Chemistry Reference
In-Depth Information
With the effectiveness and accuracy, Wang-Landau sampling is believed to be
one of the feasible methods for such systems, and its performance has been proven
using the HP sequences. Recently, Swetnam et al. have proposed ways to improve
the efficiency of simulating lattice peptides adsorption (including homopolymers
and HP sequences) using Wang-Landau sampling [
55
]. The improvement scheme
is in two aspects: the first one is to reduce the time used during the process of select-
ing a valid pull move that brings the polymer from one conformation to another.
It is made possible by not counting all available moves given a conformation. The
second proposed improvement is to shift the surface accordingly so that it is always
touching the polymer. In this way, every state generated would be a state absorbed
to the surface, and time would not be wasted in simulating desorbed conformations.
These reduce the computation time to a certain extent and will allow simulations of
larger systems.
7.5 Conclusion
In this work, we have reviewed a minimalistic lattice model for proteins, the HP
model, and some numerical methods to study HP benchmark sequences. We have
also illustrated how the HP model can be used to study the effects of protein-surface
interactions via a coarse-grained approach. In spite of the simplicity of the model,
it successfully recovers major features found in real proteins and shows how the
presence of a surface affects the conformations of proteins. Nevertheless, the use of
coarse-grained models to study peptide-substrate activities is still in its initial stage,
and the richness and complexities in thermodynamics properties are yet to under-
stand thoroughly. Further developments and advancements are certainly essential in
this emerging area.
Acknowledgments
This research was supported by NSF Grant DMR-0810223 and NIH Grant
1R01GM075331.
References
1. J.D. Bryngelson, J.N. Onuchic, N.D. Socci, P.G. Wolynes, Funnels, pathways and the energy
landscape of protein folding: a synthesis. Prot. Struct. Funct. Genet.
21
, 167 (1995)
2. J.N. Onuchic, Z. Luthey-Schulten, P.G. Wolynes, Theory of protein folding: the energy land-
scape perspective. Ann. Rev. Phys. Chem.
48
, 545 (1997)
3. C.B. Anfinsen, Principles that govern the folding of protein chains. Science
181
, 223 (1973)
4. G. MacBeath, S.L. Schreiber, Printing proteins as microarrays for high-throughput function
determination. Science
289
, 1760 (2000)
5. R. Fernandez-Lafuente et al., Immobilization of lipases by selective adsorption on hydropho-
bic supports. Chem. Phys. Lipids
93
, 185 (1998)
6. R.S. Kane, A.D. Stroock, Nanobiotechnology: protein-nanomaterial interactions. Biotechnol.
Prog.
23
, 316 (2007)
