Question

compare and contrast nmr and x ray crystallography for protein structure determination.

Answer 1

generally we have several methods by which one can get information about the proteins. X-ray and NMR structures of the same protein have more differences than various X-ray structures obtained for the protein, and even more than various NMR structures of the protein. the main differences between NMR and X-ray structures concerns the number of contacts per residue: (1) NMR structures presented in PDB have more contacts than X-ray structures at distances below 3.0 A and 4.5-6.5 A, and fewer contacts at distances of 3.0-4.5 A and 6.5-8.0 A (2) this difference in the number of contacts is greater for internal residues than for external ones, and it is larger for beta-containing proteins than for all-alpha proteins. Another significant difference is that the main-chain hydrogen bonds identified in X-ray and NMR structures often differ. Their correlation is 69% only. However, analogous difference is found for refined and rerefined NMR structures, allowing us to suggest that the observed difference in interresidue contacts of X-ray and NMR structures of the same proteins is due mainly to a difference in mathematical treatment of experimental results.

The advantages and disadvantages of NMR and X-ray crystallography.

Advantages of NMR	Disadvantages of NMR	Advantages of X-ray	Disadvantages of X-ray
1. several types of information from lots of types of experiments	1. we have lots of atoms and a lot of extracted data from a system.	1. . We can examine also by this way the solvent effect since from different solvents the same protein may crystallize into different crystalloid form.	1. the crystal structure is necessary only that proteins which can be crystallized are examinable
2. they obtain angles, distances, coupling constants, chemical shifts, rate constants etc. These are really molecular parameters which could be examined more with computers and molecular modeling procedures.	2. This is good for the more accurate determination of the structure, but not for the availability of higher molecular masses	2. So we are able to force the protein to an other form of crystallization by the change of its solvent.	2. we cannot examine solutions and the behavior of the molecules in solution
3. if we have enough strength of the magnetic field (the resolution is the function of that) than we can handle all of the atoms “personally”	3. the resolving power of NMR is less than some other type of experiments (e.g.: X-ray crystallography) since the information got from the same material is much more complex	3.we could get the whole 3D structure by the systematic analysis of a good crystallized material	3.  This happens when we try to examine powders, gases
4. With a suitable computer apparatus we can calculate the whole 3D structure	4.  the highest molecular mass which was examined successfully is just a 64kDa protein-complex		4. studying of motions are not available
5. There are lots of possibilities to collect different data-sets from different types of experiments for the ability to resolve the uncertanities of one type of measurements	5. there are lots of cases when from a given data-set - a given type of experiment - we could predict two or more possible conformations, too		5. we can get only one parameter-set so we are able to observe only one conformation
6. the motion of the segments (domains) can be examined	6. unfortunately we are just able to determine the degree of probability of being of the protein segment in the given conformation		6. there is no possibility to examine small parts in the molecule
7. this method is capable to lead us for the observation of the chemical kinetics	7. The cost of the experimental implementation is increasing with the higher strength and the complexity of the determination		7. There is no chance for direct determination of secondary structures and especially domain movements (big disadvantage against the NMR)
8.(activation-)thermodinamic (and certainly kinetic) data could be determined from a well-prepared (dynamic-)NMR experiment			8. the hydrogen in the molecules are not examinable since it has only one electron
9. we can investigate the influence of the dielectric constant, the polarity and any other properties of the solvent or some added material