Re-edited
Copyright © 2000 Aris Toharisman
Makalah Falsafah Sains (PPs 702)
Program Pasca Sarjana
Institut Pertanian
Dosen: Prof Dr Ir Rudy C Tarumingkeng
WILL NANOTECHNOLOGY ENHANCE BIOTECHNOLOGY ?
P0900004
Since several years ago the
research program in very small semiconductor structures having dimension smaller than 0.1 micrometer has been
initiated. The first advancement was
achieved by microelectronics industries when they developed in manufacturing
and machining silicon materials at the nano scale (10-9
m) or atomic scale (Laval et al.,
1995). As the technology called nanotechnology seems to offer an unprecedented
combination of scientific excitement and potential practical utility, it now
has become the most challenging technology.
Nanotechnology is defined as a “discipline in which the purpose is
to build devices and structures having every atom in the proper place” (Kaehler, 1994). The
resulting materials can be rationally designed to exhibit novel and
significantly improved optical, biological, chemical, mechanical, and
electrical properties. Since all objects in the world are composed of atoms,
the use of this technology may create various products obeying physical and
chemical law. Therefore,
nanotechnology is likely to
become the technology of choice for
many areas including biotechnology in the next few decades (Goldin et al. http://www.memagazine.org/contents/current/features/thegreat/thegreat.html.).
Biological systems are slightly different with physical processes
in which nanotechnology has been used. Kaehler (1994)
contends that biological systems are mainly based on diffusion of soft
substances rather than forced assembly of rigid parts, but they are still
parallels with nanotechnology. Many biological processes
may be recog-nized as natural nanostructure machines
whose actions are partly mechanical (Table 1).
Enzymes, for example, can be
regarded as small machines whose reactions are catalyzed by the reactants held
in specific positions; the bacteria flagella can be compared with
electromechanical machines. They can be analyzed in much the same way with non-biological
structures. They could be engineered, manipulated and manufactured and also
possible to be exploited in nanostructure design and development (Laval et al., 1995; Kaehler,
1994; Murphy et al., 1994; Fahy, 1993).
Laval et al. (1995)
suggests that the use of
nanotechnology focusing on manipulating
individual cell or molecule will develop molecular-scale processes on
biotechnology such as nanobioreactors.
Biotechnological concept has one useful characteristic that is the ability of
self-replication. Cells and molecules
are capable of making of copies of their selves. These phenomena will be interesting in terms
of economical aspects and perhaps may promote the emerging of biotechnology.
Table 1. Biological Counterparts of Machine
Components (Drexler, 1992)
____________________________________________________________
Macroscopic
Devices Cellular/Molecular Analog
____________________________________________________________
Cables Collagen
Containers,
pipelines Vesicles, endoplasmic reticulum
Conveyor
belts Axoplasmic flow
Rotary
motors, bearings Flagellar
electrostatic motor
Memory: ROM,
RAM DNA, mRNA
Robotics
assembly lines mRNA + ribosomes
____________________________________________________________
Protein Engineering
Protein is one of the most important substances in biotechnology
and involves in much of the progress in
biotechnology research and development. Nature has created a diverse of
proteins that fold into unique structures to do specific biochemical functions
such as enzymatic catalysis, coordinated motions, mechanical supports, immune
protections, and so on. Unfortunately,
in nature proteins are built blindly and they are evolving by a process of
mutation and selection. The process takes much time and seems to be
inefficient. The folding is difficult to predict and design because individual
amino acids have no strong natural complementarity (Anthonsen et al.,
1994; Drexler, 1999).
In order to broaden their functions, creating and modifying new proteins
should be carried out.
Protein
engineering has been used to design and constructs of novel proteins that can
be utilized at extreme conditions like high temperature, pH and salt (
However, the predicting structures from sequence and activity from
structure of high molecular proteins are not still understood very well. This is primarily due to the low degree of
protein geometry precessions (Fersht and Winter,
1992; Ponder and Richards, 1987).
Proximal Probes
Most protein structures are determined by X-ray
crystallography. This method may give
structures of atomic resolution, but requires the stable high quality
crystals. Many proteins, nonetheless,
are very difficult to be crystallized (Anthonsen et al., 1994). Accordingly, the efforts in exploitation
design principles for protein structure and function should be further
investigated.
The scanning tunneling microscope (STM) and the atomic force
microscope (AFM) termed the scanning probe microscopes (SPMs)
have become important tools in biotechnological works including the design of
proteins. Scanning probe microscopes employ very sharp probes in close proximity
to a surface to examine a particular surface-related property. In the STM, this property is local
conductivity, whereas in the AFM local topography is sampled (Roberts et al., 1994; Merkle,
1999). They are capable of imaging
surface with high resolution and can be
used to move and position atoms and
molecules precisely with or without the presence of specific added
molecular markers. Molecular resolution images have been reported for a range
of biomolecules including proteins, lipids, nucleic
acids and biomedical polymers. The
microscopes can be used to observe the motion of individual protein molecules
and the movement of enzymes during catalysis (Laval et al., 1995;
Roberts et al., 1994).
The SPMs have been carried
out in aqueous media mainly electrolyte
solution, resulting in increase the
stability and reduce the alteration of biological materials. For example, the exocytosis of a fox virus from living cell has been
observed by AFM in a liquid environment.
In contrast, the use of traditional imaging and surface-analysis
techniques requires
dissolving proteins in
organic solvents. It will alter the
macroscopic dielectric constant and lead to a much less pronounced difference
between the interior and exterior static dielectric behavior. Protein function in such media may be altered
and is poorly understood (Anthonsen et al., 1994).
Furthermore,
the SPMs can drive reactions.
The tips of the STM can act as a catalyst and can be oriented to bring
an active site of enzymes contact with substrate. It also can be utilized to
bind one molecule to another such as receptors and ligand,
antibodies and antigens, complementary strands of DNA, streptavidin
and biotin (Ragona, 1995; Cooper, 1999; Heinz and Hoh, 1999). One reagent can be brought together to catalyze
reactions at precisely determined locations (Fahy,
1993).
Therefore, the use of these microscopes can help in creating
proteins at the nanometer scale and describing protein structures cells completely
and perhaps the engineering problem of designing new proteins can be
simplified. Fahy
(1993) says that the use of proximal probes will “open the door to previously unthinkable
accomplishments”.
Future Prospects
The protein structures are determined and mapped by SPMs and then used as a basis structure for template, a list of sequence derived from a prototype structure. As soos as template has been identified, and an alignment between this template and a sequence has been defined, a 3-D model of the new and novel protein can be generated at atomic precise. Finally, the bulks of proteins, peptides or enzymes will be created and can be utilized for different purposes. This approach has been succeeded to make cinnamyl alcohol dehydrogense based on the structure of alcohol dehydrogenase (Anthonsen, 1994).
Immobilize
molecule techniques. Most of biotechnological
methods depend on interaction between molecules such as affinity chromatography, enzyme-linked immunosorbent
assays (ELISA), solid-phase synthesis and nucleic acid sequencing. Nanotechnology can be employed to control the
interaction by physically controlling their proximity, rather than relying on
random encounters in three-D space, resulting in novel various of immobilized molecules. It is possible to work with single biomolecules or to control a bi-molecular interaction which
can not be done today (Laval et al.,
1995).
The
surface coverage and
functionality of antibodies can be increased by linking with a high affinity substance.
One example process done by this approach is the linking biotinnylated
antiferrin antibodies streptavidin-coated
polyester surface resulting in dramatically of surface coverage and functional
states (Roberts, 1994).
Novel Proteins. Nanotechnology is now used
to build proteins in defined instructions (Goodsell, http://www.sigmaxi.org/amsci/articles/00articles/goodsellintro.html
). New proteins having specific functions can be built by
transferring entire domains from one protein to another. One enzyme, for example, has been joined
to the antigen-binding domains of antibodies to make enzymes that can target
blood clots or tumors. Adhesion
molecules (CD4) joined to the Fc region of antibodies
can block HIV infection of T-cells (Fersht and
Winter, 1992).
The antigen-binding in
antibodies are fashioned by
six loops, three from the heavy chains variable domain and three
from the light chain variable domain.
The loops are highly variable in sequence, allowing a great diversity of
shapes for binding to different antigens, and are supported on a b-sheet frame wok. Indeed, by transplanting the loops from one
antibody to another it is possible to transfer the antigen-binding site of a
rodent antibody and create reshaped human antibodies for therapy purposes.
Drexler
(1999) has proposed the use of artificially design proteins in which the
simultaneous use of many stabilization techniques produces a protein that is
much more stable than naturally occuring proteins.
Enzyme Production. Many kinds of enzymes working in unnatural
conditions can be built. Proteases, for
instance, have been widely used in lot of industries. It is about 600 tones of
proteases per annum are produced for use in soap powder, food, and leather
industries. The replacement of methionine side chain will make its resistance to
oxidation. The substitution residues
found in homologous thermopiles will make it more thermostable
(Fehrst and Winter, 1992). The small and stable peptide motifs bound to
a catalytic site of enzymes can improve their function for heuristic purposes.
Scientists
at
Many other projects on nano-scale machines have been developed such as the use of large-scale molecular dynamics techniques for making novel polymer, modified leucine zipper motifs as a critical element in artificial gels that can be switched on by changing pH or temperature and computer structures for DNA sequences construction (Goddard et al. http://www.foresight.org/Conferences/MNT8/Abstracts/Goddard/).
In short, nanotechnology offer the possibility of biotechnological
works varying in structures and functions and so it is undoubtedly that the
application of nanotechnology (enhanced by scanning probe microscopes) will
bring a great impact in biotechnology.
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