center for Chemical Dynamics in Living Cells , Chung-Ang University , Seoul 06974 , Korea
- Department of Chemistry , Chung-Ang University , Seoul 06974 , Korea
- National Institute of Innovative Functional Imaging , Chung-Ang University , Seoul 06974 , Korea
| | - Jaeyoung Sung
- Creative Research Initiative Center for Chemical Dynamics in Living Cells , Chung-Ang University , Seoul 06974 , Korea
- Department of Chemistry , Chung-Ang University , Seoul 06974 , Korea
- National Institute of Innovative Functional Imaging , Chung-Ang University , Seoul 06974 , Korea
| | - Kang Taek Lee
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology (GIST) , Gwangju 61005 , Korea
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11
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Park SJ, Song S, Yang GS, Kim PM, Yoon S, Kim JH, Sung J. The Chemical Fluctuation Theorem governing gene expression. Nat Commun 2018; 9:297. [PMID: 29352116 PMCID: PMC5775451 DOI: 10.1038/s41467-017-02737-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 12/20/2017] [Indexed: 11/20/2022] Open
Abstract
Gene expression is a complex stochastic process composed of numerous enzymatic reactions with rates coupled to hidden cell-state variables. Despite advances in single-cell technologies, the lack of a theory accurately describing the gene expression process has restricted a robust, quantitative understanding of gene expression variability among cells. Here we present the Chemical Fluctuation Theorem (CFT), providing an accurate relationship between the environment-coupled chemical dynamics of gene expression and gene expression variability. Combined with a general, accurate model of environment-coupled transcription processes, the CFT provides a unified explanation of mRNA variability for various experimental systems. From this analysis, we construct a quantitative model of transcription dynamics enabling analytic predictions for the dependence of mRNA noise on the mRNA lifetime distribution, confirmed against stochastic simulation. This work suggests promising new directions for quantitative investigation into cellular control over biological functions by making complex dynamics of intracellular reactions accessible to rigorous mathematical deductions. A unified framework to understand gene expression noise is still lacking. Here the authors derive a universal theorem relating the biological noise with dynamics of birth and death processes and present a model of transcription dynamics, allowing analytical prediction of the dependence of mRNA noise on mRNA lifetime variability.
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Affiliation(s)
- Seong Jun Park
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, 06974, Korea.,Department of Chemistry, Chung-Ang University, Seoul, 06974, Korea.,National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul, 06974, Korea
| | - Sanggeun Song
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, 06974, Korea.,Department of Chemistry, Chung-Ang University, Seoul, 06974, Korea.,National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul, 06974, Korea
| | - Gil-Suk Yang
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, 06974, Korea
| | - Philip M Kim
- Terrence Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics and Department of Computer Science, University of Toronto, Toronto, M5S 3E1, ON, Canada
| | - Sangwoon Yoon
- Department of Chemistry, Chung-Ang University, Seoul, 06974, Korea.
| | - Ji-Hyun Kim
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, 06974, Korea.
| | - Jaeyoung Sung
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, 06974, Korea. .,Department of Chemistry, Chung-Ang University, Seoul, 06974, Korea. .,National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul, 06974, Korea.
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12
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Jeong IC, Song S, Kim D, Park SJ, Kim JH, Sung J. Comment on "Nonrenewal Statistics in the Catalytic Activity of Enzyme Molecules at Mesoscopic Concentrations". PHYSICAL REVIEW LETTERS 2017; 119:099801. [PMID: 28949572 DOI: 10.1103/physrevlett.119.099801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Indexed: 06/07/2023]
Affiliation(s)
- In-Chun Jeong
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
- National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul 06974, Korea
| | - Sanggeun Song
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
- National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul 06974, Korea
| | - Daehyun Kim
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
- National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul 06974, Korea
| | - Seong Jun Park
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
- National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul 06974, Korea
| | - Ji-Hyun Kim
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
| | - Jaeyoung Sung
- Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
- National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul 06974, Korea
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13
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Avila TR, Piephoff DE, Cao J. Generic Schemes for Single-Molecule Kinetics. 2: Information Content of the Poisson Indicator. J Phys Chem B 2017; 121:7750-7760. [DOI: 10.1021/acs.jpcb.7b01516] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Thomas R. Avila
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - D. Evan Piephoff
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jianshu Cao
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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14
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Park SJ, Song S, Jeong IC, Koh HR, Kim JH, Sung J. Nonclassical Kinetics of Clonal yet Heterogeneous Enzymes. J Phys Chem Lett 2017; 8:3152-3158. [PMID: 28609615 DOI: 10.1021/acs.jpclett.7b01218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Enzyme-to-enzyme variation in the catalytic rate is ubiquitous among single enzymes created from the same genetic information, which persists over the lifetimes of living cells. Despite advances in single-enzyme technologies, the lack of an enzyme reaction model accounting for the heterogeneous activity of single enzymes has hindered a quantitative understanding of the nonclassical stochastic outcome of single enzyme systems. Here we present a new statistical kinetics and exactly solvable models for clonal yet heterogeneous enzymes with possibly nonergodic state dynamics and state-dependent reactivity, which enable a quantitative understanding of modern single-enzyme experimental results for the mean and fluctuation in the number of product molecules created by single enzymes. We also propose a new experimental measure of the heterogeneity and nonergodicity for a system of enzymes.
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Affiliation(s)
- Seong Jun Park
- National Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University , Seoul 06974, Korea
- National Institute of Innovative Functional Imaging, Chung-Ang University , Seoul 06974, Korea
| | - Sanggeun Song
- National Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University , Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University , Seoul 06974, Korea
- National Institute of Innovative Functional Imaging, Chung-Ang University , Seoul 06974, Korea
| | - In-Chun Jeong
- National Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University , Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University , Seoul 06974, Korea
- National Institute of Innovative Functional Imaging, Chung-Ang University , Seoul 06974, Korea
| | - Hye Ran Koh
- National Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University , Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University , Seoul 06974, Korea
| | - Ji-Hyun Kim
- National Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University , Seoul 06974, Korea
| | - Jaeyoung Sung
- National Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University , Seoul 06974, Korea
- Department of Chemistry, Chung-Ang University , Seoul 06974, Korea
- National Institute of Innovative Functional Imaging, Chung-Ang University , Seoul 06974, Korea
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15
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Singh D, Chaudhury S. Statistical properties of fluctuating enzymes with dynamic cooperativity using a first passage time distribution formalism. J Chem Phys 2017; 146:145103. [DOI: 10.1063/1.4979945] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Divya Singh
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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16
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Barato AC, Seifert U. Skewness and Kurtosis in Statistical Kinetics. PHYSICAL REVIEW LETTERS 2015; 115:188103. [PMID: 26565501 DOI: 10.1103/physrevlett.115.188103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Indexed: 06/05/2023]
Abstract
We obtain lower and upper bounds on the skewness and kurtosis associated with the cycle completion time of unicyclic enzymatic reaction schemes. Analogous to a well-known lower bound on the randomness parameter, the lower bounds on skewness and kurtosis are related to the number of intermediate states in the underlying chemical reaction network. Our results demonstrate that evaluating these higher order moments with single molecule data can lead to information about the enzymatic scheme that is not contained in the randomness parameter.
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Affiliation(s)
- Andre C Barato
- II. Institut für Theoretische Physik, Universität Stuttgart, 70550 Stuttgart, Germany
- Max Planck Institute for the Physics of Complex Systems, Nöthnizer Straße 38, 01187 Dresden, Germany
| | - Udo Seifert
- II. Institut für Theoretische Physik, Universität Stuttgart, 70550 Stuttgart, Germany
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17
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Chaudhury S. Poisson Indicator and Fano Factor for Probing Dynamic Disorder in Single-Molecule Enzyme Inhibition Kinetics. J Phys Chem B 2014; 118:10405-12. [DOI: 10.1021/jp506141v] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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18
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Moffitt JR, Bustamante C. Extracting signal from noise: kinetic mechanisms from a Michaelis-Menten-like expression for enzymatic fluctuations. FEBS J 2013; 281:498-517. [PMID: 24428386 DOI: 10.1111/febs.12545] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/17/2013] [Accepted: 09/23/2013] [Indexed: 12/25/2022]
Abstract
Enzyme-catalyzed reactions are naturally stochastic, and precision measurements of these fluctuations, made possible by single-molecule methods, promise to provide fundamentally new constraints on the possible mechanisms underlying these reactions. We review some aspects of statistical kinetics: a new field with the goal of extracting mechanistic information from statistical measures of fluctuations in chemical reactions. We focus on a widespread and important statistical measure known as the randomness parameter. This parameter is remarkably simple in that it is the squared coefficient of variation of the cycle completion times, although it places significant limits on the minimal complexity of possible enzymatic mechanisms. Recently, a general expression has been introduced for the substrate dependence of the randomness parameter that is for rate fluctuations what the Michaelis-Menten expression is for the mean rate of product generation. We discuss the information provided by the new kinetic parameters introduced by this expression and demonstrate that this expression can simplify the vast majority of published models.
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Affiliation(s)
- Jeffrey R Moffitt
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
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19
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Chaudhury S, Cao J, Sinitsyn NA. Universality of Poisson Indicator and Fano Factor of Transport Event Statistics in Ion Channels and Enzyme Kinetics. J Phys Chem B 2013. [DOI: 10.1021/jp3096659] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Srabanti Chaudhury
- Theoretical Division, Los Alamos National Laboratory, Los
Alamos, New Mexico, 87545 United States
- New Mexico Consortium,
Los Alamos, New Mexico, 87544 United States
| | - Jianshu Cao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts,
02139 United States
| | - Nikolai A. Sinitsyn
- Theoretical Division, Los Alamos National Laboratory, Los
Alamos, New Mexico, 87545 United States
- New Mexico Consortium,
Los Alamos, New Mexico, 87544 United States
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20
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Lim YR, Park SJ, Park BJ, Cao J, Silbey RJ, Sung J. Reaction Event Counting Statistics of Biopolymer Reaction Systems with Dynamic Heterogeneity. J Chem Theory Comput 2012; 8:1415-25. [DOI: 10.1021/ct200785q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Rim Lim
- Department of Chemistry, Chung-Ang
University, Seoul 156-756, Korea
| | - Seong Jun Park
- Department of Chemistry, Chung-Ang
University, Seoul 156-756, Korea
| | - Bo Jung Park
- Department of Chemistry, Chung-Ang
University, Seoul 156-756, Korea
| | - Jianshu Cao
- Department of Chemistry, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Robert J. Silbey
- Department of Chemistry, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jaeyoung Sung
- Department of Chemistry, Chung-Ang
University, Seoul 156-756, Korea
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21
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Yang S, Cao J, Silbey RJ, Sung J. Quantitative interpretation of the randomness in single enzyme turnover times. Biophys J 2011; 101:519-24. [PMID: 21806919 DOI: 10.1016/j.bpj.2011.06.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2011] [Revised: 06/09/2011] [Accepted: 06/13/2011] [Indexed: 11/28/2022] Open
Abstract
Fluctuating turnover times of a single enzyme become observable with the advent of modern cutting-edge, single enzyme experimental techniques. Although the conventional chemical kinetics and its modern generalizations could provide a good quantitative description for the mean of the enzymatic turnover times, to our knowledge there has not yet been a successful quantitative interpretation for the variance or the randomness of the enzymatic turnover times. In this review, we briefly review several theories in this field, and compare predictions of these theories to the randomness parameter data reported for β-galactosidase enzyme. We find the recently proposed kinetics for renewal reaction processes could provide an excellent quantitative interpretation of the randomness parameter data. From the analysis of the randomness parameter data of the single enzyme reaction, one can extract quantitative information about the mean lifetime of enzyme-substrate complex; the success or the failure probability of the catalytic reaction per each formation of ES complex; and the non-Poisson character of the reaction dynamics of the ES complex (which is beyond reach of the long-standing paradigm of the conventional chemical kinetics).
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Affiliation(s)
- Seongeun Yang
- Department of Chemistry, Chung-Ang University, Seoul, Korea
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22
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Berezhkovskii AM. Renewal theory for single-molecule systems with multiple reaction channels. J Chem Phys 2011; 134:074114. [PMID: 21341835 DOI: 10.1063/1.3551506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Some single-molecule systems share a common feature: the system performs different cycles returning after each cycle to the same state. In such systems we deal with renewal processes. Examples include (1) single-molecule enzymatic reactions, (2) membrane transport through single-occupancy channels, (3) single-molecule fluorescence spectroscopy, and (4) motion of molecular motors. The paper is focused on the analysis of such systems by means of the renewal theory. To be more specific, the theory of renewal processes is used to study multivariate distribution functions of the numbers of different events in a given observation time. Our main results are simple formulas derived for the Laplace transforms of the distribution functions. General results are illustrated by consideration of several examples.
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Affiliation(s)
- A M Berezhkovskii
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA.
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