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- Liwo, Jozef A., et al.
(författare)
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Origin of the Architecture of Biological Macromolecules - A Mean-Field Perspective
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 256A-256A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The structures of the key classes of biological macromolecules: proteins, nucleic acids and polysaccharides can be dissected into very regular motifs, which are alpha-, beta, and double helices and sheets. In this communication we demonstrate that these regular patterns arise as a result of dipole-dipole interactions of the polar groups (peptide, nucleic-acid-base or sugar-ring groups) and the coupling of these interactions with backbone-local interactions, described at the mean-field level; the averaging is carried out by rotating the dipole of a polar unit about its virtual-bond axis.
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| 2. |
- Sieradzan, Adam K., et al.
(författare)
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Peierls-Nabarro barrier and protein loop propagation
- 2014
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1539-3755 .- 1550-2376. ; 90:6, s. 062717-
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Tidskriftsartikel (refereegranskat)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-alpha 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 Schrodinger 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.
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