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Bloch spin waves and emergent structure in protein folding with HIV envelope glycoprotein as an example
Beijing Inst Technol, Sch Phys, Beijing 100081, Peoples R China.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics. Beijing Inst Technol, Sch Phys, Beijing 100081, Peoples R China.; Univ Tours, CNRS, UMR 6083, Lab Math & Phys Theor,Federat Denis Poisson, Parc Grandmont, F-37200 Tours, France.
Beijing Inst Technol, Sch Phys, Beijing 100081, Peoples R China.
Univ Gdansk, Fac Chem, Wita Stwosza 63, PL-80308 Gdansk, Poland.
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2016 (English)In: Physical review E, ISSN 2470-0045, Vol. 93, no 3, 032409Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
American Physical Society , 2016. Vol. 93, no 3, 032409
National Category
Subatomic Physics
Research subject
Theoretical Physics
Identifiers
URN: urn:nbn:se:uu:diva-287901DOI: 10.1103/PhysRevE.93.032409ISI: 000372425200004OAI: oai:DiVA.org:uu-287901DiVA: diva2:923573
Funder
Swedish Research CouncilCarl Tryggers foundation
Available from: 2016-04-26 Created: 2016-04-26 Last updated: 2016-04-27Bibliographically approved

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Niemi, Antti
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