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Biomolecules and Nanotechnology
Evolution has forced innovative solutions to biomolecular problems.
Some may inform the growing field of nanotechnology
David S. Goodsell
T
he term “nanotechnology” commonly refers to a speculative field
that proposes to build machinery so
small its components are measured on a
scale of billionths of a meter (nanometers) using many of the principles of
macroscopic engineering. In his books,
K. Eric Drexler has popularized the design and computer modeling of many
of these machines, including nano-scale
manipulators to build objects atom by
atom, bearings and axles built of diamond-like lattices of carbon, waterwheel-like pumps to extract and purify
molecules and tiny computers with
moving parts whose size is within
atomic scale. The goals of these compelling machines are precision, with
every structure and action controlled at
the level of individual atoms, and parsimony, performing tasks at the minimum size necessary.
You might be surprised to learn that
nanotechnology was perfected more
than three billion years ago. Indeed,
working examples of each of these machines exist today within living cells.
Nanoscale manipulators for building
molecule-sized objects were discovered
by the earliest cells and are now used to
build proteins and other molecules atom
by atom according to defined instructions. Rotating bearings are found in
many forms: Clamps that encircle DNA
David S. Goodsell is an assistant professor in the
Department of Molecular Biology at the Scripps
Research Institute. Trained in x-ray
crystallography, he now splits his time between
computer-aided drug design and research into the
basic principles of macromolecular structure and
function. His illustrated books The Machinery
of Life and Our Molecular Nature (SpringerVerlag, New York) explore biological molecules
and their diverse roles within living cells.
Address: The Scripps Research Institute,
Department of Molecular Biology, 10550 North
Torrey Pines Road, La Jolla, CA 92037. Internet:
http://www.scripps.edu/pub/goodsell
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American Scientist, Volume 88
and slide along its length may be found
in the simplest bacteria. Our own cells
contain a rotary motor used not to power
motion but instead to generate energy.
Cells use a large collection of moleculeselective pumps to import ions, amino
acids, sugars, vitamins and all of the other nutrients needed for living. Cells also
use molecular computers, which, by altering their shapes, “read” the concentration of surrounding molecules and
compute the proper functional outcome.
By evolutionary search and modification
over trillions of generations, living organisms have perfected a plethora of
molecular machines, structures and
processes. Figure 2 presents a few examples of the rich bio-nanotechnology that
may be found in every modern cell.
Biological molecules are proven examples of the feasibility, and the utility, of
nanotechnology. Our lives depend on
them. They are foreign, however, to our
everyday experience, with unusual organic shapes and unfamiliar properties.
Bio-nanomachines are often the same
size and complexity as the speculative
nanomachines being designed today, but
they bear little resemblance to the machinery of our macroscopic world. Eric
Drexler’s nanomanipulators and gears
seem more familiar, because they are
built by engineers along the familiar
rigid, rectilinear designs of our macroscopic world. To understand the organic,
flexible forms of bio-nanomachines, we
must forget the processes of design and
engineering in our familiar world and
look instead at the forces that shaped the
evolution of life.
Evolutionary Legacy
The process of evolution by natural selection places strong constraints on the
form that biological molecules may
adopt. Because genetic information is
passed directly from generation to generation, cells must maintain a living line
back to the earliest primordial cells. If a
cell fails to generate a living descendent,
all of its biological discoveries will be
lost. This is far more limiting than the
technology of our familiar world. If we
create machines that don’t function, we
scrap them and go back to the drawing
board. But if a cell takes a gamble and
changes a critical machine, it had better
get it right the first time or the result will
be disastrous.
The picture is not entirely grim, however, as cells have several levels of redundancy within which to develop new
Figure 1. Biomolecular machines are comparable in size and complexity to the engineeringinspired nanomachines currently being proposed, but the forms and characteristics of the
two are entirely different. Opposite are two
solutions to atom-level synthesis. Model
nanomanipulators (top right) build their
products one atom at a time, like robots on an
automobile assembly line. The biological
approach to protein synthesis, at bottom, is
less rigid. Many soluble machines read information from a strand of RNA, working
together to build a new protein one piece at a
time. Both of these illustrations are drawn at
the same scale, so the sizes and shapes of
the machines may be directly compared.
Individual atoms are about the size of a grain
of salt. Above are two approaches to a rotary
bearing, drawn at higher magnification to
show individual atoms. The model bearing at
left is a perfectly symmetric arrangement of
carbon in a diamondoid lattice. The bacterial
sliding clamp, by comparison, is more organic
in shape, composed of two C-shaped globular
protein chains. Atomic coordinates were
taken from file 2pol in the Protein Data Bank.
(All images were prepared by the author.)
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2000
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information storage and retrieval
(DNA, DNA polymerase, RNA)
powered motion
(flagellar motor)
warfare
(cholera toxin)
chemical catalysis
(enzymes)
novel materials
(elastin)
signal transduction
(hormone receptor)
information-driven synthesis
(ribosome)
electrical insulation
(myelin)
containment
(lipid bilayer)
infrastructure
(actin filament)
molecular
recognition
(antibody)
light emission
(luciferase)
electrical switching
(voltage-sensitive channel)
light sensing
(opsin)
photosynthesis
(reaction center)
packaging and delivery
(rhinovirus)
Figure 2. Using a few basic structural plans, cells have developed molecular nanomachines to fill every need.
machines. First, the plans for a given machine may be duplicated, which allows
the duplicate to be modified and ultimately perfected to perform a function
different from the original. This is very
common in the evolution of life. Hemoglobin, the protein that carries oxygen in
our blood, is an example. Our cells contain information for building several different types of hemoglobin. One is optimized for carrying oxygen in the blood
of adults, whereas another is found in
the blood of a fetus. The fetal hemoglobin has a higher affinity for oxygen, allowing it to capture oxygen from the
mother’s blood. About 200 million years
ago, a gene duplication allowed the fetal
hemoglobin to be perfected separately.
Second, biology seldom involves a
single cell. A population of cells—billions, trillions—is the biologically relevant entity. Within this population there
exists ample room for experimentation.
Millions of modifications may be tried,
even if most are ultimately lethal. The
population will still survive and individuals with rare improvements may
grow to dominate in later generations.
Human immunodeficiency virus (HIV)
shows the benefits of evolutionary
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small
charged
polar
hydrophobic
bulky
Figure 3. Most of the cell’s molecular machinery
is built of protein. Proteins are synthesized as a
linear chain of amino acids. The 20 biological
amino acids have diverse properties, some of
which are indicated here, which allow the creation of proteins with widely differing properties. If properly designed, with the appropriate
combination of charged and hydrophobic amino
acids , the protein chain will fold into a compact
globule when placed in water.
change, accelerated so that we can see
the effects in months instead of millennia. HIV reverse transcriptase, the enzyme that copies the virus’s genetic information, is particularly error-prone.
Because of this, the population of viruses within an infected individual contains viruses with all possible single-site
mutations—thousands of variants on
the wild-type virus. The best of these
will dominate, but even the weakest are
continually created and recreated in
subsequent generations by the low-fidelity copying mechanism. Thus, when
an infected individual is treated with
anti-HIV drugs, the population has a
wide range of different mutants to
choose from, some of which may be resistant to the drug: The virus is made
more efficient by its very inefficiency.
The hallmark of biological evolution
is the plasticity provided by mutation
and genetic recombination. Within a
population, or through genetic duplication within a single cell, a great many
variants may be tested and the occasional improvement saved.
Evolution carries with it one important drawback, however: the problem
of legacy. Once a key piece of machin-
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ery is perfected, it is difficult to replace it
or make major modifications without
killing the cell. This is particularly true
for major molecular processes, such as
protein synthesis, energy production
and reproduction, which require the
concerted action of many different molecular machines. This leads to the remarkable uniformity of all earthly living things when observed at the
molecular level. All are built of the same
basic components.
Modern Molecular Machinery
As a consequence of the evolution of life
from a single primordial cell, all known
living things on earth share a common
molecular plan. All living things are
made of four basic molecular building
blocks: protein, nucleic acid, polysaccharide and lipid. Other small molecules are
specially synthesized for specific functions, but the everyday work of the cell is
performed by the four basics. The earliest cells chose these materials to the exclusion of others, and subsequent generations of cells, right up to our own, have
been forced to work with them.
Two different approaches are taken
to synthesize these molecules, resulting in characteristic forms and functions. Proteins and nucleic acids are
built in modular form by stringing subunits together based on genetic information. Proteins and nucleic acids may
be built in any size and with subunits
in any order. This gives remarkable
flexibility to the form and function of
these molecules.
In contrast, lipids and polysaccharides are built by dedicated machines.
Each new type of lipid molecule requires the creation of an entirely new
suite of synthetic machines. Likewise, a
new suite of machines must be created
to build each new type of polysaccharide linkage. The result is that lipids and
polysaccharides appear in fewer forms
than proteins and are used in much
more limited, albeit essential, roles.
Our distant relatives developed a
standard for biological information,
choosing a particular 20 amino acids to
be used in proteins, encoded by five
types of nucleotides found in the nucleic acids DNA and RNA. Today, every
protein is made of these 20 amino acids
(at least initially). In their defense, these
primordial cells chose an excellent set
of building blocks, including flexible
and rigid components, charged, uncharged, acidic, basic and neutral amino
acids, large and small amino acids, and
several with attractive chemically reactive properties (Figure 3). The amino
acids may be used to create proteins
with a wide range of properties. These
include very flexible proteins with
changeable shapes and very rigid crosslinked proteins designed to retain their
shape under harsh conditions. Other
proteins are highly basic or highly
acidic, designed to perform their jobs
under extreme acidic or alkaline conditions. Some are covered with carbonrich groups that repel water and seek
out membranes for binding; others have
polar surfaces and perform their duties
in the watery cytoplasm.
Modular synthesis allows proteins to
be built in many shapes and sizes. As a
consequence, most of the processes of
modern cells are performed by proteins.
Evolutionary legacy, however, places
several limits on the design of proteins.
As noted above, proteins are limited to
the 20 components encoded in the DNA
genome. Evolution also limits the size of
proteins, limits them to aqueous environments and requires that they automatically assemble themselves within
the crowded confines of the cell. In spite
of these limitations, the breadth of protein form and function in modern cells is
remarkable.
The size of a protein is limited by the
error rate of the protein-synthesis machinery, which in theory could produce a
protein of any length. Missense errors,
which misread the genetic information
and substitute an incorrect amino acid at
one position, occur at an average frequency of about 1 in 2,000. For a protein
composed of 500 amino acids, one out of
four proteins will typically have an error, but nearly every protein of 2,000
amino acids will have one. More important, however, are processivity errors,
which cause protein synthesis to abort
prematurely. These errors have been estimated to occur at a rate of about 1 in
3,000, so long proteins of several thousand amino acids are only rarely constructed in full. The average size of a typical protein chain, 300 to 500 amino acids,
is the compromise adopted by most cells.
Error rates keep the chain length low, so
larger proteins must be built as complexes of multiple protein chains.
Figure 4. Molecules must perform their tasks under the cell’s very crowded conditions. They
must seek out their proper substrates and interact only with the proper partners. This cross
section through the cytoplasm of a typical human cell depicts such macromolecules. The
large purple molecules are ribosomes that are reading genetic information from the snaky
white messenger RNA molecules. At the same time, orange, L-shaped transfer RNA molecules are aligned on the ribosome in order to build a new protein. Actin filaments and intermediate filaments criss-cross the space, providing support to the cell and a scaffold for hundreds of different enzymes, which are working on their metabolic tasks. The spaces between
the macromolecules are also filled with small molecules and water, not depicted here for
clarity, forming a very busy environment. Note that this picture is a static snapshot of the
cell. In reality, all of these components are in rapid motion.
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2000
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Figure 5. Contact sites between proteins are
highly specific, ensuring that a protein interacts only with its proper partners. Enolase, an
enzyme involved in the breakdown of sugar, is
shown here. Active enolase is formed from two
identical subunits held together by an extensive protein-protein interface. As with most
proteins composed of several subunits, enolase
relies on complementary shape and a collection
of many weak interactions to ensure specificity.
In the upper illustration, the two subunits, colored green and blue, wrap arms around one another, with each arm fitting into a complementary groove. In the lower illustration, the two
subunits have been separated slightly, and lines
have been drawn to connect atoms that form
hydrogen bonds across the interface. Atomic
coordinates were taken from the file 4enl at the
Protein Data Bank.
Proteins were invented in “warm, salty
pools,” so life on earth now requires a
warm, aqueous environment (either externally or carried around inside). Water
is essential for protein structure and function because of an emergent property of
water solutions, termed the hydrophobic
effect. Water has peculiar properties,
which are used to great advantage by biological molecules. Portions of a protein
that are rich in carbon interact weakly
with water and are termed hydrophobic.
When placed in solution, these hydrophobic regions crowd together in a
globule, minimizing contact with water
and allowing the water to escape and interact with more favorable environments.
The hydrophobic effect is a major stabilizing force for protein folding, where carbon-rich portions of the chain are folded
within the protein globule (as well as for
formation of the lipid membranes that
surround every cell, where the carbonrich portions of the lipids are packed inside the membrane). Because our molecules rely on hydrophobicity for their
structural integrity, we could never live
in vacuum or in organic solvents. Our
proteins simply would not fold.
Perhaps the most difficult limitation to
overcome is the need for self-assembly.
Biological molecules are designed to assemble themselves within cells: Proteins
are created as unstructured, linear chains
of amino acids that must fold into a stable, functional conformation (sometimes
with a little chaperoning in the proper
direction). Often, the folded chain spontaneously associates with others to form
larger stable complexes. This is a major
limitation to the design of proteins: Not
only must the protein be functional in its
active conformation, but the protein
chain must also be designed to fold into
this active conformation using only the
folding tools available in the cell.
Biomolecular Self-Assembly
The forces involved in biomolecular
structure and interaction are different
from those at play in the macroscopic
world, and thus our intuition may play
us false when attempting to understand
protein self-assembly. In our macroscopic world, much of engineering is based
on the effect of gravity on solid objects.
The strength of concrete and steel and
the different frictional properties of
Teflon and rubber are familiar quantities.
The molecular world, on the other
hand, is dominated by the effect of thermal motion on the atomic interactions
within and between molecules. Molecules are endowed with kinetic energy
proportional to the temperature, which
manifests itself as translational, rotational and vibrational motion. The forces
holding molecules together are continually fighting against these motions and
are often overcome by them.
The cellular environment is unusual
in another respect, as shown in Figure 4.
Figure 6. Closed point-group symmetry combined with a subunit of a given size allow cells to create objects of a defined size. These symmetrical complexes are used for measuring nanoscale distances, surrounding molecular targets or enclosing defined volumes. DNA-binding proteins such as CAP (left, with DNA in gray) use twofold symmetry to create allosteric “calipers” that measure the repeat length of DNA.
Higher cyclic symmetries are used to make channels and cavities, such as the GroEL chaperonin (center), which uses sevenfold symmetry to
create an enclosed environment within which new proteins are folded. Cubic symmetries are used to create larger containers. Ferritin (right)
uses octahedral symmetry to create a container for iron ions, and viruses (see Figure 7) build large icosahedral capsids to enclose and deliver
their genetic material to new host cells. Atomic coordinates were taken from files 1cgp, 1der and 1hrs at the Protein Data Bank.
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American Scientist, Volume 88
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Figure 7. Quasisymmetry allows viruses to
build structures that are larger than is possible
with perfect symmetry. At top is satellite tobacco necrosis virus, which shows perfect
icosahedral symmetry. One subunit is highlighted. Exactly 60 subunits, all with identical
structures, make up the capsid. At bottom is
the tomato bushy stunt virus, which comprises
180 subunits and consequently is larger. In
this virus, the symmetry is not perfect, and the
subunits fall into three classes (red, orange and
yellow), each with slightly different structures.
Atomic coordinates were taken from the files
2tbv and 2stv at the Protein Data Bank.
Proteins are synthesized in cells and left
to float freely, diffusing to their ultimate
site of action amid a crowded collection
of competitors. Thus, a typical protein
will come into contact with thousands
of other types of proteins and must be
able to discriminate its unique target
from all others. This is quite different
from the macroscopic world, where an
engineer can selectively fit two parts together. For instance, the concept of a #6
screw would never work inside the cell.
When building a chair, we are able to
use the same screw to fasten many different pieces together, because we actively choose where each goes. In the
cell, however, each molecule must be
designed with a unique fastener, ensuring that it binds only to its proper target
and no other.
Before atomic structures of proteins
were known, physicist H. R. Crane provided two design concepts that are required for biological self-assembly. First,
“for a high degree of specificity the contact or combining spots on the two particles must be multiple and weak.” An array of many weak interactions, such that
all are needed to provide the necessary
stability, will form a specific site for interaction. If only a few very strong interactions are used, there is an increased
chance that a protein will find a similar
interaction with improper proteins.
Second, “one particle must have a
geometrical arrangement which is complementary to the arrangement on the
other.” In other words, the shape of the
interacting surfaces must form a good fit,
and this fit must be different from that
with other proteins. Specificity is provided by the complementary shape of the
interacting surfaces, fitting knobs into
holes, and by the complementary
arrangement of hydrogen-bonding
groups and charge-charge pairs. These
two principles—that protein-protein interfaces are extended, with many weak
interactions, and that protein-protein interfaces are complementary—have been
proved in numerous protein structures,
such as the one shown in Figure 5.
Symmetry of Proteins
The process of evolutionary selection
has yielded an unusual result: Evolution of proteins favors perfect symmetry. The majority of soluble and membrane-bound proteins found in cells
are symmetrical complexes formed by
several subunits. Most proteins are oligomeric, composed of multiple copies
of one or more types of subunits. Nearly all of these oligomeric proteins are
also beautifully symmetrical, with
identical subunits packed in identical
environments. A complex interplay of
conflicting functional needs has driven
evolution to this surprisingly aesthetic
conclusion.
The major evolutionary force is the
need for large proteins. Large proteins
are preferred over smaller proteins and
peptides for several reasons. Some functional roles simply require a molecule
that is physically big. Large protein
complexes form structural elements that
span entire cells; they form rings that
encircle DNA and rulers that measure
lengths of DNA; they create pores of
many sizes through cell membranes;
they form large spherical containers for
storage and delivery and small cylindrical containers that create exactly the
proper environment for protein folding.
Large proteins are also well suited for
cooperative functions, such as allostery
Figure 8. Allosteric motion of entire subunits within a complex is often used to regulate an enzyme’s activity. The active form of
fructose-1,6-bisphosphatase, an enzyme
involved in sugar metabolism, is a flat complex of four subunits, shown in profile on
top. The binding of AMP (green, lower
image) causes a scissor-like opening of the
complex, inactivating the enzyme. Atomic
coordinates were taken from files 4fbp and
5fbp at the Protein Data Bank.
(discussed below) and multivalent
binding, which require a molecule with
several identical active sites. Multivalent binding increases the binding
strength of a molecule to a target by reduction of entropy. Once one site on the
protein has bound, the other sites are
held in close proximity to the target, increasing their probability of binding.
Many of the molecules of the immune
system have a distinctive shape, composed of many flexible arms, in order to
take advantage of this cooperativity.
Large proteins also have attractive
physicochemical characteristics. They
are more stable against denaturation,
having a more stabilized internal
structure than small proteins. Large
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Figure 9. Immune system is designed for recognition of molecules on surfaces. Soluble proteins
of the immune system seek out foreign molecules on the surfaces of viruses, bacteria and cancer
cells, and cells of the immune system pass messages by contact of proteins on their surfaces. To
perform these functions, many molecules of the immune system share a similar molecular plan,
with globular binding domains, which seek out foreign molecules or pass messages, connected
by flexible linkers, which allow more latitude when searching for the target. Antibodies and protein C1 from the complement system (top) are soluble proteins with several flexible arms, allowing them to explore surfaces of invading organisms. Cell-bound molecules, such as multiple
histocompatibility complex and CD molecules (bottom), have only a single binding site and are
connected to cells with a flexible linker.
proteins also have a lower ratio of surface area to volume, making them less
prone to damage and degradation by
other enzymes.
Unfortunately, the accuracy of the
protein-synthetic machinery limits the
size of proteins that may be constructed.
As noted above, protein chains of 300
to 500 amino acids may be consistently
synthesized, but longer chains will become increasingly riddled with errors.
The answer is to build a complex from
subunits when a large protein is needed, which allows any faulty subunits to
be discarded. This also allows new possibilities for regulation: Large structures
may be built and disassembled at will,
or subunits may be transported to a distant site (or even outside the cell) and
assembled there.
Nearly all of these oligomeric proteins in cells form closed, symmetrical
complexes based on ideal point-symmetry groups. In general, if a complex
contains several identical subunits,
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American Scientist, Volume 88
they will adopt identical symmetrical
positions in the complex. Asymmetric
complexes and random aggregates are
almost completely unknown. Symmetrical association is favored over asymmetric association because it provides
stability and control. The stability of
closed, symmetrical complexes is a
consequence of two factors. First, interfaces between proteins are highly specific and highly directional, so in most
cases evolution selects and improves
only a single type of association between subunits. Second, given these
specific, directional interfaces, the maximum number of intersubunit contacts
is formed by closed complexes.
Closed, symmetrical complexes also
ensure that the level of oligomerization
is tightly controlled. Unwanted aggregation is very dangerous for cells—
pathological aggregation of mutant proteins leads to diseases such as sickle-cell
anemia, Alzheimer’s disease and prionrelated diseases. Selection of a closed,
symmetrical complex defines the size
and shape of the resultant complex.
Under special circumstances, symmetry may be broken for a given functional
need. For instance, viruses often need to
build shells that are too large to construct
with typically sized proteins in perfect
symmetry—the highest point-group
symmetry is icosahedral, so the largest
perfectly symmetrical capsid is limited
to 60 subunits. If larger shells are needed,
more subunits must be used.
Viruses often turn to quasisymmetrical complexes, where hundreds to thousands of identical subunits combine in
similar, but not perfectly symmetrical,
positions. Quasisymmetry was first conceived as a method of tiling an icosahedron with a triangular network, much
like the geodesic domes designed by
Buckminster Fuller. Protein subunits are
arranged in this triangular lattice. Small
elastic deformations allow the subunits
to adopt similar contacts in each of the
different positions. A series of different
networks can be defined containing 60T
subunits, where T is a “triangulation
number.” Only certain triangulation
numbers yielded smooth networks, according to the relation T = h2 + hk + k2,
where h and k are integers.
When structures were obtained for
viral capsids, this model for quasiequivalence was surprisingly successful. The arrangement of subunits of
most capsids corresponded closely to
one of the triangulation numbers: Examples with T = 1 (perfect icosahedral)
symmetry and T = 3 symmetry are
shown in Figure 7. However, elastic deformations were not observed. Instead,
subunits typically accommodated different positions through the use of
structural “switches,” where the subunit adopts two or more significantly
different conformations. Often, the subunits are composed of two domains
connected by a flexible linker, and flexure of the subunit is used to adopt different conformations.
Biomolecular Flexibility and Dynamics
Engineers in our macroscopic world
typically build rigid structures that stoically resist the forces of nature. Nature, however, has taken a different approach, developing machines that flex
over the course of their action. Is a totally rigid nanostructure needed or
even desired? Apparently not. In fact,
biological molecules take advantage of
flexibility for many aspects of their
function. Many of these functions
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would be severely compromised, or
not even possible, given a rigid molecule. Subtle motions can have surprisingly large effects on reaction rates or
assembly. Biological molecules are perfectly placed to take advantage of these
subtle motions. The step-by-step optimization provided by evolution allows
a moderately active protein to be improved, through small changes modifying structure and flexibility, to yield a
machine ideally tailored to fulfill its
function.
This process is easy for evolution but
far more difficult for biotechnological
design. We design our machines in one
step, instead of through many small
random optimization steps, and we expect to get it right with a minimum of
tweaking and redesign. Thus, to anticipate all of the subtle effects of motion,
our design techniques must be accurate enough to predict conformation
and flexibility of molecules at scales far
smaller than the radius of an atom.
All biological molecules are flexible to
some extent and are battered into different conformations by the constant
pressure of surrounding water and the
kinetic energy of their own atoms. At
physiological temperatures, biological
molecules constantly flex. Most of the
interactions holding a protein together
are conserved—covalent bonds remain
connected, hydrogen bonds and salt
bridges link portions of the chain—but
entire elements of secondary structure
flex, bending slightly or separating momentarily from the globule. These motions are often termed “breathing.”
Breathing is essential in the function of
myoglobin, a deep red protein that
stores oxygen in muscle cells. Oxygen
is bound to myoglobin in a pocket that
is completely buried within the protein.
Looking at the static structures provided by x-ray crystallography, there are no
channels leading into or out of the pocket. For the oxygen to enter and exit, the
molecule must breathe, transiently
forming channels that allow passage.
Many proteins use a carefully designed change of shape to regulate their
action. These allosteric (“other shape”)
proteins are composed of several subunits, each of which performs identical
functions. In the simplest model of their
action, each subunit may adopt two
conformations, one functionally active,
the other less active. Regulation is performed by propagation of the shape
change from one subunit to its neighbors. For instance, phosphofructoki-
nase, a key enzyme in sugar metabolism, uses allosteric regulation to modify its action. Phosphofructokinase is
composed of four identical subunits (a
tetramer), each containing a reactive site
for the sugar molecules. The tetramer
also contains binding sites for the energy molecule adenosine triphosphate
(ATP) in the cleft between subunits.
When ATP binds to this second site, it
forces the entire enzyme complex into a
different shape, which is less active than
the original form. In the cell, this regulation is used as a negative-feedback loop.
ATP is one of the final products of the
sugar-breaking process that the enzyme
performs. When ATP is plentiful, it
binds to the regulatory site in phosphofructokinase, shutting down its own
synthesis. The enzyme that performs
the opposite reaction, shown in Figure
8, is also allosterically regulated.
Many protein chains rely on “induced fit” to mediate their function.
The chain may remain in a partially
unfolded conformation that only completely folds when it binds to its target.
Induced fit may be used to create doorways that allow ligands to enter protein cavities that are shielded from the
surrounding environment. HIV-1 protease is an example. The active site is a
cylindrical tunnel, with the cleavage
machinery at its center. Somehow, a
polypeptide must be threaded through
this tunnel in order for the cleavage reaction to occur. This problem is solved
through the use of two flexible flaps
that cover the top of the tunnel. When
free in solution, these flaps are disordered, opening a path to the active site.
When the protease wraps around its
target, the flaps close, forming a stable
structure that positions the polypeptide accurately for cleavage.
Flexible linkages are common in the
molecular world. Protein chains may
be made more flexible through addition of many molecules of the amino
acid glycine, which are less hindered
in bond rotation because of the lack of
a side chain, or through addition of
many charged residues, which favor
exposure to solvent over forming a
compact globule. The rigid kink formed
by proline, surprisingly, is also commonly found in flexible regions, because it does not fit comfortably within compactly folded structures. The
immune system contains many examples of flexible linkages that enhance
multivalent binding, as shown in
Figure 9.
Prospects
Biological molecules are examples of
solved problems in nanotechnology—
lessons from nature that may be used to
inform our own design of nanoscale machines. The entire discipline of biotechnology has emerged to harvest this
rich field of biological wealth. We routinely edit and rewrite the information in
DNA to build custom proteins tailored
for a given need. Today, for instance, bacteria are engineered to produce hormones, genes for disease resistance are
added to agricultural plants, and cells are
cultured into artificial tissues.
Principles of protein structure and
function also yield insights for nanotechnological design and fabrication. The diversity of protein structure and function
shows the power of modular, information-driven synthesis, as well as the limitations imposed by modular design once
a dedicated modular plan is chosen. Proteins demonstrate that extended, complementary interfaces are essential prerequisites for molecular self-assembly. The
prevalence of protein complexes proves
that error-prone synthesis may be accommodated through the use of subunits and
symmetry to build large objects accurately
and economically. And contrary to our
macroscopic experience, motion and flexibility may be assets, not liabilities.
The principles observed in the mobile, organic shapes of biological molecules may be applied to the controlled
rectilinear forms of diamondoid lattices,
fullerines or whatever nanoscale primitives are ultimately successful. We must
not be too impatient, however. Nature
has had some three or four billion years
to perfect her machinery; so far, we
have had only a few decades.
Bibliography
Crane, H. R. 1950. Principles and problems of biological growth. Scientific Monthly 70:376–389.
Drexler, K. E. 1992. Nanosystems, Molecular Machinery, Manufacturing and Computation. New
York: John Wiley & Sons.
Goodsell, D. S. 1996. Our Molecular Nature: The
Body’s Motors, Machines and Messages. New
York: Springer-Verlag.
Goodsell, D. S., and A. J. Olson. 1993. Soluble proteins: Size, shape and function. Trends in Biochemical Sciences 18:65–68.
Goodsell, D. S., and A. J. Olson. 2000. Structural
symmetry and protein function. Annual Reviews in Biophysics and Biomolecular Structure 29:
105–153.
Larsen, T. A., A. J. Olson and D. S. Goodsell. 1998.
Morphology of protein–protein interfaces.
Structure 6:421–427.
Protein Data Bank is available on-line at
http://www.rcsb.org/pdb
© 2000 Sigma Xi, The Scientific Research Society. Reproduction
with permission only. Contact [email protected].
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