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Programmable Matter: One Step Closer

An article in the February 2007 Scientific American titled Molecular Lego talks about bis-amino acids and bis-peptides. These are synthetic amino acids and peptide chains formed from them.

The Protein Folding Problem

The biggest problem in programmable matter (true nanotechnology) that cropped up is the continued defiance of nature to reveal to us how proteins will fold. We can specify genes in any sequence we like and harness bacteria to build proteins out of the amino acid sequences we specify, but we have no idea how to predict the 3D shape that natural amino acids will fold into. If we could we could be building nanometer scale machines out of precisely shaped protein components today.

Getting Around the Folding Problem

BIS stands for “two”. Normal amino acids that make up the protein building blocks of life have two arms on them and they connect together into chains by linking an arm on one to an arm on another. They are rather flexible at these arm-to-arm connection points (joints) and the long chains fold at the joints into complex shapes. The forces which govern the folding are subtle and have resisted all efforts to predict. A bis-amino acid is like two normal acids tied together so that each acid has four arms instead of two. Think of two people standing back to back, tied firmly together, with outstretched arms. The two people represent ONE bis-amino acid. When two bis-amino acids join the juncture is rigid. They don’t fold. By engineering a set of bis-amino acid building blocks with the opposing dual-arms at various angles to each other complex and predictable 3D shapes can be built from them – molecular LEGO blocks.

Not There Yet

There are a range of problems with this nascent technology but none appear to be show-stoppers. The basic problems are finding a suitable set of 20 or so stable bis-amino acid building blocks like nature has done then fashion our own assembly line (a bis-ribosome if you will) for them. That doesn’t sound easy but it sounds a whole lot easier than solving the natural protein folding problem.

Further Reading

The principle investigator’s website is Schafmeister Laboratory.

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2 Responses to Programmable Matter: One Step Closer

  1. One note on protein folding –

    I’ve thought that the best way to understand protein folding was perhaps to see if we could find the cell’s own heuristics for protein folding.

    For instance, VDJ recombination and NHEJ both recombine disparate genes into hopefully foldable, workable genes. They also add non-templated codons to the joint that they are attaching. I’ve wondered for a while if these non-templated codons are the result of internal cell heuristics of structure and function. If so, perhaps a good step would be to use the cell’s own heuristics for analyzing structure and function.

  2. Advanced ID theories (like ID-steganogrphy) hints that creatures that exist today and their differences at the nucleotide level are designed to help us solve the protein folding problem. This is the fronteir of ID theory.

    There are hints sequence divergences are already used in practice to analyze proteins. One way protein engineers narrow down active sites is by looking for “conserved” sequences. There is probably a grammar out there that will open the door. It is a matter of gathering the data from the creatures and looking to reverse engineer the grammar of protein folding.

    Such exploration are the crux of the Biotic Message and the Question Intelligently Designed Steganography embedded in biology for the benefit of human scientists.

    We live on a privileged planet to help us study physics. There is every reason to believe biotic reality is even more optimized for scientific exploration. This is the next level of ID research that will set will take it to the next level as a real science. Right now were still at the Darwin-bashing stage…

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