OneG Help

I. About the OneG



OneG is a computational tool which addresses the discrepancy between the ΔGU and the ΔGHX of proteins, by systematically accounting the following factors:
(i) effect for cis-trans proline isomerisation
(ii) effect of baselines of melting curves on the estimation of ΔGU
(iii) possible existence of cryptic intermediates/higher energy metastable states in the unfolding kinetics of proteins under native conditions.

INPUTS:
1. PDB file
2. ΔGU
3. ΔGU*
4. Residue-specific kex / ΔGHX file

OUTPUTS:
1.ΔGHX
2.ΔGHX*
3. Reconciling the discrepancy between ΔGU* and ΔGHX*
If discrepancy exists, OneG accounts the discrepancy by predicting possible existance of cryptic intermediates or metastable states. The PDB files of the predicted foldons will also be displayed.



II. Know to How.

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 AMINO ACID SEQUENCE AND RELATED STRUCTURAL INFORMATION

SEQUENCE
Enter the sequence.
Ex. : LECHNQQSSQTPTTTGCSGGETNCYKKRWRDHRGYRTERGCGCPSVKNGIEINCCTTDRCNN
(Case insensetive)

POSITION OF CYSTEINE RESIDUE(S)
Mention position of cysteine residues in the protein.
Ex. : 3 17 30 36

POSITION OF CIS PROLINE(S)
Mention proline residues which are in cis conformations.
Ex. : 12 44 48 52


ENTER THE EXPERIMENTAL CONDITIONS

pH
Enter the pH meter reading (Not corrected to D2O).
Ex. : 3.2

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

OTHER CONDITIONS
Define the ionic strength as 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.


DOWNLOAD THE PYMOL FILE
Open the protein PDB file in pymol.
File->Resume->Select the pymol.pml generated by OneG.