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Marklund, Erik, Teknologie doktorORCID iD iconorcid.org/0000-0002-9804-5009
Alternative names
Publications (10 of 49) Show all publications
Brodmerkel, M. N., De Santis, E., Uetrecht, C., Caleman, C. & Marklund, E. (2024). Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles. Physical Chemistry, Chemical Physics - PCCP
Open this publication in new window or tab >>Collision induced unfolding and molecular dynamics simulations of norovirus capsid dimers reveal strain-specific stability profiles
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2024 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084Article in journal (Refereed) Published
Abstract [en]

Collision induced unfolding is method used with ion mobility mass spectrometry to examine protein structures and their stability. Such experiments yield information about higher order protein structures, yet are unable to provide details about the underlying processes. That information can however be provided using molecular dynamics simulations. Here, we investigate the collision induced unfolding of norovirus capsid dimers from the Norwalk and Kawasaki strains by employing molecular dynamics simulations over a range of temperatures, representing different levels of activation. The dimers have highly similar structures, but the activation reveals differences in the dynamics that arises in response to the activation.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2024
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-500271 (URN)10.1039/D3CP06344E (DOI)
Funder
Swedish Research Council, 2021-05988Swedish Research Council, 2020-04825Swedish Research Council, 2018-00740Swedish National Infrastructure for Computing (SNIC), 2022-22-854Swedish National Infrastructure for Computing (SNIC), 2022-22-925Swedish National Infrastructure for Computing (SNIC), 2022-22-947Swedish National Infrastructure for Computing (SNIC), 2022-5-415Swedish National Infrastructure for Computing (SNIC), 2022-23-57EU, Horizon 2020, 801406
Available from: 2023-04-13 Created: 2023-04-13 Last updated: 2024-04-11Bibliographically approved
Sendker, F. L., Lo, Y. K., Heimerl, T., Bohn, S., Persson, L. J., Mais, C.-N., . . . Hochberg, G. K. A. (2024). Emergence of fractal geometries in the evolution of a metabolic enzyme. Nature, 628(8009), 894-900
Open this publication in new window or tab >>Emergence of fractal geometries in the evolution of a metabolic enzyme
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2024 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 628, no 8009, p. 894-900Article in journal (Refereed) Published
Abstract [en]

Fractals are patterns that are self-similar across multiple length-scales1. Macroscopic fractals are common in nature2,3,4; however, so far, molecular assembly into fractals is restricted to synthetic systems5,6,7,8,9,10,11,12. Here we report the discovery of a natural protein, citrate synthase from the cyanobacterium Synechococcus elongatus, which self-assembles into Sierpiński triangles. Using cryo-electron microscopy, we reveal how the fractal assembles from a hexameric building block. Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident. Our findings expand the space of possible protein complexes and demonstrate that intricate and regulatable assemblies can evolve in a single substitution.

Place, publisher, year, edition, pages
Springer Nature, 2024
National Category
Biochemistry and Molecular Biology Evolutionary Biology Structural Biology
Research subject
Biochemistry; Biology with specialization in Molecular Evolution; Biology with specialization in Structural Biology
Identifiers
urn:nbn:se:uu:diva-529611 (URN)10.1038/s41586-024-07287-2 (DOI)001201403000010 ()38600380 (PubMedID)
Funder
Swedish Research Council, 2020-04825Max Planck SocietyGerman Research Foundation (DFG), Fo195/16-2EU, European Research Council, 101040472EU, European Research Council, 101075992EU, European Research Council, 101019765
Available from: 2024-05-29 Created: 2024-05-29 Last updated: 2024-05-30Bibliographically approved
Wollter, A., De Santis, E., Ekeberg, T., Marklund, E. G. & Caleman, C. (2024). Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging. Journal of Chemical Physics, 160(11), Article ID 114108.
Open this publication in new window or tab >>Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging
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2024 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 160, no 11, article id 114108Article in journal (Refereed) Published
Abstract [en]

Single particle imaging of proteins in the gas phase with x-ray free-electron lasers holds great potential to study fast protein dynamics, but is currently limited by weak and noisy data. A further challenge is to discover the proteins' orientation as each protein is randomly oriented when exposed to x-rays. Algorithms such as the expand, maximize, and compress (EMC) exist that can solve the orientation problem and reconstruct the three-dimensional diffraction intensity space, given sufficient measurements. If information about orientation were known, for example, by using an electric field to orient the particles, the reconstruction would benefit and potentially reach better results. We used simulated diffraction experiments to test how the reconstructions from EMC improve with particles' orientation to a preferred axis. Our reconstructions converged to correct maps of the three-dimensional diffraction space with fewer measurements if biased orientation information was considered. Even for a moderate bias, there was still significant improvement. Biased orientations also substantially improved the results in the case of missing central information, in particular in the case of small datasets. The effects were even more significant when adding a background with 50% the strength of the averaged diffraction signal photons to the diffraction patterns, sometimes reducing the data requirement for convergence by a factor of 10. This demonstrates the usefulness of having biased orientation information in single particle imaging experiments, even for a weaker bias than what was previously known. This could be a key component in overcoming the problems with background noise that currently plague these experiments.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2024
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-528478 (URN)10.1063/5.0188772 (DOI)001187986000015 ()38506290 (PubMedID)
Funder
EU, Horizon 2020, 801406EU, Horizon 2020, 101120312Swedish Research Council, 2020-04825Swedish Research Council, 2018-00740Swedish Foundation for Strategic Research, ITM17-0455Swedish Research Council, 2017-05336
Available from: 2024-05-23 Created: 2024-05-23 Last updated: 2024-05-23Bibliographically approved
Kierspel, T., Kadek, A., Barran, P., Bellina, B., Bijedic N, A., Brodmerkel, M. N., . . . Uetrecht, C. (2023). Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC. Analytical and Bioanalytical Chemistry, 415(18 SI), 4209-4220
Open this publication in new window or tab >>Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC
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2023 (English)In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 415, no 18 SI, p. 4209-4220Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Springer Nature, 2023
Keywords
SPI, X-ray, Native MS, Protein complex structure, Viral particles, Simulation, Modeling
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-500359 (URN)10.1007/s00216-023-04658-y (DOI)000963181300001 ()37014373 (PubMedID)
Funder
Swedish Research Council, 2018-00740Swedish Research Council, 2020-04825EU, Horizon 2020, 801406
Available from: 2023-04-14 Created: 2023-04-14 Last updated: 2024-01-26Bibliographically approved
Cornelius Chukwu, E., Bartl, M., Persson, L. J., Xiong, R., Cederfelt, D., Rad, F. M., . . . Widersten, M. (2023). Engineered Aldolases Catalyzing Stereoselective Aldol Reactions Between Aryl-Substituted Ketones and Aldehydes. Catalysis Science & Technology
Open this publication in new window or tab >>Engineered Aldolases Catalyzing Stereoselective Aldol Reactions Between Aryl-Substituted Ketones and Aldehydes
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2023 (English)In: Catalysis Science & Technology, ISSN 2044-4753, E-ISSN 2044-4761Article in journal (Refereed) Epub ahead of print
Abstract [en]

An A129G/R134V/S166G triple mutant of fructose 6-phosphate aldolase (FSA) from Escherichia coli was further engineered with the goal to generate new enzyme variants capable of catalyzing aldol reactions between aryl substituted ketones and aldehydes. Residues L107 and L163 were subjected to saturation mutagenesis and the resulting library of FSA variants was screened for catalytic activity with 2-hydroxyacetophenone and phenylacetaldehyde as substrates. A selection of aldolase variants was identified that catalyze the synthesis of 2,3-dihydroxy-1,4-diphenylbutanone. The most active enzyme variants contained an L163C substitution. An L107C/L163C variant was further tested for activity with substituted phenylacetaldehydes, and was shown to afford the production of the corresponding diphenyl substituted butanones with good diastereoselectivities (anti : syn dr of 10 to 30) and reasonable to good enantioselectivities of syn enantiomers (er of 5 to 25).

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2023
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-508486 (URN)10.1039/d3cy00181d (DOI)
Funder
Olle Engkvists stiftelse, 194-0638Olle Engkvists stiftelse, 218-0061
Available from: 2023-08-02 Created: 2023-08-02 Last updated: 2023-08-04
Leppert, A., Chen, G., Lama, D., Sahin, C., Railaite, V., Shilkova, O., . . . Landreh, M. (2023). Liquid-Liquid Phase Separation Primes Spider Silk Proteins for Fiber Formation via a Conditional Sticker Domain [Letter to the editor]. Nano Letters, 23(12), 5836-5841
Open this publication in new window or tab >>Liquid-Liquid Phase Separation Primes Spider Silk Proteins for Fiber Formation via a Conditional Sticker Domain
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2023 (English)In: Nano Letters, ISSN 1530-6984, E-ISSN 1530-6992, Vol. 23, no 12, p. 5836-5841Article in journal, Letter (Other academic) Published
Abstract [en]

Many protein condensates can convert to fibrillar aggregates, but the underlying mechanisms are unclear. Liquid-liquid phase separation (LLPS) of spider silk proteins, spidroins, suggests a regulatory switch between both states. Here, we combine microscopy and native mass spectrometry to investigate the influence of protein sequence, ions, and regulatory domains on spidroin LLPS. We find that salting out-effects drive LLPS via low-affinity stickers in the repeat domains. Interestingly, conditions that enable LLPS simultaneously cause dissociation of the dimeric C-terminal domain (CTD), priming it for aggregation. Since the CTD enhances LLPS of spidroins but is also required for their conversion into amyloid-like fibers, we expand the stickers and spacers-model of phase separation with the concept of folded domains as conditional stickers that represent regulatory units.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2023
Keywords
Phase separation, native mass spectrometry, stickers and spacers-model, functional amyloid
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-513014 (URN)10.1021/acs.nanolett.3c00773 (DOI)000981134300001 ()37084706 (PubMedID)
Funder
Swedish Cancer Society, 190480Swedish Research Council, 2019-01961Swedish Research Council, 2013-08807Swedish Research Council, 815357EU, Horizon 2020, 2019-01257Swedish Research Council Formas, 2019-00427Swedish Research Council FormasSwedish Research Council
Available from: 2023-10-03 Created: 2023-10-03 Last updated: 2023-10-03Bibliographically approved
Sahin, C., Motso, A., Gu, X., Feyrer, H., Lama, D., Arndt, T., . . . Landreh, M. (2023). Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures. Journal of the American Chemical Society, 145(19), 10659-10668
Open this publication in new window or tab >>Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures
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2023 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 145, no 19, p. 10659-10668Article in journal (Refereed) Published
Abstract [en]

Liquid-liquid phase separation (LLPS) of hetero-geneous ribonucleoproteins (hnRNPs) drives the formation of membraneless organelles, but structural information about their assembled states is still lacking. Here, we address this challenge through a combination of protein engineering, native ion mobility mass spectrometry, and molecular dynamics simulations. We used an LLPS-compatible spider silk domain and pH changes to control the self-assembly of the hnRNPs FUS, TDP-43, and hCPEB3, which are implicated in neurodegeneration, cancer, and memory storage. By releasing the proteins inside the mass spectrometer from their native assemblies, we could monitor conformational changes associated with liquid-liquid phase separation. We find that FUS monomers undergo an unfolded-to-globular transition, whereas TDP-43 oligomerizes into partially disordered dimers and trimers. hCPEB3, on the other hand, remains fully disordered with a preference for fibrillar aggregation over LLPS. The divergent assembly mechanisms revealed by ion mobility mass spectrometry of soluble protein species that exist under LLPS conditions suggest structurally distinct complexes inside liquid droplets that may impact RNA processing and translation depending on biological context.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2023
National Category
Biochemistry and Molecular Biology Biophysics
Identifiers
urn:nbn:se:uu:diva-511712 (URN)10.1021/jacs.3c00932 (DOI)000986603500001 ()37145883 (PubMedID)
Funder
Swedish Research CouncilEU, European Research CouncilSwedish Research Council FormasKnut and Alice Wallenberg Foundation, NNF19OC0055700Swedish Foundation for Strategic Research, 815357Swedish Foundation for Strategic Research, 2019-00427Swedish Cancer Society, CHE-1743392Swedish Cancer Society, PHY-2019745Swedish Research Council, C-0016Swedish Research Council Formas
Available from: 2023-09-28 Created: 2023-09-28 Last updated: 2023-09-28Bibliographically approved
Brodmerkel, M. N., De Santis, E., Caleman, C. & Marklund, E. (2023). Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration. The Protein Journal, 42(3), 205-218
Open this publication in new window or tab >>Rehydration Post-orientation: Investigating Field-Induced Structural Changes via Computational Rehydration
2023 (English)In: The Protein Journal, ISSN 1572-3887, E-ISSN 1875-8355, Vol. 42, no 3, p. 205-218Article in journal (Refereed) Published
Abstract [en]

Proteins can be oriented in the gas phase using strong electric fields, which brings advantages for structure determination using X-ray free electron lasers. Both the vacuum conditions and the electric-field exposure risk damaging the protein structures. Here, we employ molecular dynamics simulations to rehydrate and relax vacuum and electric-field exposed proteins in aqueous solution, which simulates a refinement of structure models derived from oriented gas-phase proteins. We find that the impact of the strong electric fields on the protein structures is of minor importance after rehydration, compared to that of vacuum exposure and ionization in electrospraying. The structures did not fully relax back to their native structure in solution on the simulated timescales of 200 ns, but they recover several features, including native-like intra-protein contacts, which suggests that the structures remain in a state from which the fully native structure is accessible. Our fndings imply that the electric fields used in native mass spectrometry are well below a destructive level, and suggest that structures inferred from X-ray difraction from gas-phase proteins are relevant for solution and in vivo conditions, at least after in silico rehydration.

Place, publisher, year, edition, pages
Springer Nature, 2023
Keywords
Molecular dynamics simulation, Protein hydration, Electric dipole, Protein structure, Structural biology, X-rays
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-499999 (URN)10.1007/s10930-023-10110-y (DOI)000966256600001 ()37031302 (PubMedID)
Funder
Swedish Research Council, 2020-04825Swedish Research Council, 2018-00740Swedish Research Council, 2021-05988EU, Horizon 2020, 801406
Available from: 2023-04-10 Created: 2023-04-10 Last updated: 2023-08-15Bibliographically approved
Allison, T. M., Degiacomi, M. T., Marklund, E., Jovine, L., Elofsson, A., Benesch, J. L. P. & Landreh, M. (2022). Complementing machine learning‐based structure predictions with native mass spectrometry. Protein Science, 31(6), Article ID e4333.
Open this publication in new window or tab >>Complementing machine learning‐based structure predictions with native mass spectrometry
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2022 (English)In: Protein Science, ISSN 0961-8368, E-ISSN 1469-896X, Vol. 31, no 6, article id e4333Article in journal (Refereed) Published
Abstract [en]

The advent of machine learning-based structure prediction algorithms such as AlphaFold2 (AF2) and RoseTTa Fold have moved the generation of accurate structural models for the entire cellular protein machinery into the reach of the scientific community. However, structure predictions of protein complexes are based on user-provided input and may require experimental validation. Mass spectrometry (MS) is a versatile, time-effective tool that provides information on post-translational modifications, ligand interactions, conformational changes, and higher-order oligomerization. Using three protein systems, we show that native MS experiments can uncover structural features of ligand interactions, homology models, and point mutations that are undetectable by AF2 alone. We conclude that machine learning can be complemented with MS to yield more accurate structural models on a small and large scale.

Place, publisher, year, edition, pages
John Wiley & SonsWiley, 2022
Keywords
integrative modeling, machine learning, protein structure prediction, structural proteomics
National Category
Biophysics Biochemistry and Molecular Biology Structural Biology Analytical Chemistry
Research subject
Chemistry with specialization in Biophysics; Biochemistry; Biology with specialization in Structural Biology; Chemistry with specialization in Analytical Chemistry
Identifiers
urn:nbn:se:uu:diva-474742 (URN)10.1002/pro.4333 (DOI)000798697700001 ()35634779 (PubMedID)
Funder
Swedish Cancer Society, 19 0480Swedish Research Council, 2019-01961
Available from: 2022-05-21 Created: 2022-05-21 Last updated: 2024-01-15Bibliographically approved
Yen, H.-Y., Abramsson, M. L., Agasid, M. T., Lama, D., Gault, J., Liko, I., . . . Landreh, M. (2022). Electrospray ionization of native membrane proteins proceeds via a charge equilibration step. RSC Advances, 12(16), 9671-9680
Open this publication in new window or tab >>Electrospray ionization of native membrane proteins proceeds via a charge equilibration step
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2022 (English)In: RSC Advances, E-ISSN 2046-2069, Vol. 12, no 16, p. 9671-9680Article in journal (Refereed) Published
Abstract [en]

Electrospray ionization mass spectrometry is increasingly applied to study the structures and interactions of membrane protein complexes. However, the charging mechanism is complicated by the presence of detergent micelles during ionization. Here, we show that the final charge of membrane proteins can be predicted by their molecular weight when released from the non-charge reducing saccharide detergents. Our data indicate that PEG detergents lower the charge depending on the number of detergent molecules in the surrounding micelle, whereas fos-choline detergents may additionally participate in ion-ion reactions after desolvation. The supercharging reagent sulfolane, on the other hand, has no discernible effect on the charge of detergent-free membrane proteins. Taking our observations into the context of protein-detergent interactions in the gas phase, we propose a charge equilibration model for the generation of native-like membrane protein ions. During ionization of the protein-detergent complex, the ESI charges are distributed between detergent and protein according to proton affinity of the detergent, number of detergent molecules, and surface area of the protein. Charge equilibration influenced by detergents determines the final charge state of membrane proteins. This process likely contributes to maintaining a native-like fold after detergent release and can be harnessed to stabilize particularly labile membrane protein complexes in the gas phase.

Place, publisher, year, edition, pages
Royal Society of Chemistry (RSC), 2022
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-472942 (URN)10.1039/d2ra01282k (DOI)000776649200001 ()35424940 (PubMedID)
Funder
Swedish Foundation for Strategic Research Swedish Cancer Society, 190480Swedish Research Council, 2019-01961Swedish Research Council, 2019-02433_VRSwedish Research Council, 2013-08807EU, Horizon 2020, 801406
Available from: 2022-04-20 Created: 2022-04-20 Last updated: 2022-09-15Bibliographically approved
Projects
Computations for structural mass spectrometry [2015-00559_VR]; Uppsala UniversityComputations for interrogating protein complex architecture [2020-04825_VR]; Uppsala University; Publications
Sendker, F. L., Lo, Y. K., Heimerl, T., Bohn, S., Persson, L. J., Mais, C.-N., . . . Hochberg, G. K. A. (2024). Emergence of fractal geometries in the evolution of a metabolic enzyme. Nature, 628(8009), 894-900
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ORCID iD: ORCID iD iconorcid.org/0000-0002-9804-5009

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