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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: 2021-02-08Bibliographically approved
In thesis
1. Polymer and Protein Physics: Simulations of Interactions and Dynamics
Open this publication in new window or tab >>Polymer and Protein Physics: Simulations of Interactions and Dynamics
2021 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Proteins can, without any exaggeration, be called the "building blocks of life". Their physical properties depend not only on the chemical structure but also on their geometric shape. In this thesis, I investigate protein geometry using several different methods.

We start with a coarse-graining model to study the general behavior of polymers. For this reason, we utilize an effective Hamiltonian that can describe the thermodynamic properties of polymer chains and reproduce secondary and tertiary structures. To investigate this model, I perform classical Monte Carlo simulations using my software package.

Another problem we address in this thesis is how to distinguish thermodynamic phases of proteins. The conventional definition of phases of polymer systems uses scaling laws. However, this method needs the chain's length to be varied, which is impossible to do with heteropolymers where the number of sites is one of the system's characteristics. We will apply renormalization group (RG) theory ideas to overcome this difficulty. We present a scaling procedure and an observable through which RG flow can define a certain polymer chain's phase.

Another part of the thesis is dedicated to the method of molecular dynamics. Our focus is on a novel experimental technique called Single Particle Imaging (SPI). The spatial orientation of the sample in this method is arbitrary. Scientists proposed to use a strong electric field to fix the orientation since most biological molecules have a non-zero dipole moment. Motivated by this, we investigate the influence of a strong electric field's ramping on the orientation of protein ubiquitin. For the same question of SPI and using the same protein, we study the reproducibility of unfolding it in a strong electric field. With the help of a new graph representation, I show different unfolding pathways as a function of the electric field's value and compare them with thermal and mechanical unfolding. I show that the RG flow observable can also detect the different ubiquitin unfolding pathways more simply.

The study described in this thesis has two types of results. One is a very concrete type, which can be utilized right away in the SPI experiments, like MS SPIDOC on the European XFEL. The other type of results are more theoretical and opens up a new field for further research. However, all of them contribute to protein science, an area vital for humanity's ability to protect us from threats such as the current COVID-19 pandemic.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2021. p. 126
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 2015
Keywords
polymers, proteins, Monte Carlo, molecular dynamics, phase diagram, renormalisation group, SPI, polymer effective model, coarse-graining
National Category
Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-434275 (URN)978-91-513-1139-5 (ISBN)
Public defence
2021-03-26, Polhemsalen, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 13:30 (English)
Opponent
Supervisors
Available from: 2021-03-04 Created: 2021-02-08 Last updated: 2021-03-29

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Sinelnikova, AnnaNiemi, AnttiNilsson, Johan

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