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  • RecA filament maintains structural integrity using ATP-driven internal dynamics
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    Views: 500, 2017.09.11 08:34:54
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    • Science Advances Vol. 3, no. 9, e1700676 (2017)
    • Sung Hyun Kim, TakKyoon Ahn, Tao Ju Cui, Sweeny Chauhan, Jaeyoung Sung, Chirlmin Joo, and Doseok Kim*
      †Department of Physics and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Republic of Korea.
      ‡Department of Bionanoscience, Kavli Institute of NanoScience, Delft University of Technology, 2628 CJ Delft, Netherlands.
      §Department of Chemistry, Chung-Ang University, Seoul, Republic of Korea.
    • http://advances.sciencemag.org/content/3/9/e1700676

    At the core of homologous DNA repair, RecA catalyzes the strand exchange reaction. This process is initiated by a RecA loading protein, which nucleates clusters of RecA proteins on single-stranded DNA. Each cluster grows to cover the single-stranded DNA but may leave 1- to 2-nucleotide (nt) gaps between the clusters due to three different structural phases of the nucleoprotein filaments. It remains to be revealed how RecA proteins eliminate the gaps to make a seamless kilobase-long filament. We develop a single-molecule fluorescence assay to observe the novel internal dynamics of the RecA filament. We directly observe the structural phases of individual RecA filaments and find that RecA proteins move their positions along the substrate DNA to change the phase of the filament. This reorganization process, which is a prerequisite step for interjoining of two adjacent clusters, requires adenosine triphosphate hydrolysis and is tightly regulated by the recombination hotspot, Chi. Furthermore, RecA proteins recognize and self-align to a 3-nt-period sequence pattern of TGG. This sequence-dependent phase bias may help the RecA filament to maintain structural integrity within the kilobase-long filament for accurate homology search and strand exchange reaction.

     

     

     

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    Fig. 1Real-time observation of RecA filament phase shifting dynamics.

    (A) Schematic of phase detection of RecA filament. The number of the gaps between a dye pair is determined by the phase of the filament and can be read by FRET efficiency. (B) Schematic of DNA immobilization on the polyethylene glycol–coated quartz slide via a streptavidin-biotin linker. (C to E) Population distributions of single-molecule FRET from (C) an 8-nt, (D) a 9-nt, and (B) a 10-nt separation of the dye pair. Gray bars are the distribution observed in the presence of 1 μM RecA and 1 mM ATP, and empty bars are obtained from bare DNA in the absence of RecA. Solid lines are Gaussian fits. (F to H) Representative single-molecule traces obtained from (F) an 8-nt, (G) a 9-nt, and (H) a 10-nt dye separation. Time traces with 32-ms time resolution (gray) were depicted with their moving average with a 1-s time window (black). (I to J) Dwell time distributions of high (I) and low (J) FRET states with a 10-nt dye separation. Solid lines are single-exponential fits. A manually given threshold value was applied to each trace to determine the transition points, and 150 traces were processed to build a dwell time histogram. The average dwell times with SEs were obtained from three independent data sets. (K) Averaged time correlation functions of single-molecule traces obtained with 8 nt (orange filled circle), 9 nt (black open circle), and 10 nt (blue filled box) in the presence of ATP and 10 nt in the presence of ATPγS (gray crosses). Solid lines are two exponential (gray) and three exponential fits (red) of the correlation functions (fit parameters are summarized in table S1).

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  • Frequency spectrum of chemical fluctuation: a probe of reaction mechanism and dynamics file
  • Views: 257
  • PLOS Computational Biology, 15(9), e1007356
  • Sanggeun Song1,2, Gil-Suk Yang1,2, Seong Jun Park1,2, Sungguan Hong2*, JiHyun Kim1*, Jaeyoung Sung1,2*
    1 Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, Korea,
    2 Department of Chemistry, Chung-Ang University, Seoul, Korea
  • 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 m...
Mar 18, 2019 12:17:32
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  • Anomalous Dynamics of in vivo Cargo Delivery by Motor Protein Multiplexes file
  • Views: 304
  • Journal of Physical Chemistry Letters 10, 3071-3079 (2019)
  • Kyujin Shin†1, Sanggeun Song†2,3,4, Yo Han Song†1, Seungsoo Hahn2,5, Ji-Hyun Kim2, Gibok Lee1, In-Chun Jeong2,3,4, Jaeyoung Sung*2,3,4, and Kang Taek Lee*1
    1 Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Korea.
    2 Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul, 06974, Korea.
    3 Department of Chemistry, Chung-Ang University, Seoul, 06974, Korea.
    4 National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul, 06974, Korea.
    5 Da Vinci College of General Education, Chung-Ang University, Seoul, 06974, Korea.
  • Vesicle-transport conducted by motor-protein-multiplexes, ubiquitous among eukaryotes, shows mysterious stochastic dynamics, qualitatively different from dynamics of thermal motion and artificial active matter; the relationship between in vivo vesicle-delivery dynamics and dynamics of the underlying...
May 13, 2019 02:22:51
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  • Counting statistics of single molecule reaction events and reaction dynamics of a single molecule file
  • Views: 313
  • Chemical Physics Letters, Volume 415, Issues 1–3, Pages 10–14
  • Jaeyoung Sung(a,b) Robert J. Silbey(a)*
    a. Department of Chemistry, Massachusetts Institute of Technology, Building 6-123, 77 Massachusetts Avenue, Cambridge, MA 02139-4307, USA
    b. Department of Chemistry, Chung-Ang University, Seoul 156-756, Republic of Korea
  • We present an exact form for counting statistics of single-molecule (SM) reaction events for a molecule with arbitrary hidden dynamical processes coupled to the reaction, examples of which can be found in many single biopolymer experiments. The result suggests a novel SM experimental observable, H, ...
Mar 04, 2016 15:46:32
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  • Contribution of ​RNA polymerase concentration variation to protein expression noise file
  • Views: 374
  • Nature Communications 5, Article number: 4761
  • Sora Yang, Seunghyeon Kim, Yu Rim Lim, Cheolhee Kim, Hyeong Jeon An, Ji-Hyun Kim, Jaeyoung Sung* & Nam Ki Lee*
  • Cell-to-cell variation in gene expression, or noise, is a general phenomenon observed within cell populations. Transcription is known to be the key stage of gene expression where noise is generated, however, how variation in ​RNA polymerase (​RNAP) concentration contributes to gene expression noise ...
Mar 04, 2016 16:16:16
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  • Transport Dynamics of Complex Fluids file
  • Views: 380
  • Proceedings of the National Academy of Sciences of the United States of America 116 (26), 12733-12742 (2019)
  • Sanggeun Song1,2,3, Seong Jun Park1,2,3, Minjung Kim4, Jun Soo Kim5, Bong June Sung6, Sangyoub Lee4, Ji-Hyun Kim*1 and Jaeyoung Sung*1,2,3
    1 Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Republic of Korea
    2 Department of Chemistry, Chung-Ang University, Seoul 06974, Republic of Korea
    3 National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul 06974, Republic of Korea
    4 Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
    5 Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
    6 Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
  • Thermal motion in complex fluids is a complicated stochastic process but ubiquitously exhibits initial ballistic, intermediate sub-diffusive, and long-time diffusive motion, unless interrupted. Despite its relevance to numerous dynamical processes of interest in modern science, a unified, quantitati...
Mar 18, 2019 11:53:21
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  • Reaction Event Counting Statistics of Biopolymer Reaction Systems with Dynamic Heterogeneity file
  • Views: 382
  • Journal of Chemical Theory and Computation, 8 (4), 2012, pp 1415–1425
  • Yu Rim Lim †, Seong Jun Park †, Bo Jung Park †, Jianshu Cao *‡, Robert J. Silbey ‡, and Jaeyoung Sung *†§
    † Department of Chemistry, Chung-Ang University, Seoul 156-756, Korea
    ‡ Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
  • We investigate the reaction event counting statistics (RECS) of an elementary biopolymer reaction in which the rate coefficient is dependent on states of the biopolymer and the surrounding environment and discover a universal kinetic phase transition in the RECS of the reaction system with dynamic h...
Mar 04, 2016 16:09:30
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Mar 04, 2016 16:02:49
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  • RecA filament maintains structural integrity using ATP-driven internal dynamics file
  • Views: 500
  • Science Advances Vol. 3, no. 9, e1700676 (2017)
  • Sung Hyun Kim, TakKyoon Ahn, Tao Ju Cui, Sweeny Chauhan, Jaeyoung Sung, Chirlmin Joo, and Doseok Kim*
    †Department of Physics and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Republic of Korea.
    ‡Department of Bionanoscience, Kavli Institute of NanoScience, Delft University of Technology, 2628 CJ Delft, Netherlands.
    §Department of Chemistry, Chung-Ang University, Seoul, Republic of Korea.
  • At the core of homologous DNA repair, RecA catalyzes the strand exchange reaction. This process is initiated by a RecA loading protein, which nucleates clusters of RecA proteins on single-stranded DNA. Each cluster grows to cover the single-stranded DNA but may leave 1- to 2-nucleotide (nt) gaps betw...
Sep 11, 2017 08:34:54
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  • The Chemical Fluctuation Theorem governing gene expression file
  • Views: 534
  • Nature Communications 9, Article number: 297 (2018)
  • Seong Jun Park1-3, Sanggeun Song1-3, Gil-Suk Yang1, Philip M. Kim4, Sangwoon Yoon2*, Ji-Hyun Kim1*, and Jaeyoung Sung1-3*
    1 Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea.
    2 Department of Chemistry, Chung-Ang University, Seoul 06974, Korea.
    3 National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul 06974, Korea.
    4 Terrence Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics and Department of Computer Science, University of Toronto, Toronto M5S 3E1, Canada.
  • 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 unders...
Dec 18, 2017 20:33:39
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  • Quantitative understanding of probabilistic behavior of living cells operated by vibrant reaction networks file
  • Views: 540
  • Physical Review X 5, 031014 (2015)
  • Yu Rim Lim,1,* Ji-Hyun Kim,2,*,† Seong Jun Park,1 Gil-Suk Yang,1 Sanggeun Song,1 Suk-kyu Chang,1 Nam Ki Lee,3 and Jaeyoung Sung1,‡
    1Department of Chemistry and Institute of Innovative Functional Imaging, Chung-Ang University, Seoul 156-756, Korea.
    2Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139, U. S. A.
    3Department of Physics and School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Korea.
  • For quantitative understanding of probabilistic behaviors of living cells, it is essential to construct a correct mathematical description of intracellular networks interacting with complex cell environments, which has been a formidable task. Here, we present a novel model and stochastic kinetics fo...
Mar 04, 2016 16:18:44
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  • Nonclassical Kinetics of Clonal yet Heterogeneous Enzymes file
  • Views: 603
  • The Journal of Physical Chemistry Letters, 8, 3152-3158 (2017)
  • Seong Jun Park†§⊥, Sanggeun Song†‡§⊥, In-Chun Jeong†‡§, Hye Ran Koh†‡, Ji-Hyun Kim*†, and 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
  • 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 acti...
Jun 27, 2017 17:44:12
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  • Quantitative Interpretation of the Randomness in Single Enzyme Turnover Times file
  • Views: 667
  • Biophysical Journal, Volume 101, Issue 3, Pages 519–524
  • Seongeun Yang,† Jianshu Cao,‡ Robert J. Silbey,‡* and Jaeyoung Sung†*
    †Department of Chemistry, Chung-Ang University, Seoul, Korea; and ‡Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
  • 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 turnov...
Mar 04, 2016 16:05:40
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  • Comment on “Nonrenewal Statistics in the Catalytic Activity of Enzyme Molecules at Mesoscopic Concentrations” file
  • Views: 735
  • Physical Review Letters 119, 099801 (2017)
  • In-Chun Jeong, Sanggeun Song, Daehyun Kim, Seong Jun Park, Ji-Hyun Kim, and 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
  • Comment on “Nonrenewal Statistics in the Catalytic Activity of Enzyme Molecules at Mesoscopic Concentrations” Figure 1 A system of N enzymes (a) under the synchronized initial condition and (b) in the steady state. Figure 2 Comparison between theory and simulation.
Sep 05, 2017 09:03:42
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