ArticleBiophysical journal2007
Multiscale modeling of nucleosome dynamics.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 1 of them a synthesis that pooled it.
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Who cites it
52 citing papers in PubMed, 1 synthesis or guideline pooled it, 112 citations in OpenAlex.
- An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review.Journal of infection and public health · 2022Pooled it
- Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations.Journal of chemical information and modeling · 2024Article
- Computational insights into the cross-talk between medin and Aβ: implications for age-related vascular risk factors in Alzheimer's disease.Briefings in bioinformatics · 2024Article
- In Silico Analysis of the Effect ofMedicina (Kaunas, Lithuania) · 2023Article
- Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes.PLoS computational biology · 2023Article
- Nucleosome destabilization by polyamines.Archives of biochemistry and biophysics · 2022Article
- Protobiotic Systems Chemistry Analyzed by Molecular Dynamics.Life (Basel, Switzerland) · 2019Review
- Molecular Mechanism of Spontaneous Nucleosome Unraveling.Journal of molecular biology · 2019Article
- Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core.Epigenetics & chromatin · 2018Article
- Mapping allosteric linkage to channel gating by extracellular domains in the human epithelial sodium channel.The Journal of biological chemistry · 2018Article
- Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins.The Journal of chemical physics · 2018Article
- Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[a]pyrene-Derived Lesion.Biochemistry · 2017Article
- Programming of Essential Hypertension: What Pediatric Cardiologists Need to Know.Pediatric cardiology · 2015Review
- Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations.PLoS computational biology · 2015Article
- Rational Coupled Dynamics Network Manipulation Rescues Disease-Relevant Mutant Cystic Fibrosis Transmembrane Conductance Regulator.Chemical science · 2015Article
- Molecular dynamics simulations: advances and applications.Advances and applications in bioinformatics and chemistry : AABC · 2015Review
- The role of histone tails in the nucleosome: a computational study.Biophysical journal · 2014Article
- Close encounters with DNA.Journal of physics. Condensed matter : an Institute of Physics journal · 2014Review
- Rational design of a ligand-controlled protein conformational switch.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Conformational changes relevant to channel activity and folding within the first nucleotide binding domain of the cystic fibrosis transmembrane conductance regulator.The Journal of biological chemistry · 2012Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleosomes form the fundamental building blocks of chromatin. Subtle modifications of the constituent histone tails mediate chromatin stability and regulate gene expression. For this reason, it is important to understand structural dynamics of nucleosomes at atomic levels. We report a novel multiscale model of the fundamental chromatin unit, a nucleosome, using a simplified model for rapid discrete molecular dynamics simulations and an all-atom model for detailed structural investigation. Using a simplified structural model, we perform equilibrium simulations of a single nucleosome at various temperatures. We further reconstruct all-atom nucleosome structures from simulation trajectories. We find that histone tails bind to nucleosomal DNA via strong salt-bridge interactions over a wide range of temperatures, suggesting a mechanism of chromatin structural organization whereby histone tails regulate inter- and intranucleosomal assemblies via binding with nucleosomal DNA. We identify specific regions of the histone core H2A/H2B-H4/H3-H3/H4-H2B/H2A, termed "cold sites", which retain a significant fraction of contacts with adjoining residues throughout the simulation, indicating their functional role in nucleosome organization. Cold sites are clustered around H3-H3, H2A-H4 and H4-H2A interhistone interfaces, indicating the necessity of these contacts for nucleosome stability. Essential dynamics analysis of simulation trajectories shows that bending across the H3-H3 is a prominent mode of intranucleosomal dynamics. We postulate that effects of salts on mononucleosomes can be modeled in discrete molecular dynamics by modulating histone-DNA interaction potentials. Local fluctuations in nucleosomal DNA vary significantly along the DNA sequence, suggesting that only a fraction of histone-DNA contacts make strong interactions dominating mononucleosomal dynamics. Our findings suggest that histone tails have a direct functional role in stabilizing higher-order chromatin structure, mediated by salt-bridge interactions with adjacent DNA.
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