OneG-Vali

OneG-Vali


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OneG-Vali can be used to:

1. Detection, estimation and validation of cryptic intermediates by OneG-Vali.
    Inputs:
    • PDB ID/File
    • Residue specific kex/ΔGHX
    • ΔGU
    • Cm


2.Validating cryptic intermediates detected by experimental methods.
    Inputs:
    • ΔG and m from optical methods
    • No. of foldons and no. of residues in each foldon
    • ΔG and m for each foldon

I. Know to How.


STAGE I

ENTER / UPLOAD THE PDB FILE
Ex. : 1COD
Note: Make sure the residue number of the PDB file starts with '1' and ends with 'n' without missing numbers. Also make sure residues represented in 'SEQRES' and in atomic coordinates are identical to each other.

ENTER THE EXPERIMENTAL CONDITIONS

pH
Enter the pH meter reading (OneG-Vali accounts for the effect of D2O).
Ex. : 3.2

TEMPERATURE
Enter the temperature in Kelvin .
Ex. : 293 (If the temperature is 20 oC).

OTHER CONDITIONS
Define the ionic strength is either low (< 0.5 M) or high (> 0.5 M).

CALCULATION OF FREE ENERGY EXCHANGE OF PROTEINS
Upload file containing kex values (in min-1).
OR
Upload file containing ΔGHX values (in kcal/mol).
Check example.


STAGE II

ENTER ΔGU
Enter the ΔGU of the protein (in kcal/mol).


STAGE III

ENTER ΔGU* (Optional)
ΔGU* is ΔGU corrected to the effect of baselines of melting curves.

ENTER THE Cm VALUE
Enter the Cm value (in M).


STAGE IV

VALIDATION OF CRYPTIC INTERMEDIATES
It validates the predictions by comparing the multistate unfolding signal and pseudo two-state signal of proteins.


DOWNLOADABLE FILES
Text files: Population of native, intermediate and unfolded states of the protein at every 0.1M (0 - 7M) denaturant concentration (population.zip).
                 Multistate unfolding signal and Pseudo Two-state unfolding signal of proteins at every 0.1M (0 - 7M) denaturant concentration (signal.zip).

Atom file : "atom.pdb" (atomic coordiantes of foldons).

Pymol file: Please view the protein PDB in pymol and use the "pymol.pml" file to view the foldons of the protein in Pymol
open protein PDB file → Go to file → Resume → Select the downloaded pymol.pml file.