Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

Zavadlav, Julija; Podgornik, Rudolf; Melo, Manuel N.; Marrink, Siewert J.; Praprotnik, Matej

doi:10.1140/epjst/e2016-60117-8

Cited by 24 publications

(14 citation statements)

References 68 publications

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“…where C is an appropriately chosen numerical prefactor. The TD force depends on the molecule type, i.e., we use two different ones that correspond to sodium and chloride ions (8,34,74). For water, we set F TD water ¼ 0.…”

Section: Methodsmentioning

confidence: 99%

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Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

Zavadlav

Sablić

Podgornik

et al. 2018

Biophysical Journal

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The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only at specific ionic conditions: either at nominally zero salt concentration, i.e., including only counterions enforcing the system's electroneutrality, or at excessive salt concentrations. Here, we introduce an efficient molecular dynamics simulation approach for an atomistic DNA molecule at realistic physiological ionic conditions. The simulations are performed by employing the open-boundary molecular dynamics method that allows for simulation of open systems that can exchange mass and linear momentum with the environment. In our open-boundary molecular dynamics approach, the computational burden is drastically alleviated by embedding the DNA molecule in a mixed explicit/implicit salt-bathing solution. In the explicit domain, the water molecules and ions are both overtly present in the system, whereas in the implicit water domain, only the ions are explicitly present and the water is described as a continuous dielectric medium. Water molecules are inserted and deleted into/from the system in the intermediate buffer domain that acts as a water reservoir to the explicit domain, with both water molecules and ions free to enter or leave the explicit domain. Our approach is general and allows for efficient molecular simulations of biomolecules solvated in bathing salt solutions at any ionic strength condition.

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Section: Methodsmentioning

confidence: 99%

“…To effectively correct the unwanted density undulations, the TD force is applied (17,35,73). For ions, these effects are drastically more pronounced than for water (8,74). To demonstrate this point, we plot in Fig.…”

Section: Open-boundary Multiscale Solvationmentioning

confidence: 99%

Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

Zavadlav

Sablić

Podgornik

et al. 2018

Biophysical Journal

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“…Only recently it became feasible to set up an all-atom MD simulation for a larger set of DNA molecules [51,53] characterized by a single packing geometry with only a partial characterization of the DNA countercharge and solvent ordering. This approach has been later extended by the applications of the multiscale MD technique AdResS (Adaptive Resolution Scheme) [54][55][56][57][58][59][60][61][62][63][64][65][66][67], which has been already successfully applied to various biological systems [68][69][70][71][72][73][74][75][76][77], enabling a concurrent and consistent coupling between the atomistic (AT) and the coarse-grained (CG) representations with a key feature of allowing molecules to freely move not only in real space but also in the resolution space across different regions and change their resolution on the fly according to their position in the computational domain.…”

Section: Simulating Dna Arraysmentioning

confidence: 99%

“…Here, we start to describe our efforts to achieve this goal by employing AdResS, most straightforwardly implementable for a single DNA molecule embedded in a multiscale salt solution [70,71]. We focus on (spatially varying) dielectric properties of solvent and the DNA molecule itself.…”

Section: Adaptive Resolution Simulations Of a Dna Molecule Solvated Imentioning

confidence: 99%

Molecular Dynamics Simulation of High Density DNA Arrays

2018

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Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine) counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and consequently identify the most important contribution to the DNA-DNA interactions at high DNA densities.

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“…Similarly, Zorkot et al look at the effects of electrostatic and hydrodynamic interactions on the electric current through nanopores, finding that, contrary to expectation, the exponent of the current's power spectral density is not affected by the neutral solvent-at least in the frequency range studied [13]. And Zavadlav et al demonstrate that adaptive methods can be pushed to the extreme by coupling an atomistic model of DNA with a coarse-grained (MARTINI-level) representation of a salt solution [14].…”

mentioning

confidence: 97%

Editorial

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Deserno

Dünweg

et al. 2016

Eur. Phys. J. Spec. Top.

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Abstract. This special topics issue offers a broad perspective on recent theoretical and computational soft matter science, providing state of the art advances in many of its sub-fields. As is befitting for a discipline as diverse as soft matter, the papers collected here span a considerable range of subjects and questions, but they also illustrate numerous connections into both fundamental science and technological/industrial applications, which have accompanied the field since its earliest days. This issue is dedicated to Kurt Kremer, on the occasion of his 60 th birthday, honouring his role in establishing this exciting field and consolidating its standing in the frame of current science and technology.

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Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

Cited by 24 publications

References 68 publications

Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

Molecular Dynamics Simulation of High Density DNA Arrays

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