Salt Bridges
A salt bridge is the combination of two non-covalent interactions: a hydrogen bond and a ionic bonding.
This interaction is one of the most important forces in biological systems and the most commonly observed
contribution to the stability of unfavorably folded protein conformations.
The distance between residues participating in salt bridges is usually below 4 Å, and thus is the
cutoff we use in ProteinTools to render salt bridges in proteins.
Charge Segregation
We compute (κ) and the Fraction of Charged Residues (FCR) using
CIDER from the
Pappu Lab.
(κ) (kappa) is a measure of the extent of charge segregation in a sequence[1].
FCR is the fraction of charged residues in a sequence.
These values can be use to predict compactness of proteins.
A plot of the FCR (x-axis) and (κ) (y-axis) has been used to characterize designed proteins [2].
Basak et. al observed that a designed ΑΒ protein presented an unusually high but balanced composition of
charged side chains, differentiating this designed protein from the entire proteome of Sulfolobus solfataricus.
It remains to be studied, whether this is the case for other designed proteins.
References
- [1] Das & Pappu (2013) Proceedings of the National Academy of Sciences USA. 110: 13392-13397
- [2] Sujit Basak, R Paul Nobrega, Davide Tavella, Laura M Deveau, Nobuyasu Koga, Rie Tatsumi-Koga, David Baker, Francesca Massi, C Robert Matthews.
Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein.
Proceedings of the National Academy of Sciences 116 (14), 6806-6811.
Proceedings of the National Academy of Sciences 116 (14), 6806-6811