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« Hard Enough To Scratch Diamond | Main | Planar Assembly of Loose Parts »

September 14, 2009

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flashgordon

I remember seeing a physorg article about the two women who came up with this; it was mentioned how they've been very active in patenting this; just comes to show you that those who do not have their eyes on science are very narrow(closed systems!) minded!(they've never thought of this!)

What's that Leonardo Da Vinci quote? Those who go against being scientific are bound to mess up!(not exactly the same words but the same thought!)

flashgordon

more,

the Alexandrians had steam engines, but they did not have the scientific philosophical mind to see what to do with it.

flashgordon

Here's another example!

America(really, humanity) has had the ability to tap the resources of space and solve all their problems; but, they do not seem to be able to put the two together!

Paul S

Chances are the main reason carbohydrate polymers have been neglected is that they're less versatile than polypeptides and nucleic acids. Also, if you want to make a complex carbohydrate sequence (multiple different monomers in a specific arrangement) there isn't any pre-existing biochemical machinery (e.g. genes) that you can co-opt to do it consistently every time.

It's not the ability to create side-chains. You can do that with amino acids. It's not the ability to cross-link. One amino acid - cysteine - is specialized for exactly that role. Nor is cross-linking all that difficult in wet chemistry: we do it in polymer products ranging from paint to tires. Chitin, BTW, is not heavily cross-linked. Its durability comes in part from extensive hydrogen bonding between polymer chains, and hydrogen bonds aren't "chemical bonds" in the usual sense of that term.

Stiffness may or may not scale well - I'm not enough of a materials chemist to know. But I do know that the stiffness of chitin in arthropods comes from the addition of a strong protein matrix to the chitin - at which point you've got a much more complex material. Pure chitin is tough, but not very stiff at all. In fact it's used as surgical thread.

So my guess is that it's simply that carbohydrates aren't as generally interesting and useful as peptides. Basically, there's very little that a carbohydrate polymer could do that a peptide could not. The main advantages carbohydrates have as biological building materials (chitin, lignin, etc.) are simplicity and ubiquity (carbohydrates are produced from air by photosynthesis).

Chris Phoenix

Paul, many thanks for this information.

I suspect you're right that carbohydrates have been less studied because there's no direct way to make them in engineered sequence in organisms. But this is part of why I suspected that they might reward further study, once new synthetic methods (based on mechanosynthesis) are developed.

Does your mention of cysteine as a cross-linker refer to its role in zinc fingers? I've recently proposed attaching diverse cysteine-containing proteins (or Schafmeister polymers) to a DNA scaffold, then stirring in zinc to cross-link them into a large engineered heterogeneous structure, but I wasn't sure how strong the zinc finger bond is, compared to the backbone bonds.

I agree that, in theory, almost anything could be done with peptides. The trouble is that even the reverse folding problem is still being researched (almost 30 years after Drexler's PNAS paper). I'm really looking for something with the ease of structure prediction of DNA or Schafmeister polymers, but stronger than DNA.

Anyway, this was just speculation, started by learning that carbohydrate sequences can now be built under direct automated control. If carbohydrates aren't suitable, that's fine.

Chris

Paul S

Well. once you have true mechanosythesis, the sky's the limit. You can build pretty much anything then. In a scenario like that then you might want to use carbopolymers because they're cheap, and because they don't use amide bonds like peptides do, which could give them solvent resistance and other chemical properties that would be useful for specific applications where peptides might be less suitable.

Another possible application might be in materials where you want conformational folding to be either very simple or basically non-existent. Predicting the final conformation of a long chain of diverse carbohydrate monomers might not be a lot easier than predicting protein folding, especially if the monomers are modified by side groups. But a simple polymer containing one or two subunits might be easier. Insufficient data at the moment.

Zinc fingers are one of the biological functions of cysteine, but it's not the same as crosslinking. Zinc fingers occur biologically as a means of stabilizing a certain protein conformation - to keep something where it needs to be in a wider range of temperature, pH, and ionic environments. In a case like that what you have is a zinc ion interacting with cysteine and/or histidine as lilgands.

http://en.wikipedia.org/wiki/File:Zinc_finger_rendered.png

The interaction here is between the charged zinc ion and the highly polar electron-rich side groups on histidine and cysteine. It's fairly strong, but it's not a covalent bond or even a true ionic bond.

Cysteine cross-linking comes from covalent disulfide bonds between cysteine sidegroups in different regions of the protein.

http://en.wikipedia.org/wiki/Cysteine#Disulfide_bonds

Disulfide bonds are extremely durable. They help to lock a protein into a conformation that might otherwise not be very stable at all.

Chris Phoenix

Fascinating. So it sounds like adding zinc won't do what I want, but adding protein disulfide isomerase could link up lots of cysteines in parallel, strongly.

I've started to think that there's no bright line between "true" mechanosynthesis and partial systems. For example, there might be a system that used a light-activated molecule to mechanically cover or uncover a reaction site on a different molecule. This could be addressed with ~1/2 micron resolution in an array, allowing parallel fabrication of thousands of copies of millions of different molecules. Is this mechanosynthesis? I don't know.

So I'm thinking about primitive mechanosynthesis-like systems that might initially only be able to do one or two kinds of chemistry. I'm looking for polymers and other molecular building block systems that might allow building primitive nanomachines that could be used for more flexible mechanochemistry...

Chris

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