Friday, August 18, 2006

Irreducibly Complex Protein Folding Mechanism

A post at iDesign@UCI entitled 'Chaperonin Design' is based on an article in 'Nature' about proteins known as chaperonins. The italicized article follows along with my comments in bold print.


A recent article in Nature explored the means by which certain proteins called chaperonins work. Chaperonins are proteins which help other proteins fold correctly. Specifically, they provide a "cage" in which the target protein can fold without interference. Artificially growing or shrinking the size of the cage can make certain proteins fold more quickly or slowly, but the overall size of the cage seems to be optimal given the number of proteins which this chaperonin interacts with.

There are a number of indicators of intelligent causality alluded to in this post. The indicators, which fall within the purview of circumstantial evidence, will be individually identified. There is an optimal relationship between the two proteins; specifically the size fit. Alone this signifies very little. However when considered in conjunction with other factors, which include the alternative stochastic process said to generate the cited proteins, the optimal fit becomes a relevant factor.


Because the cell is so crowded with large molecules, it is energetically favorable for newly transcribed proteins to fold compactly, reducing the volume they occupy. If it weren't for chaperonins, this tendency would cause partially complete amino acid chains to bind with each other (there are many of these chains in close proximity because mRNA is transcribed by many ribosomes at once).

Chaperonins counteract a natural tendency for proteins to fold following transcription. Folding without chaperonins would result in dysfunctional tertiary structures.


The upshot is that chaperonins use the energetic effects of crowding to stimulate folding while at the same time eliminating the negative effects of crowding - promiscuous binding to anything in the area. This is a neat trick. In the final paragraph of the article, the author (who, of course, credits natural selection with chaperonin design) even exhorts human designers to follow the example of chaperonins:

"It is a testament to the ingenuity of natural selection that the chaperonin cage not only combats aggregation caused by crowding outside the cage but also uses crowding to accelerate protein folding inside the cage. Nanoengineers trying to improve the yield of therapeutic proteins could profit from studying the tricks of the chaperonin nanocage."


Good suggestion. However should natural selection be credited with generating this phenomenon? What experimental evidence validates the belief that such protein pairings co-evolve? Note that the function of the chaperonin enables the functionality of its partner protein. Precision and necessity are descriptive of the protein relationship. There is no indication that either qualities allow for compromise in function i.e. an envisioned scenario wherein a fit becomes progressively more precise while lesser function becomes gradually maximized. Yet that would be what a natural selection paradigm would generally call for.

If chaperonin function is dependent on an exact fit to the folding protein and the folding protein lacks function without a chaperonin then we have a purposeful relationship. This one enables a more complex cellular function through a problem solving device in the form of the chaperonin protein. Does this type of phenomenon yield to a natural selection explanation? Why? Based on what experimental evidence?

What experimental evidence would implicate an intelligent cause? One could argue that evidence is already at hand in the form of purpose, precision and necessity. The argument against this has been the adaquacy of a non-telic (in the sense that the generating process is actually stochastic in nature and outcomes selected as theorized) natural selection based explanation. Natural selection then would be the testing target and coding genes for the cited proteins the experimental focus in an appropriate organism.

2 Comments:

At 8:26 AM, Anonymous Doug said...

Great article!
By the way, I love the site. Just started coming here a couple of weeks ago.

 
At 2:15 PM, Anonymous Doug said...

As we start developing a stronger understanding of life at the molecular/biochemical level - a top-down approach, opposed to the bottom-up approach of reductionism, is becoming more prominent. This approach is becoming almost necessary to make sense of the various functions within the cell. With all of the occurrences of seemingly IC structures or Whole Package Phenomena (WPP - to borrow from Dr. G. Simmons) even the strict materialist will have to start placing agent-laden/goal-directed terms to describe the workings of natural selection.

Similar to philosophers' attempts to understand the mind; teleological concepts/terms/and assumptions will have to be smuggled in, in order to present a coherent picture of the cell.

 

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