I have a protein 3D model, and the VMD program label the oxygens of a aspartate as OD1 and OD2. I read about this and apparently OD1 is a inner oxygen and OD2 is the outer oxygen (also I don't understand this description), but the oxygen of the carbonyl can be any of these. So, how can I know what is the oxygen of the carbonyl? It is for describing a hydrogen bond.
Hi
For Glutamate both the oxygen are involve in formation of hydrogen bond with Arginine as I have observed during MD simulation not the carbonyl oxygen only. So for Aspartate both oxygen will form hydrogen bond with hydrogen bond donor.
Dear marta,
First I should notice that aspartate does not have any carbonyl group in its structure.
OD1 and OD2 are in the carboxyl group of aspartate sidechain . generally carboxyl groups are resonance stabilized because the negative charge is distributed between the two oxygen atoms. Each of the carbon-oxygen bonds in carboxyl anion has partial double-bond character and same bond length.
Best,
HHA
Dear Marta,
I recommend that you first review some basic organic chemistry.
As Hamed states, the COO of the aspartate side chain will have the negative charge equally distributed between the 2 oxygen atoms, in a 'resonance state'. Therefore asking 'which is which' is really a non-question. You should think of both oxygens as equivalent, each with both partial double bond and single bond character.
I have no idea what you mean when you talk about 'inner and outer oxygen'.
Thanks, I'm reading about this. So, as you say, is more convienient schematize the hydrogen bond of aspartate how a carboxyl group without hydrogen and negative charge equally distributed between the 2 oxygen atoms than a carboxyl group with hydrogen (see figure).
The oxygen of the carbonyl (C=O) is the oxigen in the carboxyl group without hydrogen and the oxygen of the hydroxyl (-O-H) is the oxygen in the carboxyl group with hydrogen.
I still don't understand the description of inner and outer oxygen (OD1 and OD2) , I read this in the paper "The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease" of JOANNA TRYLSKA, 2003
You have drawn 2 different forms. The top one is the protonated form - which would be present at a pH lower than around 4.5. The charged form, which would be present at lower concentrations of protons i.e. higher pH (approximately 4.5 and above, i.e. including 'physiological pH') is the form that we are referring to as being in 'resonance' with the negative charge equally distributed between the 2 oxygens.
I would say this is not question of nomenclature (OD1, OD2). You need some physical rationale for attaching H to any of these oxygen. It may come from structural evidence of H-bond, from spectroscopy (i.e. 3hJNC' NMR spin-spin coupling), from force-field MD simulation, or QM calculations.
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology