Component of a Biomolecular Assembly Line
peptide synthetase.”
A Tanovic, SA Samel, LO Essen, MA Marahiel, Science, 321: 659-63 (2008).
Cells use what are, in effect, molecular assembly lines to manufacture a range of complex molecular products. In these assembly-line machines, devices in series add parts to a workpiece, using swinging arms to pass the workpiece from one device to the next. Biochemists recently learned in greater detail how these biomolecular assembly lines work, and are considering how to string devices together to make artificial machines that work the same way.
I’ve long been interested in these biomolecular machines, and was reminded of the recent work last week when I saw that Chemical & Engineering News highlighted it as one of the top 12 developments in molecular science in 2008. The machine in question is a “modular nonribosomal peptide synthetase”, kin to the machines that manufacture penicillin, vancomycin, and a number of other antibiotics. The working principle extends to the fabrication of other molecules, such as polyketides. In each instance, the molecular product is a set of linked monomers, sometimes a simple chain, sometimes branched or cyclical. A nice review. is available, courtesy of the open-publication policy of the American Society for Microbiology.
BTW, although fatty acid synthases had been thought to work by a swinging-arm mechanism, they instead use an alternative,* performing a series of catalytic operations on intermediates linked to carrier proteins confined to reaction chambers.
Assembly-line mechanosynthesis with soft constraints
The assembly lines in modular, nonribosomal peptide synthetases consist of a series of enzymes, and the transfer of a workpiece from one arm to the next is accomplished by the same catalyzed reaction that adds the next monomer. The arms themselves thrash to and fro in a constrained Brownian dance. In typical metabolic processes, by contrast, freely diffusive Brownian motion effects transfers from enzyme to enzyme. The constrained motion imposed by the flexible, swinging arms of biomolecular assembly lines provides a soft form of mechanosynthetic control, and the consequences of this illustrate two fundamental advantages of mechanically guided reactions.
The first advantage is quantitative, a matter of speed: Productive, reaction-producing molecular encounters occur more frequently when the reactants are constrained to close proximity than when they are released to diffuse in the solvent. This motion constraint increases what is called the “effective concentration” of the reaction, and increases in effective concentration contribute greatly to reaction-rate acceleration in enzymatic catalysis. Increases in effective concentration are a natural consequence of mechanically guided motions.
The second, more important advantage is qualitative, a matter of direction: In the absence of mechanical constraints on motion, reaction sequences (and reaction sites) can be controlled only by intrinsic properties of the molecules themselves — either by inherent reaction selectivity directed by very local structural features (as in classical organic synthesis), or by selective binding of the reactants by enzymes, based on less-local properties such as molecular shape, charge distribution, and hydrogen-bonding geometries. These conditions for selectivity can be difficult to meet. With mechanical constraints on motion, by contrast, reaction sites and sequences can be more nearly independent of the structure of the reactants. In both ribosomes and the modular, nonribosomal peptide synthetases, monomers are added at specific sites on a growing structure, and in a particular sequence, because the machinery allows monomers to encounter the structure in only at the correct sites, and only in the correct sequence.
This qualitative advantage is what enables mechanosynthetic processes to make structures of great complexity: Mechanically guided reactions can be highly specific, independent of the size, complexity, or structural regularity of the molecules under construction. This principle is as applicable to ribosomes as it is to other productive nanosystems, and scales all the way up to molecular manufacturing.
The shared architecture of manufacturing, molecular biology, and molecular manufacturing
In the molecular-manufacturing architecture described in Nanosystems, simple assembly-line mechanisms — not elaborate, programmable machines — perform the overwhelming majority of fabrication operations. For repetitive, high-throughput fabrication, specialized assembly-line mechanisms have great advantages in size, complexity, and energy cost, and the fundamental reasons for these advantages are the same in biological metabolism as they are in the manufacture of the components that compose most of the artifacts around us.
Programmable machines are necessary only at the higher levels of production, where they are used to make the relatively small number of specialized machines that in turn make huge numbers of identical parts. Again we see this both in manufacturing and biological metabolism. And in each instance, even the programmable machines themselves are substantially specialized: A ribosome can make any of an effectively unlimited number of different products, but only if each is the right sort of peptide sequence. Likewise for a milling machine, provided that the product is made of the right sort of material and formed into a suitable shape.
Are the most specialized machines programmable? Yes, in a sense: not from one operation to the next, but before they start, when they are designed and manufactured.
* As is often true, uncertainty about how nature implements a function (defining a problem in science) points to a choice of potential implementations for that function — providing an opportunity in engineering. This is an aspect of “The Antiparallel Structures of Science and Engineering”.
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Chris Phoenix 01.05.09 at 11:18 pm UTC
There is a blurry line between “programmable” and “not programmable.” It requires no computation for a machine to follow a fixed trajectory. Likewise, a machine can have several alternative trajectories, with an external input selecting the trajectory to follow, and it requires no computation to follow each trajectory. It also requires no computation to enter the selected path – mechanically, the selector may be as simple as a railroad track switch.
Now here’s the interesting bit: a machine to set the selector switches may itself be following a fixed trajectory. Thus, stepping through a long sequence of switch settings may incur no computational cost, as long as the data for the sequence is pre-existing in the machine, either built in, or pre-loaded into a memory. The cost to load a sequence of switch settings into a memory is not zero, but if the sequence is to be re-used many times, the cost per operation can be arbitrarily small.
A very loose analogy is the way a DMA controller can transfer large amounts of data without requiring CPU operations, though of course today’s DMA controllers do not use reversible logic.
The design space of polymers is ridiculously large. Out of trillions of possible combinations, there may be a dozen Kaehler brackets that the designer wants to use over and over. Pre-load the recipes for those brackets, and your non-computing stepping machine can build any bracket any time on command.
Go back one more level, and sequences of brackets may themselves be transmitted without computation, to build standard housings and such. But if someone invents a better housing design, you don’t have to redesign and rebuild the mechanical components of your factory, just download a new recipe (at non-zero but trivial cost).
I proposed a similar system in my “Primitive Nanofactory” paper: http://jetpress.org/volume13/Nanofactory.htm
A Jacquard loom is an example of a machine that has a small repertoire of operations, selectable by outside input. In such a machine, the operations are designed in advance, but the selection of the operations is made while the machine is running. (Again, I’m not trying to argue that such machines are small or simple – just that they don’t have to incur kT bit-erasure losses. The theoretical computational cost is zero, though the mechanical energy cost of friction won’t be zero.)
It’s worth noting that a machine may store lots of internal state as it works – indeed, the entire mechanical configuration of any mechanical system can be viewed as its internal state – but traversing a set of states along a fixed trajectory does not have to cost any bit-erasure energy. This includes things like counters that count to a pre-set value.
So we could imagine a “programmable” molecular fabrication system as a two-part machine, where the first part is analogous to a Jacquard loom and the second part selects the set of data to be processed next. The first part would perform sequences of operations, each operation being fixed at design time, and the sequence being controlled by the data fed in. The second part would simply send “cards” to the machine, one at a time. It would have a memory store for card stacks, and a counter that presented the cards to the first part by setting the switches. Which stack of cards it presented would be controlled by – guess what – externally set selector switches.
Suppose the mechanical end-effector of your fabrication system can do any of sixteen mechanosynthetic operations including NO-OP, depending on the configuration of four knobs presented to it by other machinery. There is no computational cost in this part of the system – no bit erasure – the machine is simply following trajectories that are fixed for the duration of the trajectory.
A 128-bit (16-byte) recipe can be viewed as a sequence of 32 instructions. For example, it could represent a sequence of up to 32 Schafmeister monomers to be added to a polymer (from a palette of up to 15 distinct monomers).
A mechanical system can be built that will step for a fixed range (set by external selector switches) through the contents of a (mechanically stored) memory, presenting it four bits at a time to an output device. Since the sequence of presentation is fixed, there’s no theoretical kT cost to run the counter/stepper. Presenting four bits – for example, trying to drive spring-loaded rods past cams, where the end of each rod is the knob that “programs” the first machine (”loom”) – is also reversible. (This design, of course, is inspired by the computer chapter of Nanosystems.) So this recipe-presenter system requires no computational cost, assuming the recipes are pre-loaded and the recipe-selector is externally presented.
A system with 512 bytes of storage – comparable to the earliest electronic computers, which were built one vacuum tube at a time – could store up to 32 16-byte recipes (perhaps Kaehler brackets), and present them one recipe at a time, one step at a time, to a fully deterministic mechanical molecular fabrication system.
A single five-bit code presented to this system can control the deposition of up to 32 monomers. Repeated presentations of codes will add further strings to the polymer. The design space grows rapidly.
For the energy cost of copying 512 bytes of data once – trivial – this system can deposit up to 32 monomers, according to one of 32 recipes, for every five bits presented to it. Clearly, this fits most people’s definition of “programmable.” But the system does no actual computation on the data – it just mechanically follows what it is given.
Again, I am not proposing that such a system would be useful. I am only arguing that long strings of data can be can be used to select sequences of operations out of a huge design space, at a computational cost of well under one bit per operation.
jim moore 01.06.09 at 6:03 pm UTC
What I think has real short term potential is to attach the molecular assembly lines to a membrane so that you keep your reactants on one side and your producd(s) on the other side. Just being able to avoid the giant hassle of separating and purifying the product is huge gain in manufacturability.
Steve 01.07.09 at 5:49 am UTC
To Jim Moore:
By the time proteins can be custom-designed to meet whatever manufacturing need arises, the need for purifying products will vanish because it will be possible to arrange self-assembly of macroscale structures as is seen in biology.
To Dr. Drexler:
“Productive, reaction-producing molecular encounters occur more frequently when the reactants are constrained to close proximity than when they are released to diffuse in the solvent.”
That depends on how much solvent you have. If you’re dependent on a particular product being passed from enzyme to enzyme, and a Brownian collision knocks it off of the machinery (which I would expect to be a relatively frequent occurrence, given the violence of Brownian motion and the need for the product being passed to be relatively weakly held), it’s completely lost if the process occurs in a large solution. In a smaller compartment such as a cell, however, diffusion is a perfectly effective way to transfer molecules from one enzyme to the next, and it conveniently allows the enzymes to be located anywhere within the cell. After all, releasing two molecules at opposite ends of a 1-micron cell will result in their interacting within 1 second. (Need them to interact faster? Just decrease the size of the cell.) I honestly see no reason why molecular assembly needs to resemble current manufacturing at all, when the same results can be had with significantly less effort by co-opting nature’s flawlessly engineered methods.
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