Marklund Group

Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles

Brodmerkel, Maxim N.; De Santis, Emiliano; Uetrecht, Charlotte; Caleman, Carl et al.

Part of Physical Chemistry, Chemical Physics - PCCP, 2024

• DOI for Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles

Emergence of fractal geometries in the evolution of a metabolic enzyme

Sendker, Franziska L.; Lo, Yat Kei; Heimerl, Thomas; Bohn, Stefan et al.

Part of Nature, p. 894-900, 2024

• DOI for Emergence of fractal geometries in the evolution of a metabolic enzyme
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Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging

Wollter, August; De Santis, Emiliano; Ekeberg, Tomas; Marklund, Erik G. et al.

Part of Journal of Chemical Physics, 2024

• DOI for Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging
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High-Performance Molecular Dynamics Simulations for Native Mass Spectrometry of Large Protein Complexes with the Fast Multipole Method

Persson, Louise; Sahin, Cagla; Landreh, Michael; Marklund, Erik

Part of Analytical Chemistry, p. 15023-15030, 2024

• DOI for High-Performance Molecular Dynamics Simulations for Native Mass Spectrometry of Large Protein Complexes with the Fast Multipole Method
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Engineered Aldolases Catalyzing Stereoselective Aldol Reactions Between Aryl-Substituted Ketones and Aldehydes

Cornelius Chukwu, Eugenia; Bartl, Michael; Persson, Louise J.; Xiong, Ruisheng et al.

Part of Catalysis Science & Technology, 2023

• DOI for Engineered Aldolases Catalyzing Stereoselective Aldol Reactions Between Aryl-Substituted Ketones and Aldehydes
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Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration

Brodmerkel, Maxim N.; De Santis, Emiliano; Caleman, Carl; Marklund, Erik

Part of The Protein Journal, p. 205-218, 2023

• DOI for Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration
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Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures

Sahin, Cagla; Motso, Aikaterini; Gu, Xinyu; Feyrer, Hannes et al.

Part of Journal of the American Chemical Society, p. 10659-10668, 2023

• DOI for Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures
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Liquid-Liquid Phase Separation Primes Spider Silk Proteins for Fiber Formation via a Conditional Sticker Domain

Leppert, Axel; Chen, Gefei; Lama, Dilraj; Sahin, Cagla et al.

Part of Nano Letters, p. 5836-5841, 2023

• DOI for Liquid-Liquid Phase Separation Primes Spider Silk Proteins for Fiber Formation via a Conditional Sticker Domain
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Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC

Kierspel, Thomas; Kadek, Alan; Barran, Perdita; Bellina, Bruno et al.

Part of Analytical and Bioanalytical Chemistry, p. 4209-4220, 2023

• DOI for Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC
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Structural Basis for Dityrosine-Mediated Inhibition of α-Synuclein Fibrillization

Sahin, Cagla; Østerlund, Eva Christina; Österlund, Nicklas; Costeira-Paulo, Joana et al.

Part of Journal of the American Chemical Society, p. 11949-11954, 2022

• DOI for Structural Basis for Dityrosine-Mediated Inhibition of α-Synuclein Fibrillization
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Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins

Brodmerkel, Maxim N.; De Santis, Emiliano; Uetrecht, Charlotte; Caleman, Carl et al.

Part of Current Research in Structural Biology, p. 338-348, 2022

• DOI for Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins
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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
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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
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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
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CCS for Modelling 3D Structures

Marklund, Erik G.; Degiacomi, Matteo T.; Politis, Argyris; Landreh, Michael

Part of Ion Mobility-Mass Spectrometry, p. 183-205, Royal Society of Chemistry, 2021

• DOI for CCS for Modelling 3D Structures

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

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

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

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

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
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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
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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
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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

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.

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

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

Structural Heterogeneity in Single Particle Imaging Using X-ray Lasers

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

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

• DOI for Structural Heterogeneity in Single Particle Imaging Using X-ray Lasers
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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
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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
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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
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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

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

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

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
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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
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Mass Spectrometry Reveals the Direct Action of a Chemical Chaperone

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

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

• DOI for Mass Spectrometry Reveals the Direct Action of a Chemical Chaperone
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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

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

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

• DOI for Controlling Protein Orientation in Vacuum Using Electric Fields
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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

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.

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, 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

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

Marklund, Erik

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

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
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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