Deyu Lu, Aleksei Aksimentiev, Amy Y. Shih, Eduardo Cruz-Chu, Peter L.
Freddolino, Anton Arkhipov, and Klaus Schulten.
The role of molecular modeling in bionanotechnology.
Physical Biology, 3:S40-S53, 2006.
(PMC: 2430730)
LU2006
Molecular modeling is advocated here as a key methodology for research
and development in bionanotechnology. Molecular modeling provides
nanoscale images at atomic and even electronic resolution, predicts
the nanoscale interaction of yet unfamiliar combinations of biological
and inorganic materials, and can evaluate strategies for redesigning
biopolymers for nanotechnological uses. The methodology is
illustrated in this paper through three case studies. The first
involves the use of single-walled carbon nanotubes as biomedical
sensors where a computationally efficient, yet accurate description of
the influence of biomolecules on nanotube electronic properties and a
description of nanotube - biomolecule interactions were developed;
this development furnishes the ability to test nanotube electronic
properties in realistic biological environments. The second case
study involves the use of nanopores manufactured into electronic
nanodevices based on silicon compounds for single molecule electrical
recording, in particular, for DNA sequencing. Here, modeling
combining classical molecular dynamics, material science, and device
physics, describes the interaction of biopolymers, e.g., DNA, with
silicon nitrate and silicon oxide pores, furnishes accurate dynamic
images of pore translocation processes, and predicts signals. The
third case study involves the development of nanoscale lipid bilayers
for the study of embedded membrane proteins and cholesterol.
Molecular modeling tested scaffold proteins, redesigned lipoproteins
found in mammalian plasma that hold the discoidal membranes in shape,
and predicted the assembly as well as final structure of the
nanodiscs. In entirely new technological areas like bionanotechnology
qualitative concepts, pictures, and suggestions are sorely needed;
these three case studies document that molecular modeling can serve a
critical role in this respect, even though it may still fall short on
quantitative precision.
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