Mass Spectrometry for Single Particle Imaging of Dipole Oriented protein Complexes

Livrables

Stability range and charge distribution of electrosprayed ions

MD simulations and pilot studies will be performed.

The final scientific results will be collected by the HPI and published And an official press release will be published via the common public website of the project as well as the website of the European Commission

Evaluation of X-MS-I based SPI

Structure analysis of lowpopulated transient complexes of different viruses will be evaluated including time frames for data acquisition and analysis

Instrumental settings for structural integrity

IM, action-FRET and UVPD in comparison to available solution phase data and structures will be used to confirm structural integrity of protein complexes in the gas phase.

Dissemination and Exploitation plan

The HPI is going to outline a dissemination and exploitation plan which will be updated on a regular basis as the project proceeds.

X-MS-I prototype design for integration

The X-MS-I prototype for European XFEL will include the aerolens, digital ion trap, IM and orientation device. Ions will follow a linear trajectory. A short ToF with VMI detector will be added behind the interaction region to allow for offline system testing, online quality control of the samples and monitoring mass selectivity of ions that have not been hit by the laser pulse.

Requirements from simulations for SPI experiments

Methods for integrating actionFRET and IM data with MD simulations have been successfully developed so that now the necessary requirements for performing the actual experiments can be documented

Evaluation of component tests

Methods for ion gating acceleration and trapping of high mass ions at intermediate pressure in the hybrid RF ion guide of the aerolens will be tested to enhance desolvation while maintaining structural integrity of the proteins under investigation

Benchmarking simulations of X-MS-I for SPI experiments

Simulations of system and beamline

Software pipeline for device modelling

The aerolens, digital ion trap and IM cell will be characterised for large ions using ion optical modelling prior to manufacturing. Required pressures, theoretical performance for trapping, mass selection and combination with IM device have to be defined to inform benchmarking in WP4. This will culminate in a software pipeline for simulation, testing, evaluation and implementation of instrumentation.

Public and internal web services, logo

The European XFEL-partner is going to establishing a cooperative internet working platform at the start of the project to facilitate communication, spreading of knowledge, internal publication of results and reports.

Prototype comprising X-MS-I and experimental chamber installed

The final prototype experimental chamber accommodating X-MS-I will be installed at the SPB/SFX instrument.

Data management plan

The HPI is going to generate a data management plan which meets the needs of the project and participating partners and this document will be updated on a regular basis as the work proceeds.

Publications

Polymer and Protein Physics, Simulations of Interactions and Dynamics.

Auteurs: Anna Sinelnikova
Publié dans: 2021
Éditeur: Acta Universitatis Upsaliensis

Theoretical and Biochemical: Advancing Protein Structure Investigations with Complementing Computations

Auteurs: Brodmerkel, Maxim N.
Publié dans: 2023, ISSN 1651-6214
Éditeur: Uppsala: Acta Universitatis Upsaliensis, 2023. , p. 96

Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins.

Auteurs: Maxim N. Brodmerkel, Emiliano De Santis, Charlotte Uetrecht, Carl Caleman, Erik G. Marklund.
Publié dans: Current Research in Structural Biology, 2022, ISSN 2665-928X
Éditeur: Elsevier B.V.
DOI: 10.1016/j.crstbi.2022.10.001

Commissioning the digital mass-filter/ion-trap module for the MS SPIDOC prototype.

Auteurs: Florian Simke, Paul Fischer, Tomislav Damjanović, Alan Kádek, Thomas Kierspel, Kristina Lorenzen, Charlotte Uetrecht. and Lutz Schweikhard
Publié dans: Journal of Instrumentation, Numéro Vol. 18, 2023, ISSN 1748-0221
Éditeur: Institute of Physics
DOI: 10.1088/1748-0221/18/10/p10021

Structural Heterogeneity in Single Particle Imaging Using X-ray Lasers

Auteurs: Thomas Mandl, Christofer Östlin, Ibrahim E. Dawod, Maxim N. Brodmerkel, Erik G. Marklund, Andrew V. Martin, Nicusor Timneanu, Carl Caleman
Publié dans: The Journal of Physical Chemistry Letters, Numéro 11/15, 2020, Page(s) 6077-6083, ISSN 1948-7185
Éditeur: American Chemical Society
DOI: 10.1021/acs.jpclett.0c01144

Ion mobility mass spectrometry and molecular dynamics simulations unravel the conformational stability of zinc metallothionein-2 species.

Auteurs: Manuel David Peris-Díaz, Alexey Barkhanskiy, Ellen Liggett, Perdita Barran
Publié dans: Chemical Communication, 2023, ISSN 1359-7345
Éditeur: Royal Society of Chemistry
DOI: 10.1039/d2cc06559b

Electrospray ionization of native membrane proteins proceeds via a charge equilibration step. RSC Advances

Auteurs: Hsin-Yung Yen, Mia L. Abramsson, Mark T. Agasid, Dilraj Lama, Joseph Gault, Idlir Liko, Margit Kaldmäe, Mihkel Saluri, Abdul Aziz Qureshi, Albert Suades, David Drew, Matteo T. Degiacomi, Erik G. Marklund, Timothy M. Allison, Carol V. Robinson and Michael Landreh.
Publié dans: RSC Advances, 2022, ISSN 2046-2069
Éditeur: Royal Society of Chemistry
DOI: 10.1039/d2ra01282k

In a flash of light: X-ray free electron lasers meet native mass spectrometry

Auteurs: Alan Kadek, Kristina Lorenzen, Charlotte Uetrecht
Publié dans: Drug Discovery Today: Technologies, 2021, ISSN 1740-6749
Éditeur: Elsevier BV
DOI: 10.1016/j.ddtec.2021.07.001

Reproducibility in the unfolding process of protein induced by an external electric field

Auteurs: Anna Sinelnikova, Thomas Mandl, Christofer Östlin, Oscar Grånäs, Maxim N. Brodmerkel, Erik G. Marklund, Carl Caleman
Publié dans: Chemical Science, Numéro 12/6, 2021, Page(s) 2030-2038, ISSN 2041-6520
Éditeur: Royal Society of Chemistry
DOI: 10.1039/d0sc06008a

Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC.

Auteurs: Thomas Kierspel, Alan Kadek, Perdita Barran, Bruno Bellina, Adi Bijedic, Maxim N. Brodmerkel, Jan Commandeur, Carl Caleman, Tomislav Damjanović, Ibrahim Dawod, Emiliano De Santis, Alexandros Lekkas, Kristina Lorenzen, Luis López Morillo, Thomas Mandl, Erik G. Marklund, Dimitris Papanastasiou, Lennart A. I. Ramakers, Lutz Schweikhard, Florian Simke, Anna Sinelnikova, Athanasios Smyrnakis, Nicusor
Publié dans: Analytical and Bioanalytical Chemistry, 2023, ISSN 1618-2642
Éditeur: Springer Verlag
DOI: 10.1007/s00216-023-04658-y

Simulations of a digital ion filter and a digital ion trap for heavy biomolecules

Auteurs: Florian Simke, Paul Fischer, Gerrit Marx, Lutz Schweikhard
Publié dans: International Journal of Mass Spectrometry, Numéro Volume 473, 2022, ISSN 1387-3806
Éditeur: Elsevier BV
DOI: 10.1016/j.ijms.2021.116779

Interplay between chromophore binding and domain assembly by the B 12 -dependent photoreceptor protein, CarH

Auteurs: Inês S. Camacho, Rachelle Black, Derren J. Heyes, Linus O. Johannissen, Lennart A. I. Ramakers, Bruno Bellina, Perdita E. Barran, Sam Hay, Alex R. Jones
Publié dans: Chemical Science, Numéro 12/24, 2021, Page(s) 8333-8341, ISSN 2041-6520
Éditeur: Royal Society of Chemistry
DOI: 10.1039/d1sc00522g

Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration

Auteurs: Maxim N. Brodmerkel, Emiliano De Santis, Carl Caleman & Erik G. Marklund
Publié dans: The Protein Journal, 2023, ISSN 1572-3887
Éditeur: Springer Verlag
DOI: 10.1007/s10930-023-10110-y

The XBI BioLab for life science experiments at the European XFEL

Auteurs: Huijong Han, Ekaterina Round, Robin Schubert, Yasmin Gül, Jana Makroczyová, Domingo Meza, Philipp Heuser, Martin Aepfelbacher, Imrich Barák, Christian Betzel, Petra Fromme, Inari Kursula, Poul Nissen, Elena Tereschenko, Joachim Schulz, Charlotte Uetrecht, Jozef Ulicný, Matthias Wilmanns, Janos Hajdu, Victor S. Lamzin, Kristina Lorenzen
Publié dans: Journal of Applied Crystallography, Numéro 54/1, 2021, Page(s) 7-21, ISSN 1600-5767
Éditeur: IUCr Journals
DOI: 10.1107/s1600576720013989

Characterization of native protein structure with ion mobility mass spectrometry, multiplexed fragmentation strategies and multivariant analysis

Auteurs: Rachelle Black, Alexey Barkhanskiy, Lennart A.I. Ramakers, Alina Theisen, Jeffery M. Brown, Bruno Bellina, Drupad K. Trivedi, Perdita E. Barran
Publié dans: International Journal of Mass Spectrometry, Numéro 464, 2021, Page(s) 116588, ISSN 1387-3806
Éditeur: Elsevier BV
DOI: 10.1016/j.ijms.2021.116588

Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status

Auteurs: Jasmin Dülfer, Hao Yan, Maxim N. Brodmerkel, Robert Creutznacher, Alvaro Mallagaray, Thomas Peters, Carl Caleman, Erik G. Marklund, Charlotte Uetrecht
Publié dans: Molecules, Numéro 26/8, 2021, Page(s) 2125, ISSN 1420-3049
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26082125

Formation and Characterisation of Polymetallic Rings in vacuo.

Auteurs: Niklas Geue, Grigore Timco, George Whitehead, Eric McInnes, Neil Burton, Richard Winpenny and Perdita Barran
Publié dans: Nature Synthesis, Numéro 2, 2023, Page(s) 926–936, ISSN 2731-0582
Éditeur: Springer Nature
DOI: 10.1038/s44160-023-00383-7

Disassembly Mechanisms and Energetics of Polymetallic Rings and Rotaxanes

Auteurs: Niklas Geue, Tom S. Bennett, Alexandra-Ana-Maria Arama, Lennart A. I. Ramakers, George F. S. Whitehead, Grigore A. Timco, P. B. Armentrout, Eric J. L. McInnes, Neil A. Burton, Richard E. P. Winpenny, and Perdita E. Barran
Publié dans: Journal of the American Chemical Society, 2022, ISSN 0002-7863
Éditeur: American Chemical Society
DOI: 10.1021/jacs.2c07522

Charge Engineering Reveals the Roles of Ionizable Side Chains in Electrospray Ionization Mass Spectrometry

Auteurs: Mia L. Abramsson, Cagla Sahin, Jonathan T. S. Hopper, Rui M. M. Branca, Jens Danielsson, Mingming Xu, Shane A. Chandler, Nicklas Österlund, Leopold L. Ilag, Axel Leppert, Joana Costeira-Paulo, Lisa Lang, Kaare Teilum, Arthur Laganowsky, Justin L. P. Benesch, Mikael Oliveberg, Carol V. Robinson, Erik G. Marklund, Timothy M. Allison, Jakob R. Winther, and Michael Landreh
Publié dans: JACS Au, 2021, ISSN 0002-7863
Éditeur: American Chemical Society
DOI: 10.1021/jacsau.1c00458

Protein orientation in time-dependent electric fields: orientation before destruction

Auteurs: Anna Sinelnikova, Thomas Mandl, Harald Agelii, Oscar Grånäs, Erik G. Marklund, Carl Caleman, Emiliano De Santis
Publié dans: Biophysical Journal, Numéro 120/17, 2021, Page(s) 3709-3717, ISSN 0006-3495
Éditeur: Biophysical Society
DOI: 10.1016/j.bpj.2021.07.017

Chapter 10. Photoactivation and Dissociation in Biomolecular Mass Spectrometry

Auteurs: Rachelle Black, Perdita E. Barran, Lennart A. I. Ramakers
Publié dans: Advanced Fragmentation Methods in Biomolecular Mass Spectrometry - Probing Primary and Higher Order Structure with Electrons, Photons and Surfaces, 2020, Page(s) 235-280, ISBN 978-1-83916-104-9
Éditeur: Royal Society of Chemistry
DOI: 10.1039/9781839161056-00235

Norovirus Superstar

Auteurs: Véro Mischitz
Publié dans: 2021
Éditeur: European XFEL
DOI: 10.22003/xfel.eu-comic-2021-001-en

Deciphering the antioxidative role of p53 against H2O2-induced DNA damage using ion mobility mass spectrometry.

Auteurs: Manuel David Peris-Díaz ,Artur Krężel and Perdita Barran.
Publié dans: ChemRxiv, 2022, ISSN 2573-2293
Éditeur: ChemRxiv
DOI: 10.26434/chemrxiv-2022-f6mjt

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