Secondary-structure phases of a hydrophobic-polar heteropolymer model

3 Secondary-structure phases of a hydrophobic-polar heteropolymer model 

Proteins form the most prominent class of polymers, where different types of secondary structures occur, typically within the same molecule. It is therefore useful to extend the homopolymer model employed in the previous section by introducing two types of monomers which can be hydrophobic or polar. For this purpose, we will now combine the already introduced and for the line-like heteropolymers in Chapter 8 extensively studied AB model with the thickness constraint. 

In order to get an impression of the effects caused by introducing a sequence-dependent model, we here consider an exemplified Fibonacci sequence AB2AB2ABAB2AB with 13 

For smaller thickness constraints, structures with helical properties are found, which depends on the monomer sequence. We note here a very pronounced conformational 

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