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Reproducibility in the unfolding process of protein induced by an external electric field
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, Chemical and Bio-Molecular Physics. University of Applied Sciences Technikum Wien, Höchstädtplatz 6, A-1200 Wien, Austria .
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.ORCID iD: 0000-0002-0021-4354
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.ORCID iD: 0000-0002-1482-2182
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2021 (English)In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 12, no 6, p. 2030-2038Article in journal (Refereed) Published
Abstract [en]

The dynamics of proteins are crucial for their function. However, commonly used techniques for studying protein structures are limited in monitoring time-resolved dynamics at high resolution. Combining electric fields with existing techniques to study gas phase proteins, such as Single Particle Imaging using Free-electron Lasers and gas phase Small Angle X-ray Scattering, has the potential to open up a new era in time-resolved studies of gas phase protein dynamics. Using molecular dynamics simulations, we identify well-defined unfolding pathways of a protein, induced by experimentally achievable external electric fields. Our simulations show that strong electric fields in conjunction with short pulsed X-ray sources such as Free-electron Lasers can be a new path for imaging dynamics of gas-phase proteins at high spatial and temporal resolution.

Place, publisher, year, edition, pages
Royal Society of Chemistry (RSC) Royal Society of Chemistry, 2021. Vol. 12, no 6, p. 2030-2038
National Category
Biophysics Physical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-429912DOI: 10.1039/D0SC06008AISI: 000619216100039OAI: oai:DiVA.org:uu-429912DiVA, id: diva2:1514528
Funder
EU, Horizon 2020, 801406Swedish Research Council, 2018-00740Available from: 2021-01-06 Created: 2021-01-06 Last updated: 2024-01-15Bibliographically 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, AnnaMandl, ThomasÖstlin, ChristoferGrånäs, OscarBrodmerkel, Maxim N.Marklund, ErikCaleman, Carl

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