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Multiple scales and phases in discrete chains with application to folded proteins
Stockholms universitet, Nordiska institutet för teoretisk fysik (Nordita). Uppsala University, Sweden; Far Eastern Federal University, Russia; Beijing Institute of Technology, People's Republic of China.
Antal upphovsmän: 42018 (Engelska)Ingår i: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 97, nr 5, artikel-id 052107Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
2018. Vol. 97, nr 5, artikel-id 052107
Nationell ämneskategori
Fysik
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URN: urn:nbn:se:su:diva-157785DOI: 10.1103/PhysRevE.97.052107ISI: 000432978200001PubMedID: 29906880OAI: oai:DiVA.org:su-157785DiVA, id: diva2:1235584
Tillgänglig från: 2018-07-26 Skapad: 2018-07-26 Senast uppdaterad: 2018-07-26Bibliografiskt granskad

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Niemi, Antti J.
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Nordiska institutet för teoretisk fysik (Nordita)
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Physical review. E
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