are there any experiments which can be done to identify the divalentmetal ion bound to the protein? Any chemical or biophysical tools which can be used to identify thedivalent metal ion bound to protein. Can we use mass spec or nmr o do so? but chemical techniques would be more helpful
ok, simpler methods:
1. The alkali, earth alkaline elements and copper reveal themselves nicely from their bunsen flames
2. for specific metal ions such as Fe2+, Fe3+, Co2+, Ni2+, VO2+, Al3+, Cu2+, Cr3+ there are specific colour or precipitation reactions such as the prussian blue reaction for Fe2+ and Fe3+ or the SCN- reaction for Fe2+ ...
For details see analytical textbooks such as the Jander/Blasius.
The problem with both of these types of reaction is that the amount of metal ions in a metalloenzyme (metal containing protein) is usually very small and the metal content can be overlooked.
The best example for this is urease, which was crystallised as early as 1926. But the two containing nickel atoms have not been found till the dawn of modern methods such as the ones described in my previous post (approx. 1980). The classical wet-chemistry analysis as described in this post was obviously not sufficient to trace metal ions.
Hello, Shilpi Nagpal ,
from the bioinformatic point of view, you can easily predict the type of metal ion binding to your protein as a first useful step before starting lab experiments. There is a very user-friendly tool:
https://zhanglab.ccmb.med.umich.edu/IonCom/
you can upload your protein sequence or PDB structure on this server and wait for results.
citation " IonCom is an ligand-specific method for small ligand (including metal and acid radical ions) binding site prediction. Starting from given sequences or structures of the query proteins, IonCom performs a composite binding-site prediction that combines ab initio training and template-based transferals. To enhance specificity and sensitivity, the server focuses on binding site prediction of thirteen most important small ligand molecules, including nine metal ions (Zn2+, Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+, K+) and four acid radical ions (CO32-, NO2-, SO42-, PO43-)."
Hope this help
you can see many FTIR study, like this papers -infrared studies of interaction between metal ions and Ca”-binding proteins
Marker bands for identifying the types of coordination of the side-chain
COO- groups to metal ions in pike parvalbumin (p1 = 4.10)
Masayuki Naraa, Mitsuo Tasumia,*, Masaru Tanokurab, Toshifumi Hiraoki”, Michio Yazawad,
Akihiro Tsutsumi”
Now the chemical answer:
1. Elemental analysis using Atomic absorption spectroscopy (AAS), Energy- dispersive X-ray Spectroscopy (EDX) or other element-specific X-ray spectroscopy
2. MS quite generally. If the metal has a characteristic isotopic pattern such as Mn, Co, Ni, Cu it might work out very well
3. EPR spectroscopy. Paramagnetic metal cations are frequently easily detected.
4. NMR. only for metal ions with a suitable nuclear spin: Mn, Co, V
Hope this helps.
And forget about the "four acid radical ions (CO32-, NO2-, SO42-, PO43-." Sorry, Martin, but they are in now way radicals.
Hi,Axel, I was wondering can we use something like chemical tests which we do to determine the inorganic cations in salt analysis? I am asking coz they will be easy to perform, I mean just denature the protein in such a way that metal ion is not bound anymore and then do the inorganic salt analysis?
ok, simpler methods:
1. The alkali, earth alkaline elements and copper reveal themselves nicely from their bunsen flames
2. for specific metal ions such as Fe2+, Fe3+, Co2+, Ni2+, VO2+, Al3+, Cu2+, Cr3+ there are specific colour or precipitation reactions such as the prussian blue reaction for Fe2+ and Fe3+ or the SCN- reaction for Fe2+ ...
For details see analytical textbooks such as the Jander/Blasius.
The problem with both of these types of reaction is that the amount of metal ions in a metalloenzyme (metal containing protein) is usually very small and the metal content can be overlooked.
The best example for this is urease, which was crystallised as early as 1926. But the two containing nickel atoms have not been found till the dawn of modern methods such as the ones described in my previous post (approx. 1980). The classical wet-chemistry analysis as described in this post was obviously not sufficient to trace metal ions.
@Shilpi Nagpal:
The answer on your question depends a little on what elements it might be. Depending on that information there might be some easy methods, as Axel Klein pointed out, but as long as you're suspecting everything, you need a multi-element method like XRF, ICP-MS (or maybe neutron activation, if you have access) which are by nature more complicated.
- Badges
- Science topic