Transcript Slide 1

Molecular Dynamics Simulations of
Compressional Metalloprotein Deformation
Andrew
1
1
Hung ,
Jianwei
2
Zhao ,
Jason J.
2
Davis ,
Mark S. P.
1
Sansom
Department of Biochemistry, University of Oxford, South Parks Road, Oxford, U.K. OX1 3QU
2 Department of Chemistry, University of Oxford, South Parks Road, Oxford, U.K. OX1 3QU
Background
AFM Tip-Protein-Surface Model
Azurin, a Cu metalloprotein, is a biological electron transfer
agent. An understanding of the process of electron transfer
through this protein is of immense technological interest in the
development of new molecular electronic devices1. Recently,
the conduction properties of azurin were studied by conducting
atomic force microscopy (C-AFM)2. In this experiment, the
protein is immobilised to the AFM tip, and tunneling currents
through the protein were measured at a range of bias voltages
while under various extents of applied compressive force.
3-dimensional periodic boundary conditions. Surface constructed from
united-atom CH4 molecules. Azurin obtained from PDB file 4AZU5 ,
with all non-protein molecules removed. Compression of the protein
achieved by stepwise reduction of the z-direction cell length. MD runs
performed at each tip-surface distance.
Figure 3. Stepwise compression of azurin at (z) 42 Å, 27 Å and 17 Å
Preliminary Results
Figure 1. Schematic of a typical C-AFM experiment2.
Current-bias voltage I(V)
curves were acquired at
different values of applied
force2 (differentiated by
colour), as shown in
Figure 2. Fitting each
curve to a modified
Simmons model, a curve
of tunneling barrier height
φ0 vs. applied force was
obtained. φ0 was found to
initially
decrease
monotonously with force,
but becomes constant
above ~30nN.
Secondary structural features were maintained from initial tip-surface
separation of 42 Å to ~25 Å. Packing density increases with
compression within this range. At lower separations, protein unfolding
occurs, and density decreases with compression. Consistent with AFM
conduction experiments which showed decrease in φ0 with compression
up to a certain critical point before reaching a constant, minimum value.
Figure 2. Current with
respect to bias voltage I(V)
curves for varying degrees of
applied force. (black = lowest
applied force, yellow =
highest)
Current Work
Molecular simulations have been performed to determine a
possible mechanism for this behaviour, with particular focus
on the structure and packing density (ρ) changes with
respect to compression, as φ0 is believed to be related to ρ.
Computational Details
Molecular dynamics (MD) simulations were performed under
constant particle number, volume and temperature (NVT)
conditions using
GROMACS3 The GROMOS96 forcefield
parameters were employed with time steps of 2 fs. Potential energy
cut-off radii of 10 Å were used for van der Waals’ and electrostatic
interactions. Bond lengths were constrained via the LINCS
algorithm. The protein was coupled to a temperature bath at 300 K.
Energy minimisation and 100ps of equilibration were performed on
the protein at each compression distance, with a subsequent
100ps of simulation collected on which analyses were performed.
Analyses of MD trajectories were performed using the suite of
software included in the GROMACS software. Visualisation of
system geometries and evaluation of protein secondary structure
were performed using the program VMD4.
Figure 4. Secondary structure (a) and protein atomic packing density (b)
as a function of tip-surface distance. Red = α-helix, yellow = β-strands
Further Work
Preliminary results from the current MD simulations have shown that
simulations can contribute to our understanding of protein-mediated
tunneling under compressive stress. Work in progress include studying
the effects of hydration waters, Cu coordination changes under
compression, and using a more realistic AFM tip and surface model.
References
1
R. Rinaldi et al., Adv. Mat. 14, p1453 (2002)
2 J. Zhao, J. J. Davis, Nanotechnology 14(9), p1023 (2003)
3 D. van der Spoel et al., Gromacs User Manual version 3.1, Groningen, The
Netherlands, Internet : www.gromacs.org (2002)
4 W. Humphrey et al., J. Molec. Graphics 14(1), p33 (1996)
5 H. Nar et al., J. Mol. Biol. 218, p427 (1991)