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  • 1. Kierspel, Thomas
    et al.
    Kadek, Alan
    Barran, Perdita
    Bellina, Bruno
    Bijedic N, Adi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi.
    Brodmerkel, Maxim N.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Commandeur, Jan
    Caleman, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Kemisk och biomolekylär fysik. Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, E22607, Hamburg, Germany.
    Damjanović, Tomislav
    Dawod, Ibrahim
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Kemisk och biomolekylär fysik. European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
    De Santis, Emiliano
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Lekkas, Alexandros
    Lorenzen, Kristina
    López Morillo, Luis
    Mandl, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Kemisk och biomolekylär fysik. University of Applied Sciences Technikum Wien, Höchstädtpl. 6, 1200, Vienna, Austria.
    Marklund, Erik G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Papanastasiou, Dimitris
    Ramakers, Lennart A. I.
    Schweikhard, Lutz
    Simke, Florian
    Sinelnikova, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Smyrnakis, Athanasios
    Timneanu, Nicusor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Kemisk och biomolekylär fysik.
    Uetrecht, Charlotte
    Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC2023Inngår i: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 415, nr 18 SI, s. 4209-4220Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    MS SPIDOC is a novel sample delivery system designed for single (isolated) particle imaging at X-ray Free-Electron Lasers that is adaptable towards most large-scale facility beamlines. Biological samples can range from small proteins to MDa particles. Following nano-electrospray ionization, ionic samples can be m/z-filtered and structurally separated before being oriented at the interaction zone. Here, we present the simulation package developed alongside this prototype. The first part describes how the front-to-end ion trajectory simulations have been conducted. Highlighted is a quadrant lens; a simple but efficient device that steers the ion beam within the vicinity of the strong DC orientation field in the interaction zone to ensure spatial overlap with the X-rays. The second part focuses on protein orientation and discusses its potential with respect to diffractive imaging methods. Last, coherent diffractive imaging of prototypical T = 1 and T = 3 norovirus capsids is shown. We use realistic experimental parameters from the SPB/SFX instrument at the European XFEL to demonstrate that low-resolution diffractive imaging data (q < 0.3 nm−1) can be collected with only a few X-ray pulses. Such low-resolution data are sufficient to distinguish between both symmetries of the capsids, allowing to probe low abundant species in a beam if MS SPIDOC is used as sample delivery.

    Fulltekst (pdf)
    fulltext
  • 2.
    Sinelnikova, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Data Reduction & Error Analysis in brief2017Annet (Annet vitenskapelig)
    Abstract [en]

    This booklet was written to give an idea about how errors propagate in physical measurements. For this purpose we will first discuss what a measurement of a physical quantity means and where errors come from. Then we will show how to write down the result in a proper way, using a scientific notation. We then discuss how to compute errors in different cases, in direct and indirect measurements. Finally, we give an example that explicitly shows how to use the methods.

    The booklet can be useful for students who do laboratory work in physics. It might be used as a reference source for data reduction and propagation of errors.

    Fulltekst (pdf)
    fulltext
  • 3.
    Sinelnikova, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Polymer and Protein Physics: Simulations of Interactions and Dynamics2021Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

    Delarbeid
    1. Phase diagram and the pseudogap state in a linear chiral homopolymer model
    Åpne denne publikasjonen i ny fane eller vindu >>Phase diagram and the pseudogap state in a linear chiral homopolymer model
    2015 (engelsk)Inngår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 92, nr 3, artikkel-id 032602Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    The phase structure of a single self-interacting homopolymer chain is investigated in terms of a universal theoretical model, designed to describe the chain in the infrared limit of slow spatial variations. The effects of chirality are studied and compared with the influence of a short-range attractive interaction between monomers, at various ambient temperature values. In the high-temperature limit the homopolymer chain is in the self-avoiding random walk phase. At very low temperatures two different phases are possible: When short-range attractive interactions dominate over chirality, the chain collapses into a space-filling conformation. But when the attractive interactions weaken, there is a low-temperature unfolding transition and the chain becomes like a straight rod. Between the high- and low-temperature limits, several intermediate states are observed, including the theta regime and pseudogap state, which is a novel form of phase state in the context of polymer chains. Applications to polymers and proteins, in particular collagen, are suggested.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-264627 (URN)10.1103/PhysRevE.92.032602 (DOI)000361310700003 ()
    Forskningsfinansiär
    Swedish Research CouncilCarl Tryggers foundation
    Tilgjengelig fra: 2015-10-26 Laget: 2015-10-15 Sist oppdatert: 2021-02-08bibliografisk kontrollert
    2. Multiple scales and phases in discrete chains with application to folded proteins
    Åpne denne publikasjonen i ny fane eller vindu >>Multiple scales and phases in discrete chains with application to folded proteins
    2018 (engelsk)Inngår i: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 97, nr 5, artikkel-id 052107Artikkel i tidsskrift (Fagfellevurdert) 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.

    sted, utgiver, år, opplag, sider
    American Physical Society, 2018
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-357014 (URN)10.1103/PhysRevE.97.052107 (DOI)000432978200001 ()
    Forskningsfinansiär
    Knut and Alice Wallenberg FoundationSwedish Research Council
    Tilgjengelig fra: 2018-08-13 Laget: 2018-08-13 Sist oppdatert: 2021-02-08bibliografisk kontrollert
    3. RG Smoothing Algorithm Which Makes Data Compression
    Åpne denne publikasjonen i ny fane eller vindu >>RG Smoothing Algorithm Which Makes Data Compression
    2018 (engelsk)Inngår i: arXiv preprint arXiv:1806.01663Artikkel i tidsskrift (Annet vitenskapelig) Published
    Abstract [en]

    I describe a new method for smoothing a one-dimensional curve in Euclidian space with an arbitrary number of dimensions. The basic idea is borrowed from renormalization group theory which previously was applied to biological macromolecules. There are two crucial differences from other smoothing methods that make the algorithm unique: data compression and recursive implementation. One of the simplest forms of the method that is described in this article has only one free parameter - the number of iterative steps. This means that hardware implementation should be relatively easy because each loop is simple and strictly defined. The method could be beneficially applied to pattern recognition and data compression in future studies.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-434242 (URN)
    Tilgjengelig fra: 2021-02-06 Laget: 2021-02-06 Sist oppdatert: 2021-11-10bibliografisk kontrollert
    4. Reproducibility in the unfolding process of protein induced by an external electric field
    Åpne denne publikasjonen i ny fane eller vindu >>Reproducibility in the unfolding process of protein induced by an external electric field
    Vise andre…
    2021 (engelsk)Inngår i: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 12, nr 6, s. 2030-2038Artikkel i tidsskrift (Fagfellevurdert) 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.

    sted, utgiver, år, opplag, sider
    Royal Society of ChemistryRoyal Society of Chemistry (RSC), 2021
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-429912 (URN)10.1039/D0SC06008A (DOI)000619216100039 ()
    Forskningsfinansiär
    EU, Horizon 2020, 801406Swedish Research Council, 2018-00740
    Tilgjengelig fra: 2021-01-06 Laget: 2021-01-06 Sist oppdatert: 2024-01-15bibliografisk kontrollert
    5. Orientation before destruction. A multiscale molecular dynamics study
    Åpne denne publikasjonen i ny fane eller vindu >>Orientation before destruction. A multiscale molecular dynamics study
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    The emergence of ultra-fast X-ray free-electron lasers opens the possibility of imaging single molecules in the gas phase at atomic resolution. The main disadvantage of this imaging technique is the unknown orientation of the sample exposed to the X-ray beam, making the three-dimensional reconstruction not trivial. The induced orientation of molecules prior to X-ray exposure can be highly beneficial, as it significantly reduces the number of collected diffraction patterns whilst improving the quality of the reconstructed structure. We present here the possibility of protein orientation using a time-dependent external electric field. We used ab initio simulations on Trp-cage protein to provide a qualitative estimation of the field strength required to break protein bonds, with 45 V/nm as a breaking point value. Furthermore, we simulated, in a classical molecular dynamics approach, the orientation of ubiquitin protein by exposing it to different time-dependent electric fields. The protein structure was preserved for all samples at the moment orientation was achieved, which we denote `orientation before destruction'. Moreover, we find that the minimal field strength required to induce orientation within ten ns of electric field exposure was of the order of 0.5 V/nm. Our results help explain the process of field orientation of proteins and can support the design of instruments for protein orientation.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-434280 (URN)
    Tilgjengelig fra: 2021-02-08 Laget: 2021-02-08 Sist oppdatert: 2021-02-08
    6. NMR Refinement and Peptide Folding Using the GROMACS Software
    Åpne denne publikasjonen i ny fane eller vindu >>NMR Refinement and Peptide Folding Using the GROMACS Software
    2021 (engelsk)Inngår i: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 75, nr 4-5, s. 143-149Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Nuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations. Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software. With this package, it is possible to model distance restraints, dihedral restraints, and orientation restraints. The output from the script is validated by performing simulations with and without restraints, including the ab initio refinement of one peptide.

    sted, utgiver, år, opplag, sider
    Springer NatureSpringer Nature, 2021
    Emneord
    Python, NMR-STAR, Force Field, Amber, Charmm
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-434243 (URN)10.1007/s10858-021-00363-z (DOI)000634305400001 ()33778935 (PubMedID)
    Tilgjengelig fra: 2021-02-06 Laget: 2021-02-06 Sist oppdatert: 2024-01-15bibliografisk kontrollert
    Fulltekst (pdf)
    fulltext
    Download (jpg)
    presentationsbild
  • 4.
    Sinelnikova, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    RG Smoothing Algorithm Which Makes Data Compression2018Inngår i: arXiv preprint arXiv:1806.01663Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    I describe a new method for smoothing a one-dimensional curve in Euclidian space with an arbitrary number of dimensions. The basic idea is borrowed from renormalization group theory which previously was applied to biological macromolecules. There are two crucial differences from other smoothing methods that make the algorithm unique: data compression and recursive implementation. One of the simplest forms of the method that is described in this article has only one free parameter - the number of iterative steps. This means that hardware implementation should be relatively easy because each loop is simple and strictly defined. The method could be beneficially applied to pattern recognition and data compression in future studies.

  • 5.
    Sinelnikova, Anna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Mandl, Thomas
    Agelii, Harald
    Grånäs, Oscar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Marklund, Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Caleman, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    De Santis, Emiliano
    Orientation before destruction. A multiscale molecular dynamics studyManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    The emergence of ultra-fast X-ray free-electron lasers opens the possibility of imaging single molecules in the gas phase at atomic resolution. The main disadvantage of this imaging technique is the unknown orientation of the sample exposed to the X-ray beam, making the three-dimensional reconstruction not trivial. The induced orientation of molecules prior to X-ray exposure can be highly beneficial, as it significantly reduces the number of collected diffraction patterns whilst improving the quality of the reconstructed structure. We present here the possibility of protein orientation using a time-dependent external electric field. We used ab initio simulations on Trp-cage protein to provide a qualitative estimation of the field strength required to break protein bonds, with 45 V/nm as a breaking point value. Furthermore, we simulated, in a classical molecular dynamics approach, the orientation of ubiquitin protein by exposing it to different time-dependent electric fields. The protein structure was preserved for all samples at the moment orientation was achieved, which we denote `orientation before destruction'. Moreover, we find that the minimal field strength required to induce orientation within ten ns of electric field exposure was of the order of 0.5 V/nm. Our results help explain the process of field orientation of proteins and can support the design of instruments for protein orientation.

  • 6.
    Sinelnikova, Anna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Mandl, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Kemisk och biomolekylär fysik. ty of Applied Sciences Technikum Wien, Wien, Austria.
    Agelii, Harald
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi.
    Grånäs, Oscar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Marklund, Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Caleman, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Kemisk och biomolekylär fysik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Center for Free-Electron Laser Science, DESY,Hamburg, Germany.
    De Santis, Emiliano
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Kemisk och biomolekylär fysik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Protein orientation in time-dependent electric fields: orientation before destruction2021Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 120, nr 17, s. 3709-3717, artikkel-id S0006-3495(21)00603-2Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Proteins often have nonzero electric dipole moments, making them interact with external electric fields and offering a means for controlling their orientation. One application that is known to benefit from orientation control is single-particle imaging with x-ray free-electron lasers, in which diffraction is recorded from proteins in the gas phase to determine their structures. To this point, theoretical investigations into this phenomenon have assumed that the field experienced by the proteins is constant or a perfect step function, whereas any real-world pulse will be smooth. Here, we explore the possibility of orienting gas-phase proteins using time-dependent electric fields. We performed ab initio simulations to estimate the field strength required to break protein bonds, with 45 V/nm as a breaking point value. We then simulated ubiquitin in time-dependent electric fields using classical molecular dynamics. The minimal field strength required for orientation within 10 ns was on the order of 0.5 V/nm. Although high fields can be destructive for the structure, the structures in our simulations were preserved until orientation was achieved regardless of field strength, a principle we denote "orientation before destruction."

    Fulltekst (pdf)
    fulltext
  • 7.
    Sinelnikova, Anna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Mandl, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Kemisk och biomolekylär fysik. University of Applied Sciences Technikum Wien, Höchstädtplatz 6, A-1200 Wien, Austria .
    Östlin, Christofer
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Grånäs, Oscar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Brodmerkel, Maxim N.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Marklund, Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Caleman, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Kemisk och biomolekylär fysik.
    Reproducibility in the unfolding process of protein induced by an external electric field2021Inngår i: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 12, nr 6, s. 2030-2038Artikkel i tidsskrift (Fagfellevurdert)
    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.

    Fulltekst (pdf)
    Article
    Download (pdf)
    Supplementary information
  • 8.
    Sinelnikova, Anna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Niemi, Antti
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Teoretisk fysik. 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.
    Nilsson, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Ulybyshev, M.
    Univ Regensburg, Inst Theoret Phys, Univ Str 31, D-93053 Regensburg, Germany.
    Multiple scales and phases in discrete chains with application to folded proteins2018Inngår i: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 97, nr 5, artikkel-id 052107Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 9.
    Sinelnikova, Anna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Van der Spoel, David
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Beräkningsbiologi och bioinformatik.
    NMR Refinement and Peptide Folding Using the GROMACS Software2021Inngår i: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 75, nr 4-5, s. 143-149Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Nuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations. Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software. With this package, it is possible to model distance restraints, dihedral restraints, and orientation restraints. The output from the script is validated by performing simulations with and without restraints, including the ab initio refinement of one peptide.

    Fulltekst (pdf)
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