(1) AFMB - CNRS 31, Chemin Joseph Aiguier. Marseille, France
(2) UCMB (CP 160/16) Free University of Brussels, Av. P. Heger,
1050, Brussels Belgium
Barnase is a small ribonuclease from Bacillus Amyloliquefaciens.
It is an alpha+beta protein consisting of three hydrophobic
cores.
Secondary structure and hydrophobic cores formation/disruption
along the folding/unfolding pathway has been widely studied
by the group of A. Fersht (Cambridge, UK), using the protein
engineering method.
In order to characterize, at atomic level, secondary structure
and hydrophobic cores disruption of barnase, three MD simulations
at 300 K, 450 K and 600 K were carried out. Simulations were
performed with all atoms explicitly present, in a cubic box
of water molecules, using periodic boundary conditions.
Other barnase unfolding simulations were previously reported (1).
In those cases the analysis was mainly based on some global parameters,
such as the C-alpha r.m.s. from the starting structure, the radius of gyration
and the energy of denaturation.
In the case of this study, few global parameters, such as C-alpha r.m.s. from
the starting structure and accessible volume, were followed during the
unfolding simulations, to get a general view of the evolution of the
system.
Subsequently the trajectories were divided into bins of 100 conformers
and the analysis of the process was carried out on each bin separately.
The analysis of specific features focused on the following properties:
1- main-chain-main-chain hydrogen bonds to check secondary structure
persistence.
2- Interactions between apolar protons in different side chains to
follow the formation/disruption of hydrophobic clusters.
3- Persistences, volumes and residues participating in all packing
defects encountered along the trajectories, i.e.:
- empty cavities to explore the correlation between cavity formation
and hydrophobic core disruption;
- cavities filled by water molecules to monitor solvent penetration
into barnase's hydrophobic cores.
The analysis of the enormous amount of data obtained for the specific
parameters previously reported required the development of new representation
methods which will be presented.
References
(1) A. Caflisch & M. Karplus. (1995) J. Mol. Biol. 252, 672-708