Simulation of DNA double-strand dissociation and formation during replica-exchange molecular dynamics simulations
Identifieur interne : 001137 ( Main/Exploration ); précédent : 001136; suivant : 001138Simulation of DNA double-strand dissociation and formation during replica-exchange molecular dynamics simulations
Auteurs : Srinivasaraghavan Kannan [Allemagne] ; Martin Zacharias [Allemagne]Source :
- Physical Chemistry Chemical Physics [ 1463-9076 ] ; 2009.
English descriptors
- Teeft :
- Average structure, Backbone distance, Base pairs, Bond angle, Bond length, Centroid, Chem, Cluster centroids, Complete disruption, Conformation, Conformational, Conformational cluster, Conformational states, Control simulations, Correct hydrogen bonds, Dihedral terms, Distance distributions, Distance restraint, Dominant state, Dsdna, Dsdna formation, Duplex, Duplex formation, Duplex stability, Dynamics, Energetic changes, Energetic contributions, Enthalpy change, Error bars, Formation simulation, Formation simulations, Free energy, Free energy barrier, Free energy change, Free energy curve, Full duplex structure, Good agreement, Hairpin loop structure, Heavy atoms, Hydrogen bond population, Intermediate structures, Jacobs university bremen, Kcal, Lower panels, Modesto orozco, Molecular dynamics, Molecular dynamics simulations, Monovalent salt, Nucleic, Nucleic acid, Nucleic acid backbone, Nucleic acids, Owner societies, Phys, Potential energy, Present study, Quadratic distance, Reference distance, Reference distances, Reference replica, Remd, Remd simulation, Remd simulations, Remd umbrella sampling simulations, Replica, Rmsd, Simulation, Simulation temperatures, Single strand, Single strands, Solvation contributions, Standard state conditions, Strand, Strand association, Strand separation, Structure prediction, Terminal base pairs, Umbrella sampling, Umbrella sampling simulations, Umbrella sampling window, Weighted histogram analysis method.
Abstract
The process of DNA double-strand (dsDNA) formation for a four-base pair (dCGCG)2 model system was studied using umbrella sampling combined with replica-exchange molecular dynamics simulations (REMD) and a generalized Born continuum solvent model. Disruption of dsDNA during the simulations was achieved by stepwise increasing the reference distance in a quadratic restraining potential between the nucleic acid backbone of the two DNA strands. During the reverse simulation (stepwise decrease of the distance starting from completely separated and unfolded single strands) full reformation of a dsDNA in close agreement with B-form geometry was achieved during REMD but not continuous MD simulations. The simulations allowed the calculation of a potential of mean force for the dsDNA formation along the reaction coordinate and were used to characterize intermediate structures. In addition, it was possible to analyze the change of various energetic contributions during disruption and formation of dsDNA that favor or disfavor duplex formation. The calculated free energy change of 3.2 (1.5) kcal mol1 and enthalpy change of 37 kcal mol1 for (dCGCG)2 duplex formation was in good agreement with corresponding experimental values of 3.9 kcal mol1 and 38.5 kcal mol1, respectively.
Url:
DOI: 10.1039/b910792b
Affiliations:
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Chem. Chem. Phys.</title><idno type="ISSN">1463-9076</idno><idno type="eISSN">1463-9084</idno><imprint><publisher>The Royal Society of Chemistry.</publisher><date type="published" when="2009">2009</date><biblScope unit="volume">11</biblScope><biblScope unit="issue">45</biblScope><biblScope unit="page" from="10589">10589</biblScope><biblScope unit="page" to="10595">10595</biblScope></imprint><idno type="ISSN">1463-9076</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1463-9076</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Average structure</term><term>Backbone distance</term><term>Base pairs</term><term>Bond angle</term><term>Bond length</term><term>Centroid</term><term>Chem</term><term>Cluster centroids</term><term>Complete disruption</term><term>Conformation</term><term>Conformational</term><term>Conformational cluster</term><term>Conformational states</term><term>Control simulations</term><term>Correct hydrogen bonds</term><term>Dihedral terms</term><term>Distance distributions</term><term>Distance restraint</term><term>Dominant state</term><term>Dsdna</term><term>Dsdna formation</term><term>Duplex</term><term>Duplex formation</term><term>Duplex stability</term><term>Dynamics</term><term>Energetic changes</term><term>Energetic contributions</term><term>Enthalpy change</term><term>Error bars</term><term>Formation simulation</term><term>Formation simulations</term><term>Free energy</term><term>Free energy barrier</term><term>Free energy change</term><term>Free energy curve</term><term>Full duplex structure</term><term>Good agreement</term><term>Hairpin loop structure</term><term>Heavy atoms</term><term>Hydrogen bond population</term><term>Intermediate structures</term><term>Jacobs university bremen</term><term>Kcal</term><term>Lower panels</term><term>Modesto orozco</term><term>Molecular dynamics</term><term>Molecular dynamics simulations</term><term>Monovalent salt</term><term>Nucleic</term><term>Nucleic acid</term><term>Nucleic acid backbone</term><term>Nucleic acids</term><term>Owner societies</term><term>Phys</term><term>Potential energy</term><term>Present study</term><term>Quadratic distance</term><term>Reference distance</term><term>Reference distances</term><term>Reference replica</term><term>Remd</term><term>Remd simulation</term><term>Remd simulations</term><term>Remd umbrella sampling simulations</term><term>Replica</term><term>Rmsd</term><term>Simulation</term><term>Simulation temperatures</term><term>Single strand</term><term>Single strands</term><term>Solvation contributions</term><term>Standard state conditions</term><term>Strand</term><term>Strand association</term><term>Strand separation</term><term>Structure prediction</term><term>Terminal base pairs</term><term>Umbrella sampling</term><term>Umbrella sampling simulations</term><term>Umbrella sampling window</term><term>Weighted histogram analysis method</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract">The process of DNA double-strand (dsDNA) formation for a four-base pair (dCGCG)2 model system was studied using umbrella sampling combined with replica-exchange molecular dynamics simulations (REMD) and a generalized Born continuum solvent model. Disruption of dsDNA during the simulations was achieved by stepwise increasing the reference distance in a quadratic restraining potential between the nucleic acid backbone of the two DNA strands. During the reverse simulation (stepwise decrease of the distance starting from completely separated and unfolded single strands) full reformation of a dsDNA in close agreement with B-form geometry was achieved during REMD but not continuous MD simulations. The simulations allowed the calculation of a potential of mean force for the dsDNA formation along the reaction coordinate and were used to characterize intermediate structures. In addition, it was possible to analyze the change of various energetic contributions during disruption and formation of dsDNA that favor or disfavor duplex formation. The calculated free energy change of 3.2 (1.5) kcal mol1 and enthalpy change of 37 kcal mol1 for (dCGCG)2 duplex formation was in good agreement with corresponding experimental values of 3.9 kcal mol1 and 38.5 kcal mol1, respectively.</div></front></TEI><affiliations><list><country><li>Allemagne</li></country><region><li>Brême (Land)</li></region><settlement><li>Brême</li></settlement></list><tree><country name="Allemagne"><region name="Brême (Land)"><name sortKey="Kannan, Srinivasaraghavan" sort="Kannan, Srinivasaraghavan" uniqKey="Kannan S" first="Srinivasaraghavan" last="Kannan">Srinivasaraghavan Kannan</name></region><name sortKey="Zacharias, Martin" sort="Zacharias, Martin" uniqKey="Zacharias M" first="Martin" last="Zacharias">Martin Zacharias</name><name sortKey="Zacharias, Martin" sort="Zacharias, Martin" uniqKey="Zacharias M" first="Martin" last="Zacharias">Martin Zacharias</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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