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Jan Jensen edited In_the_case_of_CA__.tex
over 8 years ago
Commit id: f44be9030170dc47f3a3aa069799dae4fe6dcc77
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For C$\beta$ removing $\Delta \sigma_{1^\circ H\alpha B}^i$ decreases the RMSD by 0.2 - 0.5 ppm, while $\Delta \sigma_{BB}^{i-1}$ and $\Delta \sigma_{BB}^{i+1}$ increases and decreases the RMSD value depending on the protein. Accordingly only $\Delta \sigma_{1^\circ H\alpha B}^i$ is removed. Note that the structural models used for $\Delta \sigma_{1^\circ HB}^i$ and $\Delta \sigma_{2^\circ HB}^i$ do not contain a C$\beta$ so there is no such contribution for this nucleus.
For C' removing $\Delta \sigma_{1^\circ H B}^i$ decreases the RMSD for GB3 by 0.1 so we choose to remove this term for this atom type. Note that removing $\Delta \sigma_{2^\circ H\alpha B}^i$ increases the RMSD by 0.4 - 0.6 ppm so this term is important for accurate predictions of C' chemical shifts.
For
H H$^\text{N}$ and H$\alpha$ we choose to retain all the terms. Not surprisingly, the respective primary hydrogen bonding terms lower the RMSD by 0.4 - 0.6 ppm and are crucial for accurate predictions.
Finally, for N removing the hydrogen bonding terms involving
HA H$\alpha$ tends to lowers the RMSD slightly, so these two terms are removed. Note that $\Delta \sigma_{BB}^{i-1}$ and the two hydrogen bonding terms involving H lower the RMSD by as much as 2.6 ppm ($\Delta \sigma_{BB}^{i-1}$ for ubiquitin) and is crucial for accurate predictions.