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Guest Writer - Gastautor - Gast Schrijver


Protein Springs and Tattoo Needles

Work in progress at CRN


I'm currently investigating two topics. One is how to make the simplest possible nanoscale molecular manufacturing system. I think I've devised a version that can be developed with today's technology, but can be improved incrementally to approach the tabletop diamondoid nanofactory that is the major milestone of molecular manufacturing. The other topic is how proteins work. I think I've had an insight that solves a major mystery: how protein machines can be so efficient. And if I'm right, it means that natural protein machines have inherent performance limitations relative to artificial machines.

I'll talk about the proteins first. Natural proteins can do things that we can't yet even begin to design into artificial proteins. And although we can imagine and even design machines that do equivalent functions using other materials, we can't build them yet. Although I personally don't expect proteins to be on the critical path to molecular manufacturing, some very smart people do, both within and outside the molecular manufacturing community. And in any case, I want to know how everything at the nanoscale works.

One of the major questions about protein machines is how they can be so efficient. Some of them, like ATP synthase, are nearly 100% efficient.
ATP synthase has a fairly complex job: it has to move protons through a membrane, while simultaneously converting molecules of ADP to ATP.
That's a pump and an enzyme-style chemical reaction--very different kinds of operation--linked together through a knobby floppy molecule, yet the system wastes almost no energy as it transfers forces and manipulates chemicals. A puzzle, to be sure: how can something like a twisted-up necklace of different-sized soft rubber balls be the building material for a highly sophisticated machine?

I've been thinking about that in the back of my mind for a few months. I do that a lot: file some interesting problem, and wait for some other random idea to come along and provide a seed of insight. This time, it worked. I have been thinking recently about entropy and springiness, and I've also been thinking about what makes a nanoscale machine efficient.
And suddenly it all came together.

A nanoscale machine is efficient if its energy is balanced at each point in its action. In other words, if a motion is “downhill” (the machine has less energy at the end of the motion) then that energy must be transferred to something that can store it, or else it will be lost as heat. If a motion is “uphill” (requires energy) then that energy must be supplied from outside the machine. So a machine with large uphills and downhills in its energy-vs.-position trajectory will require a lot of power for the uphills, and will waste it on the downhills. A machine with sufficiently small uphills and downhills can be moved back and forth by random thermal motion, and in fact, many protein machines are moved this way.

A month or so ago, I read an article on ATP synthase in which the researchers claimed that the force must be constant over the trajectory, or the machine couldn't be efficient. I thought about it until I realized why this was true. So the question to be answered was, how was the force so perfectly balanced? I knew that proteins wiggled and rearranged quite a bit as they worked. How could such a seemingly ad-hoc system be perfectly balanced at each point along its trajectory?

As I said, I have been thinking recently about entropic springs.
Entropy, in this application, means that nanoscale objects (including molecular fragments) like to have freedom to wiggle. A stringy molecule that is stretched straight will not be able to wiggle. Conversely, given some slack, the molecule will coil and twist. The more slack it has, the more different ways it can twist, and the happier it will be.

Constraining these entropic wiggles, by stretching a string or squashing a blob, costs energy. At the molecular scale, this effect is large; it turns out that entropic springiness, and not covalent bond forces, is the main reason why latex rubber is springy. This means that any nanoscale wiggly thing can function as an entropic spring. I sometimes picture it as a tumbleweed with springy branches--except that there is only one object (for example, a stringy molecule) that wiggles randomly into all the different branch positions. Sometimes I compare it to a springy cotton ball.

One Saturday morning I happened to be thinking simultaneously about writhing proteins, entropic springs, and efficient machines. I suddenly realized, as I thought about the innards of a protein rearranging themselves like a nest of snakes, that installing lots of entropic springs in the middle of that complex environment would provide lots of adjustable parameters to balance whatever force the machine's function generated. Because of the complex structural rearrangement of the protein, each spring would affect a different fraction of the range of motion. Any uphills and downhills in its energy could be smoothed out.

Natural protein machines are covered and filled with floppy bits that have no obvious structural purpose. However, each of those bits is an entropic spring. As the machine twists and deforms, its various springs are compressed or allowed to expand. An entropic spring only has to be attached at one point; it will press against any surface that happens to come into its range. Compressing the spring takes energy and requires force; releasing the spring will recover the energy, driving the machine forward.

As soon as I had that picture, I realized that each entropic spring could be changed independently, by blind evolution. By simply changing the size of the molecule, its springiness would be modified. If a change in a spring increased the efficiency of the machine, it would be kept.
The interior reconfiguration of proteins would provide plenty of different environments for the springs--plenty of different variables for evolution to tweak.

Always before, when I had thought about trying to design a protein for efficiency and effectiveness, I had thought about its backbone--the molecular chain that folds up to form the structure. This is large, clumsy, and soft--not suitable for implementing subtle energy balancing.

It would be very hard (no pun intended) to design a system of trusses, using protein backbones and their folded structure, that could implement the right stiffness and springiness to balance the energy in a complex trajectory. But the protein's backbone has lots of dangling bits attached. The realization that each of those was an entropic spring, and each could be individually tuned to adjust the protein's energy at a different position, made the design task suddenly seem easy.

The task could be approached as: 1) Build a structure to perform the protein's function without worrying about efficiency and energy balance.
Make it a large structure with a fair amount of internal reconfiguration (different parts having different relative orientations at different points in the machine's motion); 2) Attach lots of entropic springs all over the structure; 3) Tune the springs by trial and error until the machine is efficient--until the energy stored by pressure on the myriad springs exactly balances the energy fluctuations that result from the machine's functioning.

I proposed this idea to a couple of expert nanoscale scientists--a molecular manufacturing theorist and a physicist. And I learned a lot.

One of the experts said that he had not previously seen the observation that adding lots of springs made it easier to fine-tune the energy accurately. That was pretty exciting. I learned that proteins do not usually disfigure themselves wildly during their operation--interior parts usually just slip past each other a bit. I watched some movies of proteins in action, and saw that they still seemed to have enough internal structural variation to cause different springs to affect different regions of the motion trajectory. So, that part of the idea still seems right.

I had originally been thinking in terms of the need to balance forces; I learned that energy is a slightly more general way to think about the problem. But in systems like these, force is a simple function of energy, and my theory translated perfectly well into a viewpoint in terms of energy. It turned out that one of my experts had studied genetic algorithms, and he warned that there is no benefit to increasing the number of evolvable variables in the system if the number of constraints increases by the same number. I hadn't expected that, and it will take more theoretical work to verify that adding extra structures in order to stick more entropic springs on them is not a zero-sum game.

But my preliminary thinking says that one piece of structure can have lots of springs, so adding extra structures is still a win.

The other expert, the physicist, asked me how much of the effect comes from entropic springiness vs. mechanical springiness. That's a very good question. I realized that there is a measurable difference between entropic springs and mechanical (covalent bond) springs: the energy stored by an entropic spring is directly proportional to the temperature. If a machine's efficiency depends on fine-tuning of entropic springs, then changing the temperature should change all the spring constants and destroy the delicate energy balance that makes it efficient. I made the prediction, therefore, that protein machines would have a narrow temperature range in which they would be efficient. Then I thought a bit more and modified this. A machine could use a big entropic spring as a thermostat, forcing itself into different internal configurations at each temperature, and fine-tuning each configuration separately. This means that a machine with temperature-sensitive springs could evolve to be insensitive to temperature. But a machine that evolved at a constant temperature, without this evolutionary pressure, should be quite sensitive to temperature.

After thinking this through, I did a quick web search for the effect of temperature on protein activity. I quickly found [a page] containing a sketch of enzyme activity vs. temperature for various enzymes. Guess what--the enzyme representing Arctic shrimp has maximum activity around
4 C, and mostly stops working just a few degrees higher. That looks like confirmation of my theory.


That web page, as well as another one, says that enzymes stop working at elevated temperatures due to denaturation--change in three-dimensional structure brought on by breaking of weak bonds in the protein. The [other web page] also asserts that the rate of enzyme activity, “like all reactions,” is governed by the Arrhenius equation, at least up to the point where the enzyme starts to denature. The Arrhenius equation says that if an action requires thermal motion to jump across an energy barrier, the rate of the action increases as a simple exponential function of temperature. But this assumes that the height of the barrier is not dependent on temperature. If the maintenance of a constant energy level (low barriers) over the range of the enzyme's motion requires finely tuned, temperature dependent mechanisms, then spoiling the tuning--by a temperature change in either direction--will decrease the enzyme's rate.


I'll go out on a limb and make a testable prediction. I predict that many enzymes that are evolved for operation in constant or nearly constant temperature will have rapid decrease of activity at higher and lower temperatures, even without structural changes. When the physical structure of some of these supposedly denatured enzymes is examined, it will be found that the enzyme is not in fact denatured: its physical structure will be largely unchanged. What will be changed is the springiness of its entropic springs.

If I am right about this, there are several consequences. First, it appears that the design of efficient protein machines may be easier than is currently believed. There's no need to design a finely-tuned structure (backbone). Design a structure that barely works, fill it with entropic springs, and fine-tune the springs by simple evolution.

Analysis of existing proteins may also become easier. The Arrhenius equation should not apply to a protein that uses entropic springs for energy balancing. If Arrhenius is being misapplied, then permission to stop using it and fudging numbers to fit around it should make protein function easier to analyze. (The fact that ‘everyone knows’ Arrhenius applies indicates that, if I am right about entropic springs being used to balance energy, I've probably discovered something new.)

Second, it may imply that much of the size and intricate reconfiguration of protein machines exists simply to provide space for enough entropic springs to allow evolutionary fine-tuning of the system. An engineered system made of stiff materials could perform an equivalent function with equivalent efficiency by using a much simpler method of force/energy compensation. For example, linking an unbalanced system to an engineered cam that moves relative to a mechanical spring will work just fine. The compression of the spring, and the height of the cam, will correspond directly to the energy being stored, so the energy required to balance the machine will directly specify the physical parameters of the cam.

The third consequence, if it turns out that protein machines depend on entropic springs, is that their speed will be limited. To be properly springy, an entropic spring has to equalize with its space; it has to have time to spread out and explore its range of motion. If the machine is moved too quickly, its springs will lose their springiness and will no longer compensate for the forces; the machine will become rapidly less efficient. Stiff mechanical springs, having fewer low-frequency degrees of freedom, can equilibrate much faster. If I understand correctly, my physics expert says that a typical small entropic spring can equilibrate in fractions of a microsecond. But stiff mechanical nanoscale springs can equilibrate in fractions of a nanosecond.

I will continue researching this. If my idea turns out to be wrong, then I will post a correction notice in our newsletter archive at the top of this article, and a retraction in the next newsletter. But if my idea is right, then it appears that natural protein machines must have substantially lower speeds than engineered nanoscale machines can achieve with the same efficiency. “Soft” and “hard” machines do indeed work differently, and the “hard” machines are simply better.


The second thing I am investigating is the design of a nanoscale molecular manufacturing system that is simple enough to be developed today, but functional enough to build rapidly improving versions and large-throughput arrays.

It may seem odd, given the ominous things CRN has said about the dangers of advanced molecular manufacturing, that I am working on something that could accelerate it. But there's a method to my madness. Our overall goal is not to retard molecular manufacturing; rather, it is to maximize the amount of thought and preparation that is done before it is developed. Currently, many people think molecular manufacturing is impossible, or at least extremely difficult, and will not even start being developed for many years. But we believe that this is not true--we’re concerned that a small group of smart people could figure out ways to develop basic capabilities fairly quickly.

The primary insights of molecular manufacturing--that stiff molecules make good building blocks, that nanoscale machines can have extremely high performance, and that general-purpose manufacturing enables rapid development of better manufacturing systems--have been published for decades. Once even a few people understand what can be done with even basic capabilities, we think they will start working to develop them. If most people do not understand the implications, they will be unprepared.
By developing and publishing ways to develop molecular manufacturing more easily, I may hasten its development, but I also expect to improve general awareness that such development is possible and may happen surprisingly soon. This is a necessary precondition for preparedness.
That's why I spend a lot of my time trying to identify ways to develop molecular manufacturing more easily.

An early goal of molecular manufacturing is to build a nanoscale machine that can be used to build more copies and better versions. This would answer nagging worries about the ability of molecular manufacturing systems to make large amounts of product, and would also enable rapid development of molecular manufacturing technologies leading to advanced nanofactories.

I’ve been looking for ways to simplify the Burch/Drexler [planar assembly nanofactory]. This method of “working backward” can be useful for planning a development pathway. If you set a plausible goal pretty far out, and then break it down into simpler steps until you get to something you can do today, then the sequence of plans forms a roadmap for how to get from today's capabilities to the end goal.


The first simplification I thought of was to have the factory place blocks that were built externally, rather than requiring it to manufacture the blocks internally. If the blocks can be prefabricated, then all the factory has to do is grab them and place them into the product in specified locations.

I went looking for ways to join prefabricated molecular blocks and found a possible solution. A couple of amino acids, cysteine and histidine, like to bind to zinc. If two of them are hooked to each block, with a zinc ion in the middle, they'll form a bond quite a bit stronger than a hydrogen bond. That seems useful, as long as you can keep the blocks from joining prematurely into a random lump. But you can do that simply by keeping zinc away.

So, mix up a feedstock with lots of molecular zinc-binding building blocks, but no zinc. Build a smart membrane with precisely spaced actuators in it that can transport blocks through the membrane. On one side of the membrane, put the feedstock solution. On the other side of the membrane, put a solution of zinc, and the product. As the blocks come through the membrane one at a time, they join up with the zinc and become “sticky”--but the mechanism can be used to retain them and force them into the right place in the product. It shouldn't require a very complex mechanism to “grab” blocks from feedstock (via Brownian assembly) through a hole in a membrane, move them a few nanometers to face the product, and stick them in place. In fact, it should be possible to do this with just one molecular actuator per position. A larger actuator can be used to move the whole network around.

Then I thought back to some stuff I knew about how to keep blocks from clumping together in solution. If you put a charge on the blocks, they will attract a ‘screen’ of counterions, and will not easily bump each other. So, it might be possible to keep blocks apart even if they would stick if they ever bumped into each other. In fact, it might be very simple. A zinc-binding attachment has four amino acids per zinc, two on each side. Zinc has a +2 charge. If the rest of the block has a -1 charge for every pair of amino acids, then when the block is bound with zinc into a product, all the charges will match up. But if it's floating in solution with zinc, then the zinc will still be attracted to the two amino acids; in this case, the block should have a positive charge, since each block will have twice as much zinc-charge associated with it in solution as when it's fastened into the product. This might be enough to keep blocks from getting close enough to bind together. But if blocks were physically pushed together, then the extra zinc would be squeezed out, and the blocks would bind into a very stable structure.

That’s the theory, at this point. It implies that you don't need a membrane, just something like a tattoo needle that attaches blocks from solution and physically pushes them into the product. I do not know yet whether this will work. I will be proposing to investigate this as part of a Phase 2 NIAC project. If the theory doesn't work, there are several other ways to fasten blocks, some triggered by light, some by pressure, and some simply by being held in place for a long enough period of time.

It appears, then, that the simplest way to build a molecular manufacturing system may be to develop a set of molecular blocks that will float separately in solution but fasten together when pushed. At first, use a single kind of block, containing a fluorescent particle.

Use a scanning probe microscope to push the blocks together. (You can scan the structure with the scanning probe microscope, or see the cluster of fluorescence with an ordinary light microscope.) Once you can build structures this way, build a structure that will perform the same function of grabbing blocks and holding them to be pushed into a product. Attach that structure to a nano-manipulator and use it to build more structures. You'd have a hard time finding the second-level structures with a scanning probe microscope, but again the cluster of fluorescence should show up just fine in a light microscope.

Once you know you can build a passive structure that builds structures when poked at a surface, the next step is to build an active structure--including an externally controlled nanoscale actuator--that builds structures. Use your scanning probe microscope with multiple block types to build an actuator that pushes its block forward. Build several of those in an array. Let them be controlled independently. You still need a large manipulator to move the array over the surface, but you can already start to increase your manufacturing throughput. By designing new block types, and new patterns of attaching the blocks together, better construction machines could be built. Sensors could be added to detect whether a block has been placed correctly. Nanoscale digital logic could be added to reduce the number of wires required to control the system. And if anyone can get this far, there should be no shortage of ideas and interest directed at getting farther.


That’s an inside look at how my thinking process works, how I develop ideas and check them with other experts, and how what I’m working on fits in with CRN’s vision and mission. Please contact me if you have any feedback.


* * * * * * * * * * * * * * * *


Since our founding two years ago, the Center for Responsible Nanotechnology has accomplished a great deal. We have published research papers, spoken at conferences, sent out press releases, and created a sizable presence on the web.

As a result of these efforts, we have seen a considerable increase in awareness of the implications of advanced nanotechnology. This is vital work that few others are doing, despite its critical importance.

Unfortunately, we’re near the end of our current funding stream and virtually operating out of our own pockets. Unless we can quickly raise the funds necessary to support our growth, CRN’s work will be severely hindered.

If we are to continue, we need to aggressively seek other sources of funding, and that includes contributions from committed individuals such as you.

Please consider making a generous contribution to CRN. Your check, in any amount, will make a real difference in helping us to build this organization and continue to inspire meaningful dialogue about our future in a world where molecular manufacturing is a reality.

To make a tax-deductible contribution, please go to our website
(http://CRNano.org) and click on the “Donate to CRN” button.

OR…you can mail a check, made out to “CRN/World Care,” addressed to:

CRN/World Care
P.O. Box 64001
Tucson, AZ 85728

CRN is an affiliate of World Care, an international, non-profit,
501(c)(3) organization.

Many thanks in advance for all the help you can give. Please feel free to contact us at info@CRNano.org if you have any questions


Chris has studied nanotechnology and molecular manufacturing for more than a decade. After successful careers in software engineering and dyslexia correction, Chris co-founded the Center for Responsible Nanotechnology in 2002, where he is Director of Research. Chris holds an MS in Computer Science from Stanford University.

Copyright © 2004-2005 Chris Phoenix


The Center for Responsible Nanotechnology(TM) (CRN) is an affiliate of World Care(R), an international, non-profit, 501(c)3 organization. All donations to CRN are handled through World Care. The opinions expressed by CRN do not necessarily reflect those of World Care



The contents of this page, including the views expressed above, are the responsibility of the author. They do not represent the views or policies of Nano Tsunami Dot Com, except where explicitly stated.



Chris Phoenix

CRN Director of Research



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