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Prion hydrophobicity along the protein chain

An online tool for this calculation and many similar ones, is provided by ProtScale at the Swiss Prot Web site.

The hydrophobicity graphic below shows where interior residues are likely to be located in the 3D prion structure; or alternatively, where a dimer or sticky surface patch might occur. Known mouse prion secondary structure overlies a colorized output of a SwissProt online tool for Kyte-Doolittle hydrophobicity, with a nine residue wide moving average window chosen as smoothing convolution. The two-fold symmetry involving the 2nd and 3rd alpha helices does _not_ show up as an obvious sequence repeat, though it could reflect an ancient divergent internal duplication still visisble in the tertiary structure.

Note the mysterious octapeptide repeat region has no prospects of either alpha helical structure or globular form, though periodicity in sequence must be reflected in periodicity in 3D structure. Repeat residues are very strongly conserved back to the Devonian. There is a 900% excess of tryptophan N-terminal over bulk protein; while these can't stack face to face without off-setting, they must be shielded from solvent. Posted 9.22.96; revised 1.2.96


Sequence fragment:23 - 230 of PAN TROGLODYTES (CHIMPANZEE) -- this does not include the signal peptide or GPI terminus, which are cleaved during maturation.

KKRPKPGGWN TGGSRYPGQG SPGGNRYPPQ GGGGWGQPHG GGWGQPHGGG WGQPHGGGWG QPHGGGWGQG GGTHSQWNKP SKPKTNMKHM AGAAAAGAVV GGLGGYMLGS AMSRPIIHFG SDYEDRYYRE NMHRYPNQVY YRPMDQYSSQ NNFVHDCVNI TIKQHTVTTT TKGENFTETD VKMMERVVEQ MCITQYERES QAYYQRGS

KYTE-DOOLITTLE Hydrophobicity Values
for mature chimp prion protein
Arg: -4.5
Ser: -0.8
Lys: -3.9
Thr: -0.7
Asn: -3.5
Gly: -0.4
Asp: -3.5
Ala: 1.8
Gln: -3.5
Met: 1.9
Glu: -3.5
Cys: 2.5
His: -3.2
Phe: 2.8
Pro: -1.6
Leu: 3.8
Tyr: -1.3
Val: 4.2
Trp: -0.9
Ile: 4.5

KYTE-DOOLITTLE Hydrophobicity Values
for Helices H1 H2 H3, as averaged over 31 species
Prion KD helices
The three helical regions reported for prion protein from NMR are generally conserved in length and sequence in homology alignment. By assigning KD hydrophobicity values and averaging, a more representative picture of side chain use is obtained. Note that helix H1 is rather anomalous in being consistently negative in the KD scale; this shows up in the associated helical wheels.

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