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Literature DB >> 31125796

Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.

Abstract

Recent advances in biotechnology such as Hi-C, CRISPR/Cas9 and ribosome display have placed nucleoprotein complexes at center stage. Understanding the structural dynamics of these complexes aids in optimizing protocols and interpreting data for these new technologies. The integration of simulation and experiment has helped advance mechanistic understanding of these systems. Coarse-grained simulations, reduced-description models, and explicit solvent molecular dynamics simulations yield useful complementary perspectives on nucleoprotein complex structural dynamics. When combined with Hi-C, cryo-EM, and single molecule measurements, these simulations integrate disparate forms of experimental data into a coherent mechanism. Published by Elsevier Ltd.

Entities: CellLine Chemical Disease Gene Mutation Species

Mesh：

Substances：
Chromatin
Nucleosomes

Year: 2019 PMID： 31125796 PMCID： PMC6730654 DOI： 10.1016/j.sbi.2019.03.004

Source DB: PubMed Journal: Curr Opin Struct Biol ISSN： 0959-440X Impact factor: 6.809

132 in total

1. Ribosomal protein L3: gatekeeper to the A site.

Authors: Arturas Meskauskas; Jonathan D Dinman
Journal: Mol Cell Date: 2007-03-23 Impact factor: 17.970

2. Modeling a self-avoiding chromatin loop: relation to the packing problem, action-at-a-distance, and nuclear context.

Authors: Michaël Bon; Davide Marenduzzo; Peter R Cook
Journal: Structure Date: 2006-02 Impact factor: 5.006

3. The structure of helix 89 of 23S rRNA is important for peptidyl transferase function of Escherichia coli ribosome.

Authors: Dmitry E Burakovsky; Petr V Sergiev; Maria A Steblyanko; Andrey L Konevega; Alexey A Bogdanov; Olga A Dontsova
Journal: FEBS Lett Date: 2011-08-27 Impact factor: 4.124

4. Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub.

Authors: Gavin D Bascom; Christopher G Myers; Tamar Schlick
Journal: Proc Natl Acad Sci U S A Date: 2019-02-04 Impact factor: 11.205

5. Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis.

Authors: Benjamin Fritch; Andrey Kosolapov; Phillip Hudson; Daniel A Nissley; H Lee Woodcock; Carol Deutsch; Edward P O'Brien
Journal: J Am Chem Soc Date: 2018-04-06 Impact factor: 15.419

6. Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations.

Authors: Jaewoon Jung; Wataru Nishima; Marcus Daniels; Gavin Bascom; Chigusa Kobayashi; Adetokunbo Adedoyin; Michael Wall; Anna Lappala; Dominic Phillips; William Fischer; Chang-Shung Tung; Tamar Schlick; Yuji Sugita; Karissa Y Sanbonmatsu
Journal: J Comput Chem Date: 2019-04-17 Impact factor: 3.376

7. Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors: Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal: Science Date: 2009-10-09 Impact factor: 47.728

5. Mechanism for the Unfolding of the TOP7 Protein in Steered Molecular Dynamics Simulations as Revealed by Mutual Information Analysis.

Authors: Ognjen Perišić; Willy Wriggers
Journal: Front Mol Biosci Date: 2021-09-30

6. Searching for Low Probability Opening Events in a DNA Sliding Clamp.

Authors: Reza Esmaeeli; Benedict Andal; Alberto Perez
Journal: Life (Basel) Date: 2022-02-09

Review 7. Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM.

Authors: Frédéric Poitevin; Artem Kushner; Xinpei Li; Khanh Dao Duc
Journal: Molecules Date: 2020-09-17 Impact factor: 4.411

7 in total

Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.

1. Ribosomal protein L3: gatekeeper to the A site.

2. Modeling a self-avoiding chromatin loop: relation to the packing problem, action-at-a-distance, and nuclear context.

3. The structure of helix 89 of 23S rRNA is important for peptidyl transferase function of Escherichia coli ribosome.

4. Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub.

5. Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis.

6. Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations.

7. Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

8. Regulation of the protein-conducting channel by a bound ribosome.

9. Non-bulk-like solvent behavior in the ribosome exit tunnel.

10. Single-molecule compaction of megabase-long chromatin molecules by multivalent cations.

1. Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks.

2. Collective mechanical responses of cadherin-based adhesive junctions as predicted by simulations.

3. Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting.

Review 4. Getting to the bottom of lncRNA mechanism: structure-function relationships.

5. Mechanism for the Unfolding of the TOP7 Protein in Steered Molecular Dynamics Simulations as Revealed by Mutual Information Analysis.

6. Searching for Low Probability Opening Events in a DNA Sliding Clamp.

Review 7. Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM.