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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Article DOI: 10.3791/63406-v • 09:17 min • March 1st, 2022
March 1st, 2022 •
*1, *1,2, 3,4, 4, 5,6,7
1Beijing Computational Science Research Center, 2Shenzhen JL Computational Science and Applied Research Institute, 3School of Medical Informatics and Engineering, Xuzhou Medical University, 4Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 5Department of Physics and Astronomy, University of California, Irvine, 6Department of Chemistry, University of California, Irvine, 7NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine
* These authors contributed equally

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The goal of this protocol is to reveal structural dynamics of one-dimensional diffusion of protein along DNA, using a plant transcription factor WRKY domain protein as an exemplary system. To do this, both atomistic and coarse-grained molecular dynamics simulations along with extensive computational samplings have been implemented.

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Structure-Based Simulation Sampling Transcription Factor Protein Movements DNA Atomic-Scale Stepping Coarse-Grained Diffusion Protocol Structural Dynamics One-dimensional Diffusion Plant Transcription Factor WRKY Domain Protein Atomic Simulations Markov State Model Construction 1-bp Stepping Motions Protein Processive Diffusions All-atom MD Trajectory Frames VMD Protein Or Nucleic Selection Alignment Root Means Square Distance Protein Backbone RMSD Trajectory Tool
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