RT Journal Article
SR Electronic
T1 SESCA: Predicting Circular Dichroism Spectra from Protein Molecular Structures
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 279752
DO 10.1101/279752
A1 Nagy, Gabor
A1 Igaev, Maxim
A1 Hoffmann, Søren V.
A1 Jones, Nykola C.
A1 Grubmüller, Helmut
YR 2019
UL http://biorxiv.org/content/early/2019/02/25/279752.abstract
AB Circular dichroism spectroscopy is a highly sensitive, but low-resolution technique to study the structure of proteins. Combined with molecular modelling or other complementary techniques, CD spectroscopy can provide essential information at higher resolution. To this end, we introduce a new computational method to calculate the electronic circular dichroism spectra of proteins from a structural model or ensemble using the average secondary structure composition and a pre-calculated set of basis spectra. We compared the predictive power of our method to existing algorithms – namely DichroCalc and PDB2CD – and found that it predicts CD spectra more accurately, with a 50% smaller average deviation from the measured CD spectra. Our results indicate that the derived basis sets are robust to experimental errors in the reference spectra and to the choice of the secondary structure classification algorithm. For over 80% of the globular reference proteins, our basis sets accurately predict the experimental spectrum solely from their secondary structure composition. For the remaining 20%, correcting for intensity normalization considerably improves the prediction power. Additionally, we show that the predictions for short peptides and intrinsically disordered proteins strongly benefit from accounting for side-chain contributions and structural flexibility.View this table: