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Eminent Domain Stuff

New London Update (2/24/06)
Coverage of the Rally at New London's City Hall (w/ pics)

Tuesday, September 28, 2004


Evolution vs. Creationism: Round 6

Not to worry, I promise this will be a short round (although not due a KO =)).

I was thinking about something Dr. Meyers wrote concerning the problem of evolving from one protein structure to another (i.e., from one function to another). He points to a few papers to illustrate the point that the transitional protein structures found in 'structural-space' between known functional protein folds are often unfolded (and therefore nonfunctional).

Just today I ran across a paper that adds an interesting twist to the discussion. The paper is by Dr. Nick Grishin at the University of Texas Southwestern Medical Center. He has done a lot of work looking at protein folds and how they relate to function and to the primary amino acid sequence of the protein.

The traditional view has been that a protein's primary (amino acid) sequence determines it's fold and therefore it's function. It has been assumed, therefore, that any proteins with similar primary sequence will have similar functions and vice versa. The newer view is that this is a bunch of washed up crap. Obviously primary sequence will determine the fold and we still use primary sequence to determine the level of 'homology' between two proteins of unknown structure. However, it's not always safe to assume that the resulting percentage is of any true value without functional data.

This principle has been reviewed by Dr. Grishin in the paper linked above. Here are a few key points from the abstract:

Significant sequence conservation, local structural resemblance, and functional similarity strongly indicate evolutionary relationships between these proteins despite pronounced structural differences at the fold level. Several mechanisms such as insertions/deletions/substitutions, circular permutations, and rearrangements in beta-sheet topologies account for the majority of detected structural irregularities. The existence of evolutionarily related proteins that possess different folds brings new challenges to the homology modeling techniques and the structure classification strategies and offers new opportunities for protein design in experimental studies.
Translation: We know that proteins with similar structure can have different primary amino acid sequences. The newer question is: Can proteins with similar primary sequences adopt distinct folds (and therefore have different functions)? The answer that Dr. Grishin finds in his review is that yes, indeed there are proteins with similar ("evolutionarily related") sequences that contain major structural differences.

Dr. Grishin points out that this poses "new challenges" to our ability to draw conclusions from primary sequence similarities. I would add that this also increases the likelihood that relatively minor changes in primary amino acid sequence (and, therefore, relatively minor changes in the genetic code) can have drastic effects on the fold and function of a protein. While obviously none of this validates Evolution as a hypothesis, it does give it a bit of additional credence.


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