Related Experiment Video
Updated: May 28, 2025
09:52
Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
Published on: January 31, 2019
11.6K
Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by
Abhik Ghosh Moulick1, Rutika Patel1,2, Augustine Onyema1,2
1Department of Chemistry, College of Staten Island, City University of New York, 2800 Victory Blvd., 6S-238, Staten Island, New York 10314, USA.
The Journal of Chemical Physics
|February 10, 2025
Summary
This study reveals that coarse-grained simulations accurately model nucleosome dynamics, showing broader DNA motion and uncovering multiple energy states. This aids understanding of DNA repositioning and sequence-dependent chromatin behavior.
Area of Science:
- Structural Biology
- Computational Biophysics
- Genomics
Background:
- Nucleosome conformational dynamics influence gene regulation and chromatin structure.
- Understanding these dynamics is crucial for deciphering cellular processes.
Purpose of the Study:
- To investigate nucleosome dynamics using molecular dynamics simulations.
- To compare all-atom and coarse-grained (CG) simulations with the SIRAH force field.
- To assess the accuracy and sampling capabilities of CG models for nucleosome behavior.
Main Methods:
- All-atom and coarse-grained molecular dynamics simulations.
- Simulations of alpha satellite palindromic and Widom-601 DNA sequences.
- Analysis of structural parameters and principal component analysis (PCA).
Main Results:
- CG simulations showed good agreement with atomistic models for structural parameters.
- CG simulations provided broader conformational sampling and enhanced DNA end breathing motion.
- PCA revealed multiple free energy minima, particularly in CG simulations, indicating complex DNA dynamics.
Conclusions:
- The SIRAH CG force field is suitable for studying large-scale nucleosome dynamics.
- CG simulations offer valuable insights into DNA repositioning and sequence-dependent nucleosome behavior.
- This work advances computational approaches for chromatin structure and function studies.
Related Concept Videos
02:10The Nucleosome Core Particle
11.9K
Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
11.9K
02:54Nucleosome Remodeling
8.9K
Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
8.9K
02:33The Nucleosome
16.0K
DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...
16.0K
01:17Studying the Cytoskeleton
5.8K
The cytoskeletal architecture can be studied using different microscopic and biochemical techniques. Electron microscopy was instrumental in discovering the cytoskeletal architecture around the 1960s, which allowed obtaining structural information at a high-resolution level. However, the sample preparation procedure often limits this ability in biological samples. Several protocols have been developed over the years to optimize sample preparation. In one of the protocols known as rotary...
5.8K
01:32Chromatin Packaging
16.6K
Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
16.6K