Selected Publications

How transcription factors (TFs) recognize their DNA sequences is often investigated complementarily by highthroughput protein binding assays (modeled by the position weight matrix, PWM) and by structural biology experiments. Here, we propose and test a new modeling method that incorporates the PWM with complex structure data. We model the specific protein−DNA interactions, PWMcos, in terms of an orientation-dependent potential function, which enables us to perform molecular dynamics simulations at unprecedentedly large scales. We show that the PWMcos model reproduces subtle specificity in the protein−DNA recognition: during the target search in genomic sequences, PU.1 moves on highly rugged landscapes and occasionally flips on DNA depending on the sequence; the TATA-binding protein exhibits two remarkably distinct binding modes, of which frequencies differ between TATA-containing and TATA-less promoters. The PWMcos is general and can be applied to any protein−DNA interactions given their PWMs and complex structure data are available.
J. Chem. Theory Comput., 2018, 14 (7), 3877-3889.

The correlation between protein binding to DNA and DNA bending has been observed in many protein-DNA complex structures. These are, however, the correlation in static structures. Due to time and spatial resolutions in experiments, little is known on the dynamic coupling between protein binding and DNA bending. Here, armed with new simulation methods, we investigated the dynamic coupling between protein binding and DNA bending for a bacterial protein HU and 14 other proteins. The sliding of positively-charged HU on negatively-charged DNA is highly coupled with local DNA distortion, which is reminiscent of polaron in physics. In shorter time scale, HU was self-trapped in a locally bent DNA leading to pauses. Spontaneous relaxation in DNA shape resulted in the sliding mode.
J. Am. Chem. Soc., 2016, 138 (27), 8512–8522.

Recent Publications

  • Nucleosomes as allosteric scaffolds for genetic regulation
    Curr. Opin. Struct. Biol., 2020, 62, 93-101.

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  • Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data
    J. Chem. Theory Comput., 2018, 14 (7), 3877-3889.

    Details Full Text

  • DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations
    Nucl. Acids Res., 2018, 46 (6), 2788-2801

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  • Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
    PLoS Comp. Biol., 2017, 13 (12), e1005880

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  • Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics
    J. Am. Chem. Soc., 2016, 138 (27), 8512–8522.

    Details Full Text

  • Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations
    Acc. Chem. Res., 2015, 48 (12), 3026–3035.

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  • Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex
    PLoS Comput. Biol., 2014, 10 (4), e1003562.

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  • Localized Frustration and Binding-Induced Conformational Change in Recognition of 5S RNA by TFIIIA Zinc Finger
    J. Phys. Chem. B, 2013, 117 (50), 15917–15925.

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  • Specific Binding of a Short miRNA Sequence by Zinc Knuckles of Lin28: A Molecular Dynamics Simulation Study
    J. Theor. Comput. Chem., 2013, 12 (8), 1341015.

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  • Low Folding Cooperativity of Hp35 Revealed by Single-Molecule Force Spectroscopy and Molecular Dynamics Simulation
    Biophys J., 2012, 102 (8), 1944-1951.

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I made a gif showing COVID19 infection distribution changes in Japan. Nothing new, just a showcase with python.


I recently got this idea that we can show all the basic trigonometric functions and the derivatives in one figure. So I spent some time to plot it with LaTeX.


This is the beginning of teaching my daughter Chinese characters.


Another LaTeX template for this years documentation.


Cheat Sheet for Maxima v5.42.2.




Yet another dictionary tool written in python. Allow regex.


My snippets for Emacs yasnippet.


A simple tool to plot information content LOGO for PWM. Image format is svg.


This is a package consisting of several small handy tools for analyzing biomolecule structures (protein, RNA, DNA) and CafeMol MD trajectories.


Simple script to perform RESPAC calculations (including APBS) for coarse-grained protein charge distributions.


My spacemacs configurations (init.el) and additional layer settings.


An Emacs major mode for editing CafeMol input file.