Oligonucleotide Analogues with a Nucleobase-Including Backbone, Part 7, Molecular Dynamics Simulation of a DNA Duplex Containing a 2′-Deoxyadenosine 8-(Hydroxymethyl)-Derived Nucleotide

Czechtizky, Werngard; Daura, Xavier; Vasella, Andrea; Gunsteren, Wilfred van

doi:10.1002/1522-2675(20010711)84:7<2132::aid-hlca2132>3.0.co;2-9

Cited by 11 publications

(5 citation statements)

References 10 publications

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“…The earlier MD simulations of DNA in aqueous solution based on the GROMOS force field37–41 made use of the parameter sets 37C4,42 43A1,19, 43 and 45A3,21 that had mainly been derived for polypeptides. Long‐time (nanosecond) nucleic‐acid simulations using the latest GROMOS 45A3 parameter set21 indicated the need and room for improvement of this set with respect to nucleic acid simulations.…”

Section: Methodsmentioning

confidence: 99%

An improved nucleic acid parameter set for the GROMOS force field

et al. 2005

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Over the past decades, the GROMOS force field for biomolecular simulation has primarily been developed for performing molecular dynamics (MD) simulations of polypeptides and, to a lesser extent, sugars. When applied to DNA, the 43A1 and 45A3 parameter sets of the years 1996 and 2001 produced rather flexible double-helical structures, in which the Watson-Crick hydrogen-bonding content was more limited than expected. To improve on the currently available parameter sets, the nucleotide backbone torsional-angle parameters and the charge distribution of the nucleotide bases are reconsidered based on quantum-chemical data. The new 45A4 parameter set resulting from this refinement appears to perform well in terms of reproducing solution NMR data and canonical hydrogen bonding. The deviation between simulated and experimental observables is now of the same order of magnitude as the uncertainty in the experimental values themselves.

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Section: Methodsmentioning

confidence: 99%

An improved nucleic acid parameter set for the GROMOS force field

et al. 2005

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“…The structural stability of proteins,138–144 peptides,145–152 sugars,126, 153 and DNA154, 155 as function of their composition, chain lengths, and solvent environment or temperature and pressure can be studied. Solvation, both in pure solvents and in mixtures, can be investigated in atomic detail 156–159.…”

Section: Examples Of Applicationmentioning

confidence: 99%

The GROMOS software for biomolecular simulation: GROMOS05

Christen¹,

Hünenberger²,

Bakowies³

et al. 2005

J Comput Chem

599

524

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We present the latest version of the Groningen Molecular Simulation program package, GROMOS05. It has been developed for the dynamical modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization. An overview of GROMOS05 is given, highlighting features not present in the last major release, GROMOS96. The organization of the program package is outlined and the included analysis package GROMOS++ is described. Finally, some applications illustrating the various available functionalities are presented.

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“…Previous GROMOS parameter sets [37C4 (Smith et al 1995;van Gunsteren and Berendsen 1987), 43A1 (Daura et al 1998; and 45A3 (Schuler et al 2001;Schuler and van Gunsteren 2000)] have proven successful in describing biochemical interactions in protein stability (Antes et al 2002;Bakowies and van Gunsteren 2002;Mark 2003, 2004;Smith et al 1995Smith et al , 1996Smith et al , 1999, peptide folding (Daura et al 1999a;Daura et al 2002;Daura et al 1997;) and protein-ligand binding (Hansson et al 1998;Marelius et al 1998;Oostenbrink et al 2000;Talhout et al 2003). They have also been used successfully in simulations involving triglycerides (Chandrasekhar and van Gunsteren 2002), membranes (Chandrasekhar et al 2003;Gla¨ttli et al, submitted) and DNA double helices (Bonvin et al 1998;Czechtizky et al 2001). For simulations of DNA double helices, a new parameter set has recently been introduced, with which it has proven to be possible to obtain stable simulations of DNA strands using a simple force field and cutoff scheme (Soares et al 2005).…”

Section: Introductionmentioning

confidence: 99%

Validation of the 53A6 GROMOS force field

et al. 2005

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The quality of biomolecular dynamics simulations relies critically on the force field that is used to describe the interactions between particles in the system. Force fields, which are generally parameterized using experimental data on small molecules, can only prove themselves in realistic simulations of relevant biomolecular systems. In this work, we begin the validation of the new 53A6 GROMOS parameter set by examining three test cases. Simulations of the well-studied 129 residue protein hen egg-white lysozyme, of the DNA dodecamer d(CGCGAATTCGCG)(2), and a proteinogenic beta(3)-dodecapeptide were performed and analysed. It was found that the new parameter set performs as well as the previous parameter sets in terms of protein (45A3) and DNA (45A4) stability and that it is better at describing the folding-unfolding balance of the peptide. The latter is a property that is directly associated with the free enthalpy of hydration, to which the 53A6 parameter set was parameterized.

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Oligonucleotide Analogues with a Nucleobase-Including Backbone, Part 7, Molecular Dynamics Simulation of a DNA Duplex Containing a 2′-Deoxyadenosine 8-(Hydroxymethyl)-Derived Nucleotide

Cited by 11 publications

References 10 publications

An improved nucleic acid parameter set for the GROMOS force field

An improved nucleic acid parameter set for the GROMOS force field

The GROMOS software for biomolecular simulation: GROMOS05

Validation of the 53A6 GROMOS force field

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