Bloch spin waves and emergent structure in protein folding with HIV envelope glycoprotein as an example

Abstract

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.

arXiv comment20 pages 29 figures

References in corpus (10)

• The Discrete Frenet Frame, Inflection Point Solitons And Curve Visualization with Applications to Folded Proteins
• Discrete Nonlinear Schrodinger Equation, Solitons and Organizing Principles for Protein Folding
• Topological Solitons and Folded Proteins
• Soliton concepts and the protein structure
• A Gauge Field Theory of Chirally Folded Homopolymers with Applications to Folded Proteins
• Phases of bosonic strings and two dimensional gauge theories
• Towards Quantitative Classification of Folded Proteins in Terms of Elementary Functions
• Peierls-Nabarro Barrier and Protein Loop Propagation
• On correlation between protein secondary structure, backbone bond angles, and side-chain orientations
• Protein loops, solitons and side-chain visualization with applications to the left-handed helix region

Cited by in corpus (3)

• Thermal unfolding of myoglobin in the Landau-Ginzburg-Wilson approach
• Towards multistage modelling of protein dynamics with monomeric Myc oncoprotein as an example
• Solution X-ray scattering (S/WAXS) and structure formation in protein dynamics