Chemistry Reference
In-Depth Information
8.0
7.0
6.0
5.0
4.0
3.0
2.0
1.0
0.0
-1.0
-2.0
s
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0
4.5
T
Fig. 7.8
A pseudophase diagram for the 103mer interacting with a surface that is attractive to both
H and P monomers. See the text for a description of the pseudophases. (From Bachmann and Janke
[
53
])
adsorbed compact (AC), adsorbed expanded (AE), adsorbed globule (AG), desorbed
compact (DC), and desorbed expanded (DE) phases (Fig.
7.8
).
7.4 What Do We Still Want to Learn?
In order to understand how a protein reacts toward various materials in a coarse-
grained perspective, simulations of HP sequences interacting with hydrophobic sur-
faces or polar surfaces will be necessary, in addition to surfaces attracting all kinds
of residues regardless of their hydrophobicity. One step further, surfaces of finite
attraction strength should be considered in order to simulate systems closer to real-
istic experimental scenarios.
We have carried out simulations on the same 103mer and physical settings as
in [
53
] using Wang-Landau sampling. In principle our preliminary results agree
with previous studies, but we got slightly different observations in the specific heat
which might lead to different transition behaviors (Li et al., unpublished). Further
investigations are definitely required before drawing any conclusion.
In fact, there are growing attention and developments in treating the problem of
protein-substrate interactions using coarse-grained models. For example, a refined
HP model is used to study the adsorption of peptides on gold and palladium surfaces
in [
54
]. Apart from the hydrophobic and polar effects among amino acid residues,
interactions due to electrostatic forces, the presence of solvents, and more detailed
substrate-amino acid interaction potentials (obtained from all-atomistic point of
view instead of just classifying the surface briefly into hydrophobic or polar) are
considered. The relative field strengths can also be adjusted by defining an interac-
tion matrix so as to introduce diversities to the interactions.
