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Multiple scales and phases in discrete chains with application to folded proteins
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics. Stockholm Univ, Nordita, Roslagstullsbacken 23, SE-10691 Stockholm, Sweden;Far Eastern Fed Univ, Sch Biomed, Lab Phys Living Matter, Vladivostok, Russia;Beijing Inst Technol, Dept Phys, Beijing 100081, Peoples R China.ORCID iD: 0000-0003-3408-5834
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
Univ Regensburg, Inst Theoret Phys, Univ Str 31, D-93053 Regensburg, Germany.
2018 (English)In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 97, no 5, article id 052107Article in journal (Refereed) Published
Abstract [en]

Chiral heteropolymers such as large globular proteins can simultaneously support multiple length scales. The interplay between the different scales brings about conformational diversity, determines the phase properties of the polymer chain, and governs the structure of the energy landscape. Most importantly, multiple scales produce complex dynamics that enable proteins to sustain live matter. However, at the moment there is incomplete understanding of how to identify and distinguish the various scales that determine the structure and dynamics of a complex protein. Here we address this impending problem. We develop a methodology with the potential to systematically identify different length scales, in the general case of a linear polymer chain. For this we introduce and analyze the properties of an order parameter that can both reveal the presence of different length scales and can also probe the phase structure. We first develop our concepts in the case of chiral homopolymers. We introduce a variant of Kadanoff's block-spin transformation to coarse grain piecewise linear chains, such as the C alpha backbone of a protein. We derive analytically, and then verify numerically, a number of properties that the order parameter can display, in the case of a chiral polymer chain. In particular, we propose that in the case of a chiral heteropolymer the order parameter can reveal traits of several different phases, contingent on the length scale at which it is scrutinized. We confirm that this is the case with crystallographic protein structures in the Protein Data Bank. Thus our results suggest relations between the scales, the phases, and the complexity of folding pathways.

Place, publisher, year, edition, pages
American Physical Society, 2018. Vol. 97, no 5, article id 052107
National Category
Physical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-357014DOI: 10.1103/PhysRevE.97.052107ISI: 000432978200001OAI: oai:DiVA.org:uu-357014DiVA, id: diva2:1238216
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilAvailable from: 2018-08-13 Created: 2018-08-13 Last updated: 2018-08-13Bibliographically approved

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Sinelnikova, AnnaNiemi, AnttiNilsson, Johan

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