Molecular dynamics simulation nucleic acids

K. E. Lind, V. Mohan, M. Manoharan, and D. M. Ferguson, Structural characteristics of 2 -0-(2-methoxyethyl)-modified nucleic acids from molecular dynamics simulations. Nucleic Acids Res 26, 3694-3799 1998. 

Zakrzewska, K. (2009b). Local and global effects of strong DNA bending induced during molecular dynamics simulations. Nucleic Acids Research, 37, 3766. 

Going beyond the mean-field level, several "hybrid" approaches are now being explored in MD simulations. Examples include a recent model [70] in which the immediate hydration of the solute is modeled explicitly by a layer of water molecules, and the GB model is used to treat the bulk continuum solvent outside the explicit simulation volume. A similar idea was recently found very effective in the context of replica-exchange simulations [71]. An explicit ion/implicit water (PB) solvation model for molecular dynamics of nucleic acids has recently been tested [72]. 

Pande V, Nilsson L (2008) Insights into stmcture, dyntimics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations. Nucleic Adds Res 36 1508-1516... 

J M 1992. Molecular Dynamics Simulation. Elementary Methods. New York, John Wiley Sons, ammon J A and S C Harvey 1987. Dynamics of Proteins and Nucleic Acids. Cambridge, Cambridge Jniversity Press. 

V. Tsui and D. A. Case, Molecular dynamics simulations of nucleic acids with a generalized bom solvation model, J. Am. Chem. Soc. 122 2489 (2000). 

Cheatham, T.E., 3rd and Young, M.A. (2000) Molecular dynamics simulation of nucleic acids successes, limitations, and promise. Biopolymers 56, 232-256. 

Banci, L. 2003. Molecular Dynamics Simulations of Metalloproteins , Curr. Opin. Chem. Biol., 7, 143. Beveridge, D. L. and McConnell, K. J. 2000. Nucleic acids theory and computer simulation, Y2K ... 

Molecular simulations are used most often for modeling proteins and nucleic acids. We mention the methods here only because they are methods for computing a free energy directly. However, they are rather complex calculations, so we will keep our comments brief. Molecular dynamics simulations give information about the variation in structure and energy of a molecule over an interval of time (78,79). In MD, each atom moves according to Newton s equations of motion for classical particles ... 

Table 21.4 Population of planar conformation of rings (with endocyclic torsion angles less than 10° ) in nucleic acid bases according to Carr-Parinello molecular dynamics simulations [45]...

The probably most delicate aspect of nucleic-acid modeling is the treatment of long-range interactions. The particle-mesh Ewald method, introduced by Darden et al. [109] [110] has yielded very promising results in a number of recent molecular-dynamics simulations of oligonucleotides... 

MacKerell AD, Jr, NK Banavali (2000) All-atom empirical force field for nucleic acids II. Application to molecular dynamics simulations of DNA and RNA in solution. J. Comput. Chem. 21 (2) 105-120... 

Langley DR (1998) Molecular dynamic simulations of environment and sequence dependent DNA conformations the development of the BMS nucleic acid force field and comparison with experimental results, J Biomol Struct, 16 487—509... 

Biochemistry and Molecular Biophysics, Vol. I, pp. 39-58, D. L. Beveridge and R. Lavery, Eds., Adenine Press, Guilderland, New York, 1991. Search Strategies, Minimization Algorithms, and Molecular Dynamics Simulations for Exploring Conformational Spaces of Nucleic Acids. 

Molecular dynamics simulations have been used in a variety of ways. They can be used to compute mechanical moduli by studying the response of a model of the bulk polymer to a constant stress or strain, and to study the diffusion of molecules in membranes and polymers.There are numerous biomolecular applications. Structural, dynamic, and thermodynamic data from molecular dynamics have provided insights into the structure-function relationships, binding affinities, mobility, and stability of proteins, nucleic acids, and other macromolecules that cannot be obtained from static models. 

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