Prediction of collagen stability from amino acid sequence.
An algorithm was derived to relate the amino acid sequence of a collagen triple helix to its thermal stability. This calculation is based on the triple helical stabilization propensities of individual residues and their intermolecular and intramolecular interactions, as quantitated by melting temperature values of host-guest peptides. Experimental melting temperature values of a number of triple helical peptides of varying length and sequence were successfully predicted by this algorithm. However, predicted T(m) values are significantly higher than experimental values when there are strings of oppositely charged residues or concentrations of like charges near the terminus. Application of the algorithm to collagen sequences highlights regions of unusually high or low stability, and these regions often correlate with biologically significant features. The prediction of stability from sequence indicates an understanding of the major forces maintaining this protein motif. The use of highly favorable KGE and KGD sequences is seen to complement the stabilizing effects of imino acids in modulating stability and may become dominant in the collagenous domains of bacterial proteins that lack hydroxyproline. The effect of single amino acid mutations in the X and Y positions can be evaluated with this algorithm. An interactive collagen stability calculator based on this algorithm is available online.
Persikov
Anton V
AV
Department of Biochemistry, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA.
Ramshaw
John A M
JA
Brodsky
Barbara
B
D000465:Algorithms; D020816:Amino Acid Motifs; D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D003094:Collagen / Q000737:chemistry*; D024042:Collagen Type I / Q000737:chemistry; D024043:Collagen Type II / Q000737:chemistry; D019281:Dimerization; D006801:Humans; D006909:Hydroxyproline / Q000737:chemistry; D009154:Mutation; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D055672:Static Electricity; D013696:Temperature
D000596:Amino Acids; D024042:Collagen Type I; D024043:Collagen Type II; D010455:Peptides; D003094:Collagen; D006909:Hydroxyproline