The bias of Charged vs. polar residues (CvP-bias) has been shown to correlate with the thermostability for eukaryotic (prokayotic) proteins (c.f. References).

Note: If you compare orthologous sequences you might want to align the sequence first and only analyze the relevant regions

N_charged

Number of charged amino acids (EDKR)

N_polar

Number of polar amino acids (STNQ)

CvP-bias

(N_charged - N_polar)/length * 100

Note:

Larger CvP values imply higher thermostability

References:

Holder et. al., 2013. Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability. Biology Direct 8:2 [Abstract]

Suhre & Claverie, 2003. Genomic correlates of hyperthermostability, an update. J Biol Chem 278:17198-17202 [Article]

Author / Contact

Steffen Schmidt

Max Planck Institute for Developmental Biology - Dept. Biochemistry
Tübingen, Germany