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SESCA: Predicting Circular Dichroism Spectra from Protein Molecular Structures

Gabor Nagy, Maxim Igaev, Søren V. Hoffmann, Nykola C. Jones, Helmut Grubmüller
doi: https://doi.org/10.1101/279752
Gabor Nagy
1Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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Maxim Igaev
1Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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Søren V. Hoffmann
2ISA, Department of Physics & Astronomy, Aarhus University, Ny Munkegade 120, DK 8000 Aarhus C, Denmark
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Nykola C. Jones
2ISA, Department of Physics & Astronomy, Aarhus University, Ny Munkegade 120, DK 8000 Aarhus C, Denmark
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Helmut Grubmüller
1Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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  • For correspondence: hgrubmu@gwdg.de
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Abstract

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.

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Posted February 25, 2019.
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SESCA: Predicting Circular Dichroism Spectra from Protein Molecular Structures
Gabor Nagy, Maxim Igaev, Søren V. Hoffmann, Nykola C. Jones, Helmut Grubmüller
bioRxiv 279752; doi: https://doi.org/10.1101/279752
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SESCA: Predicting Circular Dichroism Spectra from Protein Molecular Structures
Gabor Nagy, Maxim Igaev, Søren V. Hoffmann, Nykola C. Jones, Helmut Grubmüller
bioRxiv 279752; doi: https://doi.org/10.1101/279752

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