Details

Autor(en) / Beteiligte

• Beveridge, David L.
• Barreiro, Gabriela
• Suzie Byun, K.
• Case, David A.
• Cheatham, Thomas E.
• Dixit, Surjit B.
• Giudice, Emmanuel
• Lankas, Filip
• Lavery, Richard
• Maddocks, John H.
• Osman, Roman
• Seibert, Eleanore
• Sklenar, Heinz
• Stoll, Gautier
• Thayer, Kelly M.
• Varnai, Péter
• Young, Matthew A.

Titel

Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(C pG) Steps

Ist Teil von

• Biophysical journal, 2004-12, Vol.87 (6), p.3799-3813

Ort / Verlag

United States: Elsevier Inc

Erscheinungsjahr

2004

Link zum Volltext

Quelle

Elsevier ScienceDirect Journals Complete

Beschreibungen/Notizen

• We describe herein a computationally intensive project aimed at carrying out molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide base sequences. This initiative was undertaken by an international collaborative effort involving nine research groups, the “Ascona B-DNA Consortium” (ABC). Calculations were carried out on the 136 cases imbedded in 39 DNA oligomers with repeating tetranucleotide sequences, capped on both ends by GC pairs and each having a total length of 15 nucleotide pairs. All MD simulations were carried out using a well-defined protocol, the AMBER suite of programs, and the parm94 force field. Phase I of the ABC project involves a total of ∼0.6 μs of simulation for systems containing ∼24,000 atoms. The resulting trajectories involve 600,000 coordinate sets and represent ∼400 gigabytes of data. In this article, the research design, details of the simulation protocol, informatics issues, and the organization of the results into a web-accessible database are described. Preliminary results from 15-ns MD trajectories are presented for the d(CpG) step in its 10 unique sequence contexts, and issues of stability and convergence, the extent of quasiergodic problems, and the possibility of long-lived conformational substates are discussed.