Wednesday, December 06, 2006

Replication Fidelity & a Proline-Rich Domain

The article 'Unusual Mechanism Keeps Repair Protein Accurate', at the Science Daily website reports what is described as an unusual mechanism involved in accurate repair of DNA. The protein involved in the repair is called DNA polymerase lambda. It is but one of a group of proteins referred to as DNA polymerases.

Other proteins having repair functions have been analyzed. Some accomplish their mission due to their proof-reading regions and some are known to interact with other biochemicals to realize their function. However the protein in question apears unusual with respect to the part of it that accounts for its accuracy.

Zucai Suo, assistant professor of biochemistry and a researcher with the Ohio State University Comprehensive Cancer Center led the related study and stated: “DNA is constantly attacked and damaged by a variety of agents. The body must properly repair that damage, or it can lead to cell death or to cancer, birth defects and other diseases." Suo noted the existence of six families of DNA polymerases and the uniqueness of the mechanism associated with the polymerase studied.

There are four domains to the protein and the structure of three of them was familiar. The surprise was region two which was rich in the amino acid proline. No known function could be correlated to this proline-rich domain. This was the key to the repair accuracy. DNA needs to be replicated and needs to be replicated with great accuracy. Here was the clue as to how it is accomplished.

The details of the process remain to be fleshed out. The protein is still being studied to learn exactly how the proline-rich domain ensures replication fidelity.

The new information clearly reveals the advantage of a particular protein domain but its historic implications need not be trivialized with a selection dunnit analysis. At the very least a credible analysis of its origins would reference its function and the plausibility that DNA could have foregone it at some prior point in time.



At 9:26 AM, Blogger Doug said...

When they tested this short version of the protein, however, they found that it made up to a 100 times more mistakes than did the similar repair protein, DNA polymerase beta.

“That error rate is too high,” Suo says. “If the entire repair protein produced that many errors, it would cause more problems than it would fix.”

Very telling. Even with this protein complex working with minimal function still puts the organism at risk of demise. If you even want to call it 'minimal function', because 'doing more harm than good' doesn't even provide the organism with a potential for increased survival.

At 5:23 PM, Blogger William Bradford said...

Hi Doug. Evidence for the biological necessity of correction and repair mechanisms is so strong and the consequences accruing from their disabled function so severe, that it is difficult to conceive of any cellular life that could exist without them. But then why would such mechanisms co-evolve with or preceed the functions they repair? It is counterintuitive to a natural selection mindset.

At 3:07 PM, Blogger Doug said...

Hi William,
This is a topic that you are very knowledgeable with. Have you considered putting this to type and writing a book? There seems to be so much information that you could incorporate in a book with just this one topic. It doesn't seem to be an area that I see IDtheFuture, UncommonD, or TT touching on that much.

At 3:44 PM, Blogger William Bradford said...

I had not thought about this Doug but it may not be a bad idea. I have noticed that other IDers have not picked up on this and I think they are missing something. The topic is complex but offers a clear demarcation between the predictions of ID and those of mainstream theories. METers are boxed in by their own theories. If they contend that cells are viable without the mechanisms alluded to, they risk being refuted experimentally. If they concur as to their necessity they face the dilemna of explaining how such mechanisms came about incrementally in response to a selection paradigm. Oddly enough about the only one that has discussed this with me, other than you, is Smokey.

At 6:08 PM, Blogger William Bradford said...

Hi Doug,

Just want to let you know that I received your message and preserved the information provided. I had to reject the comment because the host allows me to only accept or reject comments. I cannot modify them or delete portions.


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