2018
DOI: 10.1016/j.bbrc.2017.09.086
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Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes

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Cited by 33 publications
(25 citation statements)
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“…Indeed, various coarse grained methods have been proposed, [16][17][18][19][20][21][22] e.g. for handling membrane proteins, 23 DNA, 24 water solutions, 25 lipid membranes, 21 and polymers. 26,27 The basic units of these CG models are typically spherical beads, which is quite reasonable for modelling alkyl chains, phosphates, and more generally biomolecules, like, e.g., in the popular MARTINI package.…”
Section: Introductionmentioning
confidence: 99%
“…Indeed, various coarse grained methods have been proposed, [16][17][18][19][20][21][22] e.g. for handling membrane proteins, 23 DNA, 24 water solutions, 25 lipid membranes, 21 and polymers. 26,27 The basic units of these CG models are typically spherical beads, which is quite reasonable for modelling alkyl chains, phosphates, and more generally biomolecules, like, e.g., in the popular MARTINI package.…”
Section: Introductionmentioning
confidence: 99%
“…Coarse-grained simulations of unrolling have been studied by Langowski and co-workers [70]. The SIRAH force field extension for protein-DNA complexes has been used to perform coarse-grained simulations of tetranucleosomes to study DNA dynamics within the context of this system [71]. Many coarse-grained models of DNA itself have been described previously [72].…”
Section: Nucleosomes Di-nucleosomes Tri-nucleosomes and Tetra-nuclmentioning
confidence: 99%
“…Recently, coarse-grained models are also being extended to study ribosome dynamics 25 and various protein-DNA transient complexes. [26][27][28] Motivated by these success stories of coarsegrained models, we speculated if coarse-grained models of proteins and small molecules can be put into play to substitute computationally expensive all-atom simulations for capturing protein-ligand recognition process on the fly. In this work, by building on popular MAR-TINI 6,29-31 coarse-grained frame-work, we report that while its vanilla implementation on protein-ligand system might fail to capture the binding event, judicious optimization of elastic network 32 in MARTINI protein model enable the simulation of the spontaneous binding process of ligand to the designated cavity at crystallographically identical pose.…”
Section: Introductionmentioning
confidence: 99%