  We inquire how structure emerges during the process of protein folding. For
this we scrutinise col- lective many-atom motions during all-atom molecular
dynamics simulations. We introduce, develop and employ various topological
techniques, in combination with analytic tools that we deduce from the concept
of integrable models and structure of discrete nonlinear Schroedinger equation.
The example we consider is an alpha-helical subunit of the HIV envelope
glycoprotein gp41. The helical structure is stable when the subunit is part of
the biological oligomer. But in isolation the helix becomes unstable, and the
monomer starts deforming. We follow the process computationally. We interpret
the evolving structure both in terms of a backbone based Heisenberg spin chain
and in terms of a side chain based XY spin chain. We find that in both cases
the formation of protein super-secondary structure is akin the formation of a
topological Bloch domain wall along a spin chain. During the process we
identify three individual Bloch walls and we show that each of them can be
modelled with a very high precision in terms of a soliton solution to a
discrete nonlinear Schroedinger equation.
