Cheng Tan

Postdoc of Computational Biophysics

Kyoto University

Biography

I am currently a postdoc in the Department of Biophysics at Kyoto University. I have started my postdoctoral research in Prof. Shoji Takada’s laboratory since 2014. My current research interests include functional mechanisms of DNA-binding proteins, the multi-scale organization of the genome, and modeling of biomolecules in molecular dynamics simulations.

I used to be a free software fanatic, with up to 10+ years of experience with various Linux distributions. For a long time, I was proud of having a signature of RMS on my doctoral dissertation. But now I prefer to use the paid software, to save my time and to focus on important things. Still, I have Arch Linux installed on my VPS.

When I was young, I bought thousands of classical music CDs and listened to 10% of them. I bought all the cello concerto scores I was able to find, pretending to read 5% of them. Although I always enjoyed being an amateur.

In order to participate in a sport without any physical contact, I started practicing the Rubik’s cube in 2009, and I was lucky enough to break a national record in a game in 2010. So I stopped practicing since then.

Anyway, welcome to my personal website!

Interests

Statistical Physics
Computer Simulations
Genome Organization
Data Visualization

Education

PhD in Physics, 2014

Nanjing University
BSc in Physics, 2007

Nanjing University

Selected Publications

Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data

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.

Cheng Tan, Shoji Takada

J. Chem. Theory Comput., 2018, XXX (XX), XXXX–XXXX.

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Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics

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.

Cheng Tan, Tsuyoshi Terakawa, Shoji Takada

J. Am. Chem. Soc., 2016, 138 (27), 8512–8522.

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Recent Publications

Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data
Cheng Tan, Shoji Takada

J. Chem. Theory Comput., 2018, XXX (XX), XXXX–XXXX.

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DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations
Giovanni B. Brandani, Toru Niina, Cheng Tan, Shoji Takada

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
Toru Niina, Giovanni B. Brandani, Cheng Tan, Shoji Takada

PLoS Comp. Biol., 2017, 13 (12), e1005880

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Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics
Cheng Tan, Tsuyoshi Terakawa, Shoji Takada

J. Am. Chem. Soc., 2016, 138 (27), 8512–8522.

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Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations
Shoji Takada, Ryo Kanada, Cheng Tan, Tsuyoshi Terakawa, Wenfei Li, Hiroo Kenzaki

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
Yunqiang Bian, Cheng Tan, Jun Wang, Yuebiao Sheng, Jian Zhang, Wei Wang

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
Cheng Tan, Wenfei Li, Wei Wang

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
Cheng Tan, Wenfei Li, Wei Wang

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
Chunmei Lv, Cheng Tan, Meng Qin, Dawei Zou, Yi Cao, Wei Wang

Biophys J., 2012, 102 (8), 1944-1951.

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