Supplementary Information for the Paper:

 Comment on 'Improving protein circular dichroism calculations in the far-ultraviolet through reparametrizing the amide chromophore' [J. Chem. Phys. 109, 782-788 (1998)].
R.W.Woody & N. Sreerama, J. Chem. Phys. 1999.

Information Available:
The  transition parameters used in the calculation:
Amide: For the two pp* transitions (NV1 and NV2), experimental transition moments (Clark, 1995) were used. The monopole charges for the np* and for transitions connecting the np* and pp* excited states were calculated from INDO/S wave functions (Ridley & Zerner, 1973) for N-methyl acetamide.
The correlation between the calculated and experimental CD at 190 nm and 220 nm for the 23 proteins. The plots of CD at 190 and 220 nm are also shown.
CD spectra of 23 proteins: CD spectra were computed using INDO/S parameters for the amide chromophore and parameters described in Grishina & Woody (Faraday Discuss., 1994, 99, 245-262) for aromatic side-chains, are compared with experimental spectra.

Transition Parameters
 
Click on the chromophore
AMIDE
PHENYLALANINE
TYROSINE
TRYPTOPHAN
 

Correlation between the Calculated and Experimental CD of 23 proteins
 
 
Method
Model
No. of Amide Transitions
Side-Chains
Correlation Coefficients
Spearman Rank Correlation
Linear Correlation
190 nm
220 nm
190 nm
220 nm
INDO/S
NMA
3
No
0.66
0.84
0.89
0.93
INDO/S
NMA
3
Yes
0.46
0.71
0.72
0.87

 

Plot of Calculated and Experimental CD for 23 proteins at 190 and 220 nm.


Comparison Theoretical and Experimental CD Spectra for 23 proteins
 
Comparison of  CD Spectra calculated with only amide transitions (dotted curve) and with amide and aromatic side-chain transitions (dashed curve) with experiment (solid curve). The PDB code of the crystal structure used in the calculation is  also given. (Please Click on the Name of the Protein )


Proteins:

       Legend:  Experiment - Solid (Red);
               Calculated with Amide Transitions - Dotted (Magenta);
               Calculated with Amide and Aromatic Transitions - Dashes (Blue)
    1. a-chymotrypsinogen 2. alcohol dehydrogenase 3. a-chymotrypsin 4. concanavalin A
    5. carbonic anhydrase 6. cytochrome c 7. elastase 8. glutathione reductase
    9. hemoglobin 10. l-immunoglobulin 11. lactate dehydrogenase 12. lysozyme
    13. myoglobin 14. papain 15. rhodanase 16. ribonuclease A
    17. ribonuclease S 18. subtilisin 19. superoxide dismutase 20. thermolysin
    21. triosephosphate isomerase 22. trypsin inhibitor 23. trypsin

Updated: April 8, 1999.