title: Peierls-Nabarro barrier and protein loop propagation.
abstract: When a self-localized quasiparticle excitation propagates along a discrete one-dimensional lattice, it becomes subject to a dissipation that converts the kinetic energy into lattice vibrations. Eventually the kinetic energy no longer enables the excitation to cross over the minimum energy barrier between neighboring sites, and the excitation becomes localized within a lattice cell. In the case of a protein, the lattice structure consists of the C(α) backbone. The self-localized quasiparticle excitation is the elemental building block of loops. It can be modeled by a kink that solves a variant of the discrete nonlinear Schrödinger equation. We study the propagation of such a kink in the case of the protein G related albumin-binding domain, using the united residue coarse-grained molecular-dynamics force field. We estimate the height of the energy barriers that the kink needs to cross over in order to propagate along the backbone lattice. We analyze how these barriers give rise to both stresses and reliefs, which control the kink movement. For this, we deform a natively folded protein structure by parallel translating the kink along the backbone away from its native position. We release the transposed kink, and we follow how it propagates along the backbone toward the native location. We observe that the dissipative forces that are exerted on the kink by the various energy barriers have a pivotal role in determining how a protein folds toward its native state.
authors.affiliation: Department of Physics and Astronomy, Uppsala University, Ångströmlaboratoriet, Lägerhyddsvägen 1, 751 20 Uppsala, Sweden and Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-952 Gdańsk, Poland.
authors.forename: Adam K
authors.initials: AK
authors.lastname: Sieradzan
authors.affiliation: Department of Physics and Astronomy, Uppsala University, Ångströmlaboratoriet, Lägerhyddsvägen 1, 751 20 Uppsala, Sweden and Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200 Tours, France and Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081, People Republic of China.
authors.forename: Antti
authors.initials: A
authors.lastname: Niemi
authors.affiliation: Department of Physics and Astronomy, Uppsala University, Ångströmlaboratoriet, Lägerhyddsvägen 1, 751 20 Uppsala, Sweden.
authors.forename: Xubiao
authors.initials: X
authors.lastname: Peng
mesh_terms: D056004:Molecular Dynamics Simulation; D009068:Movement; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D011506:Proteins