Protein Fossil Formation: A Novel Approach to Studying 3D Structures

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Discussion Overview

The discussion revolves around the concept of studying the 3D structures of proteins through a novel approach involving the creation of a "fossil" of the protein by embedding it in a solidifying material. Participants explore whether this method has been attempted and its feasibility, as well as existing techniques for studying protein structures in solution.

Discussion Character

  • Exploratory
  • Technical explanation
  • Debate/contested

Main Points Raised

  • One participant proposes the idea of embedding a protein in a material that solidifies, leaving a "fossil" of the protein to study its 3D structure.
  • Another participant mentions "molecularly imprinted polymers" as a related concept but notes a lack of studies correlating the cast with 3D structure.
  • A different participant references "negative staining electron microscopy" as a method that has been widely used for proteins, suggesting it provides useful 2D images that can be mathematically combined to model structures.
  • Concerns are raised about the limitations of X-ray crystallography and NMR, particularly their inability to show protein structures in solution without crystallization.
  • One participant counters that NMR has been used to solve protein structures in solution since the 1980s, particularly for small globular proteins, and mentions small-angle X-ray scattering as a method for determining low-resolution structures in solution.

Areas of Agreement / Disagreement

Participants express differing views on the feasibility and existing methods for studying protein structures, with some suggesting that the proposed fossilization method has not been widely explored, while others highlight established techniques that address similar challenges.

Contextual Notes

Participants note various limitations of existing methods, including the need for crystallization in X-ray studies and the specific conditions under which NMR is effective. There is also mention of qualifiers regarding the types of proteins that can be studied effectively.

Who May Find This Useful

This discussion may be of interest to researchers in biochemistry, molecular biology, and materials science, particularly those focused on protein structure analysis and innovative imaging techniques.

mather
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hello!

it is often used and in many cases safely accurate to use enlarged and mechanistic models of proteins in order to study them

given than, trying to elucidate the 3D structure of a protein, I wonder if it would be possible to somehow place the protein inside a material that would surround it, then make that material to somehow "freeze" or solidify, then somehow remove the protein and then study the "solid" material that is left, which ofcourse will have a kind of "fossil" of the protein!

studying that fossil, we could get info about protein's 3D structure!

I know there are many "somehow" in the above thought, but I wonder if that rings a bell to someone and tell me if it has already been attempted, or if it could be implemented with a specific material/method/technology he brought to mind

thanks!

PS: if not for proteins, maybe for any other 3D molecule?
 
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The closest thing I can think of is something called a "molecularly imprinted polymer". I've never heard of anyone studying the cast to correlate 3D structure.
 
I guess what you ask corresponds to what's called 'negative staining electron microscopy'.
Yes it is more than attempted, it is quite large-scale literature for proteins.
As you get a 2-D image, a large number of images are generally put together mathematically ('tomography') to get a model of the structure.
Not such fine resolution as X-ray crystallography or NMR yet quite useful.

Here are a couple of articles I quickly googled, but hopefully someone better informed can add to this.

http://www.nature.com/aps/journal/v26/n10/pdf/aps2005169a.pdf

http://www.pnas.org/content/109/4/1098.full.pdf+html
 
interesting thanks

X-ray (maybe NMR too, but me not sure) has the tremendous disadvantage that it cannot show the structure of the protein in a solution, but only after crystallizing

this is what I am thinking of overcoming...
 
mather said:
interesting thanks

X-ray (maybe NMR too, but me not sure) has the tremendous disadvantage that it cannot show the structure of the protein in a solution, but only after crystallizing

this is what I am thinking of overcoming...

People have been solving protein structures in solution via NMR since the 1980s. Now, there are numerous qualifiers here, but for small globular proteins (under 25 kDa or so), it's fairly routine. Also, small-angle (x-ray) scattering can determine low-resolution "molecular envelopes" of proteins in solution.
 

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