Collagen Stability Calculator

The objective of this website is to predict the stability of the collagen triple-helix from amino acid sequence using an algorithm based on experimental host-guest peptide thermal stability data. The algorithm is described in Persikov, A., Ramshaw, J.A. and Brodsky, B., J. Biol. Chem. (2004) Prediction of collagen stability from amino acid sequence. The algorithm can be applied to a peptide with a repeating (Gly-X-Y)n sequence, to predict the melting temperature, Tm, under standard conditions (c=1mg/ml; PBS, pH 7; average heating rate 0.1°/min). If the terminal groups of the peptide are blocked, this must be indicated, since it increases the stability.

Although collagen molecules are long and consist of multiple domains, the algorithm can be applied to predict the variations in triple-helix stability along a collagen molecule. In this case, the relative stability representing a 5-tripeptide average can be visualized as a graph. The precise average values are also given in a table, and can be used for further analysis. In this case, the values reflect relative thermal stability, but cannot be directly related to collagen melting temperatures.

Data entry format:

Enter a sequence in any of the following formats: Single amino acid code, where O= hydroxyproline: GPOGARGMOGPAGPOGAR Strings of tripeptides: GPO-GAR-GRE-GTA-GTT-GAA-GPO Use of repeating triplets: (GPO)4-(GAR)2-(GMT)3-GPO

The sequences may be entered with O as hydroxyproline (Hyp). Alternatively, since Pro are typically post-translationally modified to Hyp in the Y position, a sequence with only Pro residues can be entered, and the program will modify all Pro in the Y positions to Hyp if the appropriate box is checked.

Please check the resulting sequence after calculations are performed.

The graph of the relative stability and the table reflect the 5-tripeptide average around each tripeptide site. Entry and graphing of more than 2000 triplets is not supported.

Return to Collagen Calculator