Search Results - "Marklund, Erik. G."

Collision Cross Sections for Structural Proteomics by Marklund, Erik G., Degiacomi, Matteo T., Robinson, Carol V., Baldwin, Andrew J., Benesch, Justin L.P.

“…Ion mobility mass spectrometry (IM-MS) allows the structural interrogation of biomolecules by reporting their collision cross sections (CCSs). The major…”
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Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles by Marty, Michael T, Baldwin, Andrew J, Marklund, Erik G, Hochberg, Georg K. A, Benesch, Justin L. P, Robinson, Carol V

“…Interpretation of mass spectra is challenging because they report a ratio of two physical quantities, mass and charge, which may each have multiple components…”
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Quantitative mass imaging of single biological macromolecules by Young, Gavin, Hundt, Nikolas, Cole, Daniel, Fineberg, Adam, Andrecka, Joanna, Tyler, Andrew, Olerinyova, Anna, Ansari, Ayla, Marklund, Erik G, Collier, Miranda P, Chandler, Shane A, Tkachenko, Olga, Allen, Joel, Crispin, Max, Billington, Neil, Takagi, Yasuharu, Sellers, James R, Eichmann, Cédric, Selenko, Philipp, Frey, Lukas, Riek, Roland, Galpin, Martin R, Struwe, Weston B, Benesch, Justin L P, Kukura, Philipp

“…The cellular processes underpinning life are orchestrated by proteins and their interactions. The associated structural and dynamic heterogeneity, despite…”
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MkVsites: A tool for creating GROMACS virtual sites parameters to increase performance in all‐atom molecular dynamics simulations by Larsson, Per, Kneiszl, Rosita C., Marklund, Erik G.

“…The absolute performance of any all‐atom molecular dynamics simulation is typically limited by the length of the individual timesteps taken when integrating…”
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Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters by Landreh, Michael, Marklund, Erik G., Uzdavinys, Povilas, Degiacomi, Matteo T., Coincon, Mathieu, Gault, Joseph, Gupta, Kallol, Liko, Idlir, Benesch, Justin L. P., Drew, David, Robinson, Carol V.

“…Na + /H + antiporters are found in all kingdoms of life and exhibit catalysis rates that are among the fastest of all known secondary-active transporters. Here…”
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Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology by Allison, Timothy M, Barran, Perdita, Cianférani, Sarah, Degiacomi, Matteo T, Gabelica, Valérie, Grandori, Rita, Marklund, Erik G, Menneteau, Thomas, Migas, Lukasz G, Politis, Argyris, Sharon, Michal, Sobott, Frank, Thalassinos, Konstantinos, Benesch, Justin L. P

“…Native mass spectrometry (MS) allows the interrogation of structural aspects of macromolecules in the gas phase, under the premise of having initially…”
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Mass Spectrometry of RNA-Binding Proteins during Liquid–Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures by Sahin, Cagla, Motso, Aikaterini, Gu, Xinyu, Feyrer, Hannes, Lama, Dilraj, Arndt, Tina, Rising, Anna, Gese, Genis Valentin, Hällberg, B. Martin, Marklund, Erik. G., Schafer, Nicholas P., Petzold, Katja, Teilum, Kaare, Wolynes, Peter G., Landreh, Michael

“…Liquid–liquid phase separation (LLPS) of heterogeneous ribonucleoproteins (hnRNPs) drives the formation of membraneless organelles, but structural information…”
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Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models by Marklund, Erik G., Mahmutovic, Anel, Berg, Otto G., Hammar, Petter, van der Spoel, David, Fange, David, Elf, Johan

“…Transcription factors search for specific operator sequences by alternating rounds of 3D diffusion with rounds of 1D diffusion (sliding) along the DNA. The…”
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Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status by Dülfer, Jasmin, Yan, Hao, Brodmerkel, Maxim N, Creutznacher, Robert, Mallagaray, Alvaro, Peters, Thomas, Caleman, Carl, Marklund, Erik G, Uetrecht, Charlotte

“…Noroviruses are the major cause of viral gastroenteritis and re-emerge worldwide every year, with GII.4 currently being the most frequent human genotype. The…”
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Controlling Protein Orientation in Vacuum Using Electric Fields by Marklund, Erik G, Ekeberg, Tomas, Moog, Mathieu, Benesch, Justin L. P, Caleman, Carl

“…Single-particle imaging using X-ray free-electron lasers is an emerging technique that could provide high-resolution structures of macromolecules in the gas…”
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Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins by Brodmerkel, Maxim N., De Santis, Emiliano, Uetrecht, Charlotte, Caleman, Carl, Marklund, Erik G.

“…Proteins are innately dynamic, which is important for their functions, but which also poses significant challenges when studying their structures. Gas-phase…”
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Structural stability of electrosprayed proteins: temperature and hydration effects by Marklund, Erik G, Larsson, Daniel S D, van der Spoel, David, Patriksson, Alexandra, Caleman, Carl

“…Electrospray ionization is a gentle method for sample delivery, routinely used in gas-phase studies of proteins. It is crucial for structural investigations…”
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Charge Engineering Reveals the Roles of Ionizable Side Chains in Electrospray Ionization Mass Spectrometry by Abramsson, Mia L, Sahin, Cagla, Hopper, Jonathan T. S, Branca, Rui M. M, Danielsson, Jens, Xu, Mingming, Chandler, Shane A, Österlund, Nicklas, Ilag, Leopold L, Leppert, Axel, Costeira-Paulo, Joana, Lang, Lisa, Teilum, Kaare, Laganowsky, Arthur, Benesch, Justin L. P, Oliveberg, Mikael, Robinson, Carol V, Marklund, Erik G, Allison, Timothy M, Winther, Jakob R, Landreh, Michael

“…In solution, the charge of a protein is intricately linked to its stability, but electrospray ionization distorts this connection, potentially limiting the…”
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The lac Repressor Displays Facilitated Diffusion in Living Cells by Hammar, Petter, Leroy, Prune, Mahmutovic, Anel, Marklund, Erik G., Berg, Otto G., Elf, Johan

“…Transcription factors (TFs) are proteins that regulate the expression of genes by binding sequence-specific sites on the chromosome. It has been proposed that…”
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Weighing-up protein dynamics: the combination of native mass spectrometry and molecular dynamics simulations by Marklund, Erik G, Benesch, Justin LP

“…•Native mass spectrometry provides coarse structural and dynamics information.•Molecular dynamics simulations operate at the atomic level.•Integrating these…”
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A hydrophobic ratchet entrenches molecular complexes by Hochberg, Georg K. A., Liu, Yang, Marklund, Erik G., Metzger, Brian P. H., Laganowsky, Arthur, Thornton, Joseph W.

“…Most proteins assemble into multisubunit complexes 1 . The persistence of these complexes across evolutionary time is usually explained as the result of…”
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High-Performance Molecular Dynamics Simulations for Native Mass Spectrometry of Large Protein Complexes with the Fast Multipole Method by Persson, Louise J., Sahin, Cagla, Landreh, Michael, Marklund, Erik G.

“…Native mass spectrometry (MS) is widely employed to study the structures and assemblies of proteins ranging from small monomers to megadalton complexes…”
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Bringing Molecular Dynamics and Ion-Mobility Spectrometry Closer Together: Shape Correlations, Structure-Based Predictors, and Dissociation by Kulesza, Alexander, Marklund, Erik G, MacAleese, Luke, Chirot, Fabien, Dugourd, Philippe

“…Unfolding of proteins gives detailed information about their structure and energetics and can be probed as a response to a change of experimental conditions…”
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Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles by Brodmerkel, Maxim N, Thiede, Lars, De Santis, Emiliano, Uetrecht, Charlotte, Caleman, Carl, Marklund, Erik G

“…Collision induced unfolding (CIU) is a method used with ion mobility mass spectrometry to examine protein structures and their stability. Such experiments…”
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Protein orientation in time-dependent electric fields: orientation before destruction by Sinelnikova, Anna, Mandl, Thomas, Agelii, Harald, Grånäs, Oscar, Marklund, Erik G., Caleman, Carl, De Santis, Emiliano

“…Proteins often have nonzero electric dipole moments, making them interact with external electric fields and offering a means for controlling their orientation…”
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