Microsecond time-scale molecular dynamics simulations of the ABC oligomers
The collaborative effort of the ABC laboratories allowed the collection of microsecond scale molecular dynamics simulations on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences, using the Amber forcefield (parm99bsc0). The full MD dataset contains more than 35 million conformational snapshots of B-DNA in physiological salt conditions.
Observations include highly sequence-dependent occupancies of backbone BI/BII states, that are related to the sequence dependent multimodality of the three helical parameters shift, slide and twist.
- M. Pasi, J.H. Maddocks, D. Beveridge, T.C. Bishop, D.A. Case, T. Cheatham III, P.D. Dans, B. Jayaram, F. Lankas, C. Laughton, J. Mitchell, R. Osman, M. Orozco, A. Perez, D. Petkeviciute, N. Spackova, J. Sponer, K. Zakrzewska, R. Lavery. µABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Research 2014; doi: 10.1093/nar/gku855.