title: 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 scrutinize collective 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 Schrödinger equation. The example we consider is an α-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 supersecondary 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 precision of tenths to several angstroms in terms of a soliton solution to a discrete nonlinear Schrödinger equation.
authors.affiliation: School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China.
authors.forename: Jin
authors.initials: J
authors.lastname: Dai
authors.affiliation: School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China.|Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala, Sweden.|Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200, Tours, France.
authors.forename: Antti J
authors.initials: AJ
authors.lastname: Niemi
authors.affiliation: School of Physics, Beijing Institute of Technology, Beijing 100081, People's Republic of China.
authors.forename: Jianfeng
authors.initials: J
authors.lastname: He
authors.affiliation: Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
authors.forename: Adam
authors.initials: A
authors.lastname: Sieradzan
authors.affiliation: Institute of Information and Communication Technologies, Bulgarian Academy of Sciences, 25A, Acad. G. Bonchev Str., Sofia 1113, Bulgaria.
authors.forename: Nevena
authors.initials: N
authors.lastname: Ilieva
mesh_terms: D000595:Amino Acid Sequence; D015700:HIV Envelope Protein gp41 / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D000072756:Protein Conformation, alpha-Helical; D017510:Protein Folding; D013816:Thermodynamics
chemical_list: D015700:HIV Envelope Protein gp41