1 National Centre for Biomolecular Research and
Institute of Biophysics, Academy of Sciences of the Czech Republic,
Královopolská 135, 612 65 Brno, Czech Republic.
2 Institute of Molecular Biology and Biophysics,
CH-8093 Zurich, Switzerland
3 National Centre for Biomolecular Research,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech
Republic.
4 Departments of Medicinal Chemistry and of
Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of
Utah, 30 South 2000 East, Salt Lake City, Utah 84112-5820, USA.
Molecular dynamics
(MD) simulations with explicit solvent represent very powerful tools for
detailed insights into the structure and dynamics of various systems.
Unfortunately, MD simulations are limited to the nanosecond timescale leading
to impossibility to observe slower processes. An example of such process is the
formation of a cation-stabilized guanine quadruplex (G-DNA) stem. It is an
exceptionally slow process involving complex kinetics that has not yet been
characterized at atomic resolution. The formation of a parallel stranded G-DNA
stem consisting of four strands of d(GGGG) has been investigated using MD
simulations [1]. Rather than watching for the spontaneous formation of G-DNA,
our approach probed the stability of possible supramolecular intermediates
(including two-, three-, and four-stranded assemblies with out-of-register
basepairing between guanines) on the formation pathway. To supplement the
analysis, approximate free energies of the models have been calculated using
Molecular–Mechanics-Poisson Boltzmann-Surface Area (MM-PBSA) method.
Similar approach has
been applied in the study of various DNA duplex sequences interacting with the
minor groove binding drug 4’,6-diamidino-2-phenylindole (DAPI) [2]. Sequences
investigated include the binding modes observed experimentally, that is, AATT in d(CGCGAATTCGCG)2
and ATTG in d(GGCCAATTGG)2
and alternative shifted binding modes ATTC
and AATT,
respectively. The simulations also suggest that the DAPI molecule is able to adopt
different conformational substates accompanied by specific hydration patterns
that include long residing waters. The MM-PBSA technology has been utilized to
compare free energies of different binding modes. It is demonstrated that
explicit inclusion of a subset of bound water molecules shifts the calculated
relative binding free energies in favor of both crystallographically observed
binding modes, underlining the importance of structured hydration.
The approach applied
here serves as a prototype for qualitatively investigating other molecules
using molecular dynamics simulation and free-energy analysis.
1. R. Štefl, T.E. Cheatham, N. Špačková, E. Fadrná, I. Berger, J. Koča & J. Šponer, Biophysical Journal, 85 (2003) 1787-1804.
2. N. Špačková, T.E. Cheatham III, F. Ryjáček,
F. Lankaš, L. van Meervelt, P. Hobza & J. Šponer, Journal of the American Chemical Society, 125 (2003) 1759-1769.