Department of Chemistry - BMC

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Publications in Erik Marklund Group

Mass Spectrometry and Machine Learning Reveal Determinants of Client Recognition by Antiamyloid Chaperones

Osterlund, Nicklas; Vosselman, Thibault; Leppert, Axel; Graslund, Astrid et al.

Part of Molecular & Cellular Proteomics, 2022.

DOI for Mass Spectrometry and Machine Learning Reveal Determinants of Client Recognition by Antiamyloid Chaperones Download full text (pdf) of Mass Spectrometry and Machine Learning Reveal Determinants of Client Recognition by Antiamyloid Chaperones

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Complementing machine learning‐based structure predictions with native mass spectrometry

Allison, Timothy M.; Degiacomi, Matteo T.; Marklund, Erik; Jovine, Luca et al.

Part of Protein Science, 2022.

DOI for Complementing machine learning‐based structure predictions with native mass spectrometry Download full text (pdf) of Complementing machine learning‐based structure predictions with native mass spectrometry

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

Yen, Hsin-Yung; Abramsson, Mia L.; Agasid, Mark T.; Lama, Dilraj et al.

Part of RSC Advances, p. 9671-9680, 2022.

DOI for Electrospray ionization of native membrane proteins proceeds via a charge equilibration step Download full text (pdf) of Electrospray ionization of native membrane proteins proceeds via a charge equilibration step

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

Abramsson, Mia L.; Sahin, Cagla; Hopper, Jonathan T. S.; Branca, Rui M. M. et al.

Part of JACS Au, p. 2385-2393, 2021.

DOI for Charge Engineering Reveals the Roles of Ionizable Side Chains in Electrospray Ionization Mass Spectrometry
Protein orientation in time-dependent electric fields: orientation before destruction

Sinelnikova, Anna; Mandl, Thomas; Agelii, Harald; Grånäs, Oscar et al.

Part of Biophysical Journal, p. 3709-3717, 2021.

DOI for Protein orientation in time-dependent electric fields: orientation before destruction Download full text (pdf) of Protein orientation in time-dependent electric fields: orientation before destruction

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

Duelfer, Jasmin; Yan, Hao; Brodmerkel, Maxim N.; Creutznacher, Robert et al.

Part of Molecules, 2021.

DOI for Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status Download full text (pdf) of Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status

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Ion mobility-mass spectrometry shows stepwise protein unfolding under alkaline conditions

Sahin, Cagla; Österlund, Nicklas; Leppert, Axel; Johansson, Janne et al.

Part of Chemical Communications, p. 1450-1453, 2021.

DOI for Ion mobility-mass spectrometry shows stepwise protein unfolding under alkaline conditions
Reproducibility in the unfolding process of protein induced by an external electric field

Sinelnikova, Anna; Mandl, Thomas; Östlin, Christofer; Grånäs, Oscar et al.

Part of Chemical Science, p. 2030-2038, 2021.

DOI for Reproducibility in the unfolding process of protein induced by an external electric field Download full text (pdf) of Reproducibility in the unfolding process of protein induced by an external electric field

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A hydrophobic ratchet entrenches molecular complexes

Hochberg, Georg K. A.; Liu, Yang; Marklund, Erik; Metzger, Brian P. H. et al.

Part of Nature, p. 503-508, 2020.

DOI for A hydrophobic ratchet entrenches molecular complexes
Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology

Allison, Timothy M.; Barran, Perdita; Cianférani, Sarah; Degiacomi, Matteo T. et al.

Part of Analytical Chemistry, p. 10872-10880, 2020.

DOI for Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology
MkVsites: A tool for creating GROMACS virtual sites parameters to increase performance in all-atom molecular dynamics simulations.

Larsson, Per; Kneiszl, Rosita C.; Marklund, Erik

Part of Journal of Computational Chemistry, p. 1564-1569, 2020.

DOI for MkVsites: A tool for creating GROMACS virtual sites parameters to increase performance in all-atom molecular dynamics simulations.
Predicting the Shapes of Protein Complexes through Collision Cross Section Measurements and Database Searches

Landreh, Michael; Sahin, Cagla; Gault, Joseph; Sadeghi, Samira et al.

Part of Analytical Chemistry, p. 12297-12303, 2020.

DOI for Predicting the Shapes of Protein Complexes through Collision Cross Section Measurements and Database Searches
Software Requirements for the Analysis and Interpretation of Native Ion Mobility Mass Spectrometry Data

Allison, Timothy M.; Barran, Perdita; Benesch, Justin L. P.; Cianférani, Sarah et al.

Part of Analytical Chemistry, p. 10881-10890, 2020.

DOI for Software Requirements for the Analysis and Interpretation of Native Ion Mobility Mass Spectrometry Data
Structural Heterogeneity in Single Particle Imaging Using X-ray Lasers

Mandl, Thomas; Östlin, Christofer; Dawod, Ibrahim E.; Brodmerkel, Maxim N. et al.

Part of Journal of Physical Chemistry Letters, p. 6077-6083, 2020.

DOI for Structural Heterogeneity in Single Particle Imaging Using X-ray Lasers Download full text (pdf) of Structural Heterogeneity in Single Particle Imaging Using X-ray Lasers

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Gas-Phase Collisions with Trimethylamine-N-Oxide Enable Activation-Controlled Protein Ion Charge Reduction

Kaldmäe, Margit; Österlund, Nicklas; Lianoudaki, Danai; Sahin, Cagla et al.

Part of Journal of the American Society for Mass Spectrometry, p. 1385-1388, 2019.

DOI for Gas-Phase Collisions with Trimethylamine-N-Oxide Enable Activation-Controlled Protein Ion Charge Reduction Download full text (pdf) of Gas-Phase Collisions with Trimethylamine-N-Oxide Enable Activation-Controlled Protein Ion Charge Reduction

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Weighing-up protein dynamics: the combination of native mass spectrometry and molecular dynamics simulations

Marklund, Erik; Benesch, Justin L. P.

Part of Current opinion in structural biology, p. 50-58, 2019.

DOI for Weighing-up protein dynamics: the combination of native mass spectrometry and molecular dynamics simulations Download full text (pdf) of Weighing-up protein dynamics: the combination of native mass spectrometry and molecular dynamics simulations

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A strategy for the identification of protein architectures directly from ion mobility mass spectrometry data reveals stabilizing subunit interactions in light harvesting complexes

Kaldmae, Margit; Sahin, Cagla; Saluri, Mihkel; Marklund, Erik et al.

Part of Protein Science, p. 1024-1030, 2019.

DOI for A strategy for the identification of protein architectures directly from ion mobility mass spectrometry data reveals stabilizing subunit interactions in light harvesting complexes Download full text (pdf) of A strategy for the identification of protein architectures directly from ion mobility mass spectrometry data reveals stabilizing subunit interactions in light harvesting complexes

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Bringing Molecular Dynamics and Ion-Mobility Spectrometry Closer Together: Shape Correlations, Structure-Based Predictors, and Dissociation

Kulesza, Alexander; Marklund, Erik; MacAleese, Luke; Chirot, Fabien et al.

Part of Journal of Physical Chemistry B, p. 8317-8329, 2018.

DOI for Bringing Molecular Dynamics and Ion-Mobility Spectrometry Closer Together: Shape Correlations, Structure-Based Predictors, and Dissociation
Mass Spectrometry Reveals the Direct Action of a Chemical Chaperone

Gault, Joseph; Lianoudaki, Danai; Kaldmäe, Margit; Kronqvist, Nina et al.

Part of Journal of Physical Chemistry Letters, p. 4082-4086, 2018.

DOI for Mass Spectrometry Reveals the Direct Action of a Chemical Chaperone Download full text (pdf) of Mass Spectrometry Reveals the Direct Action of a Chemical Chaperone

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Quantitative mass imaging of single biological macromolecules

Young, Gavin; Hundt, Nikolas; Cole, Daniel; Fineberg, Adam et al.

Part of Science, p. 423-427, 2018.

DOI for Quantitative mass imaging of single biological macromolecules
Structural and functional aspects of the interaction partners of the small heat-shock protein in Synechocystis

Marklund, Erik G.; Zhang, Yichen; Basha, Eman; Benesch, Justin L P et al.

Part of Cell stress & chaperones (Print), p. 723-732, 2018.

DOI for Structural and functional aspects of the interaction partners of the small heat-shock protein in Synechocystis Download full text (pdf) of Structural and functional aspects of the interaction partners of the small heat-shock protein in Synechocystis

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Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions.

Hochberg, Georg K A; Shepherd, Dale A; Marklund, Erik G.; Santhanagoplan, Indu et al.

Part of Science, p. 930-935, 2018.

DOI for Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions.
Fundamentals of ion mobility spectrometry

Gabelica, Valérie; Marklund, Erik

Part of Current opinion in chemical biology, p. 51-59, 2018.

DOI for Fundamentals of ion mobility spectrometry
Lipids Shape the Electron Acceptor-Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase

Costeira-Paulo, Joana; Gault, Joseph; Popova, Gergana; Ladds, Marcus J G W et al.

Part of Cell Chemical Biology, p. 309-317, 2018.

DOI for Lipids Shape the Electron Acceptor-Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase Download full text (pdf) of Lipids Shape the Electron Acceptor-Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase

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Controlling Protein Orientation in Vacuum Using Electric Fields

Marklund, Erik; Ekeberg, Tomas; Moog, Mathieu; Benesch, Justin L. P. et al.

Part of Journal of Physical Chemistry Letters, p. 4540-4544, 2017.

DOI for Controlling Protein Orientation in Vacuum Using Electric Fields Download full text (pdf) of Controlling Protein Orientation in Vacuum Using Electric Fields

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Effects of Detergent Micelles on Lipid Binding to Proteins in Electrospray Ionization Mass Spectrometry

Landreh, Michael; Costeira-Paulo, Joana; Gault, Joseph; Marklund, Erik et al.

Part of Analytical Chemistry, p. 7425-7430, 2017.

DOI for Effects of Detergent Micelles on Lipid Binding to Proteins in Electrospray Ionization Mass Spectrometry

Open access
Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters

Landreh, Michael; Marklund, Erik G; Uzdavinys, Povilas; Degiacomi, Matteo T. et al.

Part of Nature Communications, 2017.

DOI for Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters Download full text (pdf) of Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters

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Mass spectrometry captures structural intermediates in protein fiber self-assembly

Landreh, Michael; Andersson, Marlene; Marklund, Erik G.; Jia, Qiupin et al.

Part of Chemical Communications, p. 3319-3322, 2017.

DOI for Mass spectrometry captures structural intermediates in protein fiber self-assembly
A hydrodynamic comparison of solution and gas phase proteins and their complexes.

Hewitt, Dominic; Marklund, Erik; Scott, David J; Robinson, Carol V et al.

Part of Journal of Physical Chemistry B, 2014.

DOI for A hydrodynamic comparison of solution and gas phase proteins and their complexes.
Collision cross sections for structural proteomics.

Marklund, Erik G; Degiacomi, Matteo T; Robinson, Carol V; Baldwin, Andrew J et al.

Part of Structure, 2015.

DOI for Collision cross sections for structural proteomics.
Molecular self-occlusion as a means for accelerating collision cross-section calculations

Marklund, Erik G.

Part of International Journal of Mass Spectrometry, p. 54-55, 2015.

DOI for Molecular self-occlusion as a means for accelerating collision cross-section calculations
Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models

Marklund, Erik G.; Mahmutovic, Anel; Berg, Otto G.; Hammar, Petter et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 19796-19801, 2013.

DOI for Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models
High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking

Ullman, Gustaf; Walldén, Mats; Marklund, Erik G.; Mahmutovic, Anel et al.

Part of Philosophical Transactions of the Royal Society of London. Biological Sciences, p. 20120025:1-8, 2013.

DOI for High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking
The lac repressor displays facilitated diffusion in living cells

Hammar, Petter; Leroy, Prune; Mahmutovic, Anel; Marklund, Erik G et al.

Part of Science, p. 1595-1598, 2012.

DOI for The lac repressor displays facilitated diffusion in living cells
Marklund, Erik

Gas-Phase Protein Structure Under the Computational Microscope: Hydration, Titration, and Temperature

2011.

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Proteins, Lipids, and Water in the Gas Phase

van der Spoel, David; Marklund, Erik G.; Larsson, Daniel S. D.; Caleman, Carl

Part of Macromolecular Bioscience, p. 50-59, 2011.

DOI for Proteins, Lipids, and Water in the Gas Phase
Structural stability of electrosprayed proteins: temperature and hydration effects

Marklund, Erik G.; Larsson, Daniel S. D.; van der Spoel, David; Patriksson, Alexandra et al.

Part of Physical Chemistry, Chemical Physics - PCCP, p. 8069-8078, 2009.

DOI for Structural stability of electrosprayed proteins: temperature and hydration effects
Formation of secondary electron cascades in single-crystalline plasma-deposited diamond upon exposure to femtosecond x-ray pulses

Gabrysch, Markus; Marklund, Erik; Hajdu, Janos; Twitchen, D. J. et al.

Part of Journal of Applied Physics, 2008.

DOI for Formation of secondary electron cascades in single-crystalline plasma-deposited diamond upon exposure to femtosecond x-ray pulses Download full text (pdf) of Formation of secondary electron cascades in single-crystalline plasma-deposited diamond upon exposure to femtosecond x-ray pulses

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Radiation damage in biological material: electronic properties and electron impact ionization in urea

Caleman, Carl; Ortiz, Carlos; Marklund, Erik; Bultmark, Fredrik et al.

Part of Europhysics letters, p. 18005-, 2009.

DOI for Radiation damage in biological material: electronic properties and electron impact ionization in urea Download full text (pdf) of Radiation damage in biological material: electronic properties and electron impact ionization in urea

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Single particle X-ray diffractive imaging

Bogan, Michael J; Benner, W Henry; Boutet, Sébastien; Rohner, Urs et al.

Part of Nano letters (Print), p. 310-6, 2008.

DOI for Single particle X-ray diffractive imaging
Proteins structures under electrospray conditions

Patriksson, Alexandra; Marklund, Erik; van der Spoel, David

Part of Biochemistry, p. 933-945, 2007.

DOI for Proteins structures under electrospray conditions