dorsal/arxiv
View SchemaA Minimal Model of B-DNA
| Authors | Alexey K. Mazur |
|---|---|
| Categories | |
| ArXiv ID | physics/9907028 |
| URL | https://arxiv.org/abs/physics/9907028 |
Abstract
Recently it has been found that stable and accurate molecular dynamics (MD) of B-DNA duplexes can be obtained in relatively inexpensive computational conditions with the bulk solvent represented implicitly, but the minor groove filled with explicit water (J. Am. Chem. Soc. 1998, 120, 10928). The present paper further explores these simulation conditions in order to understand the main factors responsible for the observed surprisingly good agreement with experimental data. It appears that in the case of the EcoRI dodecamer certain sequence specific hydration patterns in the minor groove earlier known from experimental data are formed spontaneously in the course of MD simulations. The effect is reliably reproduced in several independent computational experiments in different simulation conditions. With all major groove water removed, closely similar results are obtained, with even better reproducibility. On the other hand, without explicit hydration, metastable dynamics around a B-DNA like state can be obtained which, however, only poorly compares with experimental data. It appears, therefore, that a right-handed DNA helix with explicitly hydrated minor groove is a minimal model system where the experimental properties of B-DNA can be reproduced with non-trivial sequence-dependent effects. Its small size makes possible virtually exhaustive sampling, which is a major advantage with respect to alternative approaches. An appendix is included with a correction to the implicit leapfrog integrator used in internal coordinate MD.
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"abstract": "Recently it has been found that stable and accurate molecular dynamics (MD)\nof B-DNA duplexes can be obtained in relatively inexpensive computational\nconditions with the bulk solvent represented implicitly, but the minor groove\nfilled with explicit water (J. Am. Chem. Soc. 1998, 120, 10928). The present\npaper further explores these simulation conditions in order to understand the\nmain factors responsible for the observed surprisingly good agreement with\nexperimental data. It appears that in the case of the EcoRI dodecamer certain\nsequence specific hydration patterns in the minor groove earlier known from\nexperimental data are formed spontaneously in the course of MD simulations. The\neffect is reliably reproduced in several independent computational experiments\nin different simulation conditions. With all major groove water removed,\nclosely similar results are obtained, with even better reproducibility. On the\nother hand, without explicit hydration, metastable dynamics around a B-DNA like\nstate can be obtained which, however, only poorly compares with experimental\ndata. It appears, therefore, that a right-handed DNA helix with explicitly\nhydrated minor groove is a minimal model system where the experimental\nproperties of B-DNA can be reproduced with non-trivial sequence-dependent\neffects. Its small size makes possible virtually exhaustive sampling, which is\na major advantage with respect to alternative approaches. An appendix is\nincluded with a correction to the implicit leapfrog integrator used in internal\ncoordinate MD.",
"arxiv_id": "physics/9907028",
"authors": [
"Alexey K. Mazur"
],
"categories": [
"physics.comp-ph",
"physics.bio-ph",
"physics.chem-ph",
"q-bio.BM"
],
"title": "A Minimal Model of B-DNA",
"url": "https://arxiv.org/abs/physics/9907028"
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