JoVE Logo
Faculty Resource Center

Sign In

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

DOI :

10.3791/63406-v

March 1st, 2022

March 1st, 2022

2,772 Views

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

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.

Tags

Structure Based Simulation

-- Views

Related Videos

article

Preparing T Cell Growth Factor from Rat Splenocytes

article

Staining of Proteins in Gels with Coomassie G-250 without Organic Solvent and Acetic Acid

article

Application of Stopped-flow Kinetics Methods to Investigate the Mechanism of Action of a DNA Repair Protein

article

A Noninvasive Hair Sampling Technique to Obtain High Quality DNA from Elusive Small Mammals

article

A Practical and Novel Method to Extract Genomic DNA from Blood Collection Kits for Plasma Protein Preservation

article

Green Fluorescent Protein-based Expression Screening of Membrane Proteins in Escherichia coli

article

Sampling Blood from the Lateral Tail Vein of the Rat

article

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

article

Visualization of Surface-tethered Large DNA Molecules with a Fluorescent Protein DNA Binding Peptide

article

Advanced Confocal Microscopy Techniques to Study Protein-protein Interactions and Kinetics at DNA Lesions

JoVE Logo

Privacy

Terms of Use

Policies

Research

Education

ABOUT JoVE

Copyright © 2024 MyJoVE Corporation. All rights reserved