Foresight Update 3
page 4
A publication of the Foresight Institute
 Protein
Engineering Survey
Editor's note: Dr. Lewis, a Senior Scientist at the genetic
engineering firm Oncogen in Seattle, has prepared a survey of the
protein engineering and related fields from a nanotechnology
perspective. Excerpts follow:
A protein engineering meeting entitled "Protein domains:
molecular insights into structure/function relationships"
was held at the Waksman
Institute at Rutgers on Nov. 2-3, 1987. It was cosponsored by
the newly created Center for Advanced Biotechnology and Medicine.
The twelve talks brought together topics ranging from pure
structure determination to molecular genetics.
A recently developed alternative approach to protein structure
determination was introduced by Prof. Kurt Wuthrich
of Switzerland. He explained how new techniques in nuclear
magnetic resonance spectroscopy enable the determination of
three-dimensional protein structures in solution so that
it is not necessary to obtain a crystal to know the structure. In
addition, you can directly compare how relevant the crystal
structure is to the structure in solution. The results he
presented were impressive. The limitations of the technique at
the moment are (1) you can only do medium-size proteins, up to
25,000 daltons (about 230 amino acid units), (2) you need a 500
MHz machine, which costs over $500,000, and (3) you need several
days of CPU time on a Cray supercomputer. The significance to
nanotechnology of [this approach] is that our knowledge of the
rules governing the relationship between protein sequence and
protein structure, and between structure and function, is limited
by the number of structures that we know. At the moment, this
number is less than 200, but [new] techniques promise a rapid
increase in this number.
[The current list of known protein structures is available in the
Brookhaven Protein Data Bank.]
A novel, and controversial, presentation on protein evolution by Prof.
Russell Doolittle of UCSD is directly relevant to the
question of how many basic protein structures have been invented
by nature. If this number is very large, then we have a long way
to go to understand the structure/function motifs that nature has
invented, and to figure out what novel motifs nature missed that
we might use. Doolittle's work is not concerned directly with
three-dimensional structure, but instead with the comparison of
protein sequence information (about 30 times as many sequences as
3-D structures are known). He has shown that a surprisingly large
number of these sequences are evolutionarily related, implying
that most proteins are derived from a small number of basic
themes. Recognizing that our current databases contain proteins
chosen because someone wanted to work on them, rather than
because an attempt was made to be representative, Doolittle
estimates that there are fewer than a hundred fundamentally
different protein structures in nature, including the ones that
have not yet been described. If he is right, a solid
understanding of sequence/structure/function relationships may
not be too far off. The question then becomes: is this small
number all that you can do with proteins; that is, did nature
only make this many because the zillions of other possibilities
are redundant or useless--or did nature just get lazy when she
came up with a small number that worked so that these became
"locked in" by evolution, while other good
possibilities were ignored? Correspondingly, can we design
additional structures that will have novel and useful properties,
rather than being more minor variations on a well-studied theme?
Another meeting, "Protein Engineering '87", held at
Oxford, was reviewed by M. Gait, J. Thornton, and R. Wetzel in Protein
Engineering 1:267-270. The major topics appear to
have been the usual attempts to use site-directed mutagenesis to
improve commercially important enzymes. These experiments may be
a bit dull compared to the ultimate use of protein engineering to
develop nanotechnology, but we should remember that they are
important for two reasons: (1) they help develop the knowledge of
structure/function relationships that we need to design protein
assemblers, and (2) they have immediate commercial applications,
which will provide the near-term market force to drive
nanotechnology development. Other topics included new algorithms
for predicting structures from sequences. This effort is a bit
academic from the nanotechnology perspective; however, there was
also discussion of a new algorithm to do the reverse:
predict a sequence that should produce a desired structure. Now
this is something to follow! It is expected to be easier to do
than predicting structure from sequence, and will be the heart of
designing assemblers.
[One
paper on the Web reporting an algorithm for reverse protein
folding]
Other relevant technologies
Although the paper "The design of a biochip: a
self-assembling molecular-scale memory device," by B.H.
Robinson and N.C. Seeman
(Protein Engineering 1:295-300) was published
in a journal about protein engineering, it actually has nothing
to do with proteins. It describes the design of a computer to be
constructed using DNA, organic polymers, and metal ions. If the
construction of such a computer were actually realized, it could
utilize a readable bit of 3x104 nm3 , and
would operate at electronic speeds over short distances. A novel
feature of the design is the use of DNA for its
structural--rather than informational--content. Oligonucleotides
would be synthesized with sequences designed to give a particular
pattern of complementarity so that they could be ligated together
and would self-assemble into "nucleic acid junctions,"
a stiff scaffolding of DNA to be used to hold the working parts
of the circuits into place. Molecular architecture and computer
graphics programs to design these scaffolds are apparently
available, and some experimental work has been done. The computer
would use conducting organic polymers, such as
trans-polyacetylene (tPA), in the preliminary design. The use of
bundles of ten to twenty tPA "wires" is contemplated to
ensure that the electronic properties are characteristic of bulk
material. The problem of how to attach tPA to DNA has not been
solved, but plausible solutions are presented. Metal ions
chelated between adjacent tPA ends would serve as redox bits that
could be manipulated by a connected voltage source through use of
a suitable dopant in the polymer. A major feature is that the
conductance would be electronic rather than through
phonon-limited nuclear motion, so that speeds would be fast. The
article explores several problems involved, along with suggested
solutions, and an estimate of a decade for development. Although
molecular in scale, the individual parts would be considerably
larger than those of Drexler's suggested mechanical
nanocomputer--but they might be faster, with estimated access
times of picoseconds. Even with a relatively large bit size (by
molecular standards), a cubic cm array would hold 3.3x1016
bits, or several hundred times as much as would be needed to
store each of the estimated ten million books in existence.
[The 1989
NanoCon Conference featured talks on this topic by
Ned Seeman and by
Bruce Robinson, and an additional paper
by Ned Seeman. In 1995, Ned Seeman was awarded the
Feynman Prize for Nanotechnology.]
The "third path"
Current thinking (Update 1, p. 5) recognizes
three technological pathways to nanotechnology: (1) protein
engineering, (2) atomic manipulation through use of the scanning
tunneling microscope (STM) and related technologies, and (3)
other approaches to chemical synthesis... The third path was
briefly considered in our previous installment by way of noting a
short article in Science News that reported novel
"Cages, Cavities, and Clefts" produced by organic
chemists that are capable of recognizing atoms and small
molecules. Although these developments are currently seen in
terms of bulk-scale technology, they embody the principles of
designing specific molecular recognition, until now exclusive to
the realm of biology. These capabilities will surely become
useful in designing molecular-scale machines for manipulating
individual atoms. This area of research has been recognized by
the 1987 Nobel Prize in Chemistry, showing once again that
science at large is realizing the enormous potential of
recognition and manipulation at the atomic scale. A short summary
of the award-winning research, entitled "Chemistry in the
image of biology" appeared in Science (238:611-612).
It briefly describes how the work of the three Nobel laureates
mimics enzyme systems in function by the creation of small
organic "host molecules," typically one-tenth the size
of enzymes, that will recognize "guest molecules," such
as metal ions, and bind them to specially designed cavities,
clefts, or cages. This host-guest chemistry is essentially trying
to understand in atomic detail the general principles of how
molecules recognize and react to each other. This knowledge will
be an essential aspect of nanotechnological manipulations. It
will enable our assemblers to feel, recognize, pick up, and put
in place the atoms with which our technological dreams will be
built.
[One
example of work on host-guest and supramolecular chemistry. Another
example.]
Readers who would like full copies of Dr. Lewis's Protein
Engineering Survey may obtain them through FI.
Please include a donation of at least $1 to cover our costs.
From Foresight Update 3, originally
published 30 April 1988.
Foresight thanks Dave Kilbridge for converting Update 3 to
html for this web page.
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