Server For Computing/Predicting DEPTH, Cavity Sizes, Ligand Binding Sites and pKa

Input Output

Users can specify the 4-letter code of an existing protein structure in the PDB followed by selected chain identifiers
Example: 2FP7 (select whole structure) or 2FP7AB (select chain A and chain B)

Note: The chain identifier record is case sensitive.
Users also have the option to upload a file in PDB format.
In its current implementation, the server only processes limited???? structures per submission. For larger scale applications, the program can be downloaded and run locally.


DEPTH Algorithm

1. 2.

Output

A residue-wise plot of depth value is displayed. The plot shows both mean and standard deviation of depth values. The depth output is also available for download in tab-delimited and PDB formats. In the PDB format depth values are recorded in the b-factor column.


Binding Cavity Prediction

Using an extensive benchmark of 900 ligand bound proteins, we have established that some residues in most ligand binding cavities are simultaneously surface exposed and deep.

Options

The server predicts small molecule binding cavities on proteins. Prediction results may vary with choice of depth computation parameters. For example, using a larger value of minimum number of neighborhood waters results in the detection of larger cavities, which maybe apt for larger ligands.
The algorithm estimates the probability value of forming part of a binding cavity for every residue of the protein. Users have the option to alter the recommended cavity prediction probability threshold.

Binding cavity prediction for other biomolecule other than proteins (DNA, RNA etc) is currently not supported. (Please contact author for this application)

Output

The algorithm estimates the probability value of forming part of a binding cavity for every residue of the protein. A residue-wise probability plot is displayed. A list of residues that have probabilities greater than the threshold are displayed along with the list of residues predicted to form the binding cavities. Users can also choose to download the results in PDB (with b-factor column replaced by probability value) or tab-delimited formats.


Solvent Accessible Surface Area(ASA)

Normalized residue-wise solvent accessible surface area of protein residues are computed using the Shrake-Rupley algorithm [Shrake and Rupley, 1973]. The output is downloadable in tab-delimited format. The surface area is calculated for 5 categories of atoms including - all atoms, Main Chain, Side Chain, Polar Side Chain and Non-Polar Side Chain (i.e. carbon atoms).

Default Values

For multi domain protein, the recommended values are

  • Minimum number of neighbourhood water = 4
  • Cavity prediction probability threshold = 0.50
For single domain protein, the recommended values are
  • Minimum number of neighbourhood water = 5
  • Cavity prediction probability threshold = 0.45

predicting pKa of polar residues

pKa is a measure of acidic strength and is defined as the logarithm of the acid dissociation constant. pKa of protein residues estimates the protonation strength of its ionizable groups. Ionizable residues play a significant role in several protein functions including folding, stability, solubility, protein-protein interactions etc. To gain insight into these function, it is often crucial to accurately determine the pKa of ionizable residues. The pKa values of ionizable groups are however highly sensitive to their enviroment. This sensitivity makes pKa estimation difficult. Here we introduce a simple method for pKa prediction. pKa predictions are made for the following ionizable residues: ASP, GLU, HIS and LYS residues using the formula:

where the predicted pKa is a correction to the model pKa. The model pKa for a particular amino acid residue is determined for the case when the titratable group is completely accessible to the solvent and minimally pertubed by the surrounding environment. The correction terms are in the form of a linear combination of 6 different features including main chain depth (MCdepth), polar side chain depth (polarSCdepth), number of H-bonds donors and acceptors (no. HbondsN and no. HbondsO), the electrostatic potential centred at the titratable group considering all partial charges within a cut-off distance of 8Å (elec) and the solvent accessible area of the side chain (ASASC) . [back to top]

Output

The pKa output is represented graphically (see below) on the results page or can be downloaded in a tab separated flat file. The results for each of GLU, ASP, LYS and HIS are shown in different histograms. A horizontal line on each of the plots indicates the pka value of the model residue.


References

  1. Richards, F. M. (1974) J. Mol. Biol. 82, 1–14
  2. Chakravarty, S., Bhinge, A. and Varadarajan, R. (2002) J. Biol. Chem. 277, 31345-31353
  3. Saha, P., Barua, B., Bhattacharyya, S., Balamurali, M., M., Schief, W., R., Baker, D. and Varadarajan, R. (2011) Biochem. 50, 7891-790
  4. Nguyen, M., N., Tan, K., P. and Madhusudhan, M., S. (2011) Nucleic Acids Res. 39, W24-28
  5. Gerstein, M., Tsai, J., and Levitt, M. (1995) J. Mol. Biol. 249, 955–966

Utility of DEPTH

  • provides wider dynamic range for residue burial (as compared to accessible surface area)
  • correlates well with protein stability
  • correlates well with amide proton hydrogen exchange rates
  • predicts protein-protein interaction hot spots
  • helps explain evolutionary variability in protein sequences