The molecular dynamics thermocycler. A new approach to sample conformational space, as exemplified by the RNA hairpin.
The approach called the molecular dynamics thermocycler employs repeated cycles of heating and cooling of the model during the course of unrestrained in aqua MD simulation. It is validated by confronting results of three 1.6 ns simulations using different heating temperatures, starting from a de novo constructed 12-mer RNA hairpin model containing a UGAA loop vs. the set of NMR derived coordinates (PDB code 1AFX). The lowest average RMS deviation and best coherence with the experimentally delivered structures was identified in case of the molecular dynamics thermocycler using Tmax = 400 K.
Bielecki
Lukasz
L
Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznán, Poland.
Popenda
Mariusz
M
Adamiak
Ryszard W
RW
D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
D012313:RNA