I am looking at ways to validate experimentally to some degree the 3D structures of some theoretical models of proteins. What properties can be calculated from the structure that can be directly measured experimentally or show at least correlation with an experimental measurement?
Some I know:
1. Secondary structure: from CD or IR
2. Radius of gyration/hydrodynamic radius: from DLS or diffusion NMR. The hydrodynamic radius can be calculated from the structure by HYDROPRO
3. % amide protons not H-bonded: hydrogen exchange by mass spec or NMR, temperature dependent HSQC NMR spectra
4. Exposed cysteines: thiol modification
5. Predicted protease sensitivity ?
6. Exposed hydrophobic residues will show a correlation with certain fluorescent dyes (SYPRO orange for example)
7. Total exposed surface area should show a correlation with titration with water soluble paramagnetic in 1D NMR (not tried to my knowledge for soluble proteins, but a similar concept is used with membrane proteins).
with NMR backbone assignment
1. residue specific secondary structure: from chemical shift index
2. ligand binding site: HSQC titration
I don't think the correlation between the 3D structure and thermal stability is strong enough to serve as validation of structure.. it would be more of a prediction based upon a prediction.
The number of subunits (monomer or polymer) can be identified by native and SDS-PAGE.
You could certainly calculate the SAXS curve from any model and test as long as you can make the protein. Besides the scattering curve you could compare Dmax, Rg, Vp, P(r) - histogram of all distances, and density. A start would be with http://modbase.compbio.ucsf.edu/foxs/about.html and a look at the Bio-isis database http://www.bioisis.net tutorials
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology