If there is a structural difference that exists in the backbone and side chain dihedral angles etc. between X-ray and NMR structure of the same protein, how do we know if this difference is due to:
1. Protein having dynamic nature and being able to express it in solution, and in crystals due to crystalline contacts protein remains relatively stable?
2. Specific parameter that differs in these two experiments (Temperature, pH etc)?
Combination of both?
Does someone came across some publication that examines this question?
Best
Dear Srdjan,
First of all you have to identify the major differences between these two experimental techniques.
1. In the case of NMR you have to have your molecule in solution not interacting to each other, and molecules have to have a random orientation. Because these two features add to the quality of your data (how well you can resolve your peaks).
2. In the case of the X-ray crystallography. You have to have your molecules form close contacts, and oriented in the same way. These will make your crystals better ordered, and your diffraction better (resolution, peak quality).
And those are the biggest differences between these methods.
pH, temperature and other factors only help you to get better data (NMR) or better crystals (X-ray).
Best regards,
George.
Dear George,
thank you very much for your answer and time.
I am trying to obtain all structural differences between X-ray and NMR structures of the same protein on the large scale. To be more precise I am testing binding (docking) of both types of structures of the same protein.
Therefore, for single instance I get that one structure (NMR) has better "binding performance" compared to X-ray, and that there are structural differences.
Now, I am not sure if the structural difference observed in NMR structure is "natural" due to natural dynamic property of the protein and difference in experiment (solution vs crystal), or due to specific physical properties used in experiment such as Temperature, pH, difference in the buffer.
Basically I am interested what is the impact of physical properties used in experiment on structural differences between two structures?
Best,
Srdjan
- Badges
- Science topic
- Similar topics
- Linguistics
- Composition Studies
- Publication