Dear all,
Can I have your opinion: I have crystal structure of viral protein and has 4 dimers.
What would be the best way to identify whether the arrangement of protein in crystal structure is a functional arrangement or an artifact of crystallisation?
Thank you in advance
Dear Shymaa Damfo ,
As a crude opinion in such a specific field, there are many reasons why an artifact crystallized protein other than the protein of interest may be found in a crystal structure solution:
1) The wrong protein was purified instead of the protein of interest or undesirably co-precipitated.
2) A protein preparation for structure determination may be contaminated during the extraction, isolation, purification, or into the structure determination curse at the moment of crystal preparation (glue, nitrogen flowing for low-temperature determination, etc.).
3) A recombinant protein is expressed as a fusion protein, and only the fusion partner may crystallize; the determination would be of the wrong species.
4) The lack or presence of complementary interactions in the isolated protein system compared to the original one may promote stretching, folding, or other physical processes, resulting in no original correlation structure.
5) Human errors.
Apart from the last one, it is not easy to be sure if some determined functional arrangement is the real one. Over a crystallization process, there are so many possibilities that result in a reliable final protein structure, such as co-crystals, solvated crystals, dimers, among others, that did not represent the original protein of interest. They appear by synergic effects, lowering the final crystal energy.
Some tools like the ones available in the CCDC suite package for databank structure ranking and comparison may help identify the most common and already described protein similarities on spatial distribution and angular arrangements.
There is so much data already used in docking studies. A reliable databank of functional group arrangements and interactions may only indicate if the determined arrangement is functional or an artifact of crystalization for that particular protein class.
I believe that a blind crystal structure determination of some isolated protein of interest will hardly guarantee that the final crystallized arrangement is the original and functional one.
It should be a multidisciplinary study, checking NMR signal correlations, for instance.
Best regards,
WNM
Mr. Damfo,
All processes in the Nature are governed by corresponding exact physical laws. Simply speaking, there is a lack of ''artifact of crystallisation.'' There are only a functionally dependent processes. The 'Science,' namely, discovers these natural laws.
Dear Wagner Da Nova Mussel
Thank you very much for your answer and explanation.
So in my case the crystal structure represent the correct protein of interest. The difference between our structure and published one is the oligmerisation. (ours is four dimers (8 molecules) and published one is a dimer (2 molecules).
I think the differnce in dimerisation is related to your point no. 4. Our sequence is longer than other by almost 10 residues...so it can be the reason!
When you said multidisciplinary study, would you recommend other method other the NMR?
Thank you again,
Shymaa
Dear Bojidarka B. Ivanova
Thank you for your reply.
I can see your point, however, nature explained by physics law doesn't necessarily have a biological significance.
Best,
Shymaa
Dear Shymaa Damfo ,
Have you checked the lower symmetric representation of your crystal structure solution?
There is a possibility to represent one crystal structure by a couple of space groups, in general, with lower symmetry.
Check the uniqueness of your space group solution. The routine means checking for the coincidence of computed lines. This phenomenon infrequently occurs in low-symmetry cases and consistently in high-symmetry cases and is known as geometrical ambiguity. Therefore, it should be checked in individual cases whether or not the uniqueness of solutions is happening, A. D. Mighell, A. Santoro, Geometrical Ambiguities in the Indexing of Powder Patterns, J. Appl.Cryst., 8, pp. 372–374 (1975).
Let say P2 of much lower symmetry may represent the higher symmetric P 21 21.
Try to obtain the highest symmetric representation of your solution.
Anyway, check the asymmetric unit to see how many single molecules are considered in your solution. You may have the right solution expressed in a lower symmetric space group. The IUCr states that the final solution must be represented by the highest symmetric space group representing your solution equally.
Solid H1 and C13 NMR signal correspondence are the most usual; in general, there is no necessity of sample preparation and consequently no chance of changes with chemical manipulations. ATR-FTIR may help in some cases; it is done directly in the solid.
Best regards,
WNM
Mr. Damfo,
The fractals can be not only Natural, but also biological objects. In addition to, the following comment on: The biological objects and (subjects Humans) constitute the Nature. The theory of fractals is a part of stochastics, dealing with stochastic mathematical methods applicable to physics, chemistry and biology, because of they are capable of describing namely chemical, physical and biological phenomena.
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