Monday, June 22, 2009

Double Helix Electric Slide

This is an area of research in which we may start getting really exciting ideas into play. My own interest is derived from the apparent implied logic system that produces life itself. This is mathematically interesting and calls for a major effort in defining the parameters. If undertaken successfully, I cannot imagine any biologists ever thanking one for the implied headache.

Present efforts are focused on extracting a familiar Boolean system and some progress has been made. I am inclined to go in a different direction that may be simply a dead end but that needs to be confirmed. Even as a Boolean system, mathematics only gives us zero and one and that needs to be changed to a more generalized fuzzy logic style system all of which make ideas of rigor difficult.

In any case, this is becoming interesting and there is enough known to encourage an attempt at constructing a practical biological logic system.

Jun 17, 2009

Double helix is an 'electric slide' for proteins

Swarming proteins slide into place on DNA double helix

http://physicsworld.com/cws/article/news/39512/1

DNA may contain the blueprint for life but it takes proteins to read the plan and build an organism. The mechanism of this vital biological process has remained a mystery but now researchers in France are proposing a physical model wherein individual proteins can “slide” freely along DNA strands in search of target sequences.

The team envision the process involving ‘DNA-binding proteins’ swarming around the iconic double helix on account of electric attraction — proteins have a net positive charge and DNA has a net negative charge. Miraculously, these proteins can then bind to exactly the right section of the long, coiling DNA so they can carry out vital functions such as copying genetic information and translating genes into templates for protein production.

Vincent Dahirel of the Pierre and Marie Curie University in Paris and his colleagues have reduced this complex biological set-up into more general physical shapes. Using Monte Carlo computer simulations, DNA was modelled as a long cylinder, and the protein as one of four solids: a sphere; a cylinder; or a cube or cylinder with a groove carved in one side.

Grooved cylinders

Dahirel and colleagues find that as the first three protein-shapes approach the DNA the electric attraction continues unabated. However, in the case of grooved cylinders, the proteins start to be repelled once they get to within 0.1 to 0.75 nm of the DNA.

Dahirel and his team attribute this force to the solution that bathes these biological molecules. As the protein approaches the DNA, positively charged ions in the solution become trapped in the gap, driving more water into the region as a result of osmosis. If the inward electric attraction is balanced by the outward water pressure, the protein can slide along the helix until it reaches its target. The hydrogen-bond attraction between DNA and protein then overpowers the osmotic barrier and the two bind together.

The research is published in
Physical Review Letters.

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