Mikael Akke

2024

Interplay of halogen bonding and solvation in protein-ligand binding

Verteramo, M. L., Ignjatović, M. M., Kumar, R., Wernersson, S., Ekberg, V., Wallerstein, J., Carlström, G., Chadimová, V., Leffler, H., Zetterberg, F., Logan, D. T., Ryde, U., Akke, M. & Nilsson, U. J., 2024 Apr 19, In: iScience. 27, 4, 109636.

Research output: Contribution to journal › Article › peer-review

Open Access

Ligand-induced protein transition state stabilization switches the binding pathway from conformational selection to induced fit

Stenström, O., Diehl, C., Modig, K. & Akke, M., 2024 Apr 2, In: Proceedings of the National Academy of Sciences of the United States of America. 121, 14, p. e2317747121

Research output: Contribution to journal › Article › peer-review

Open Access

2023

Flexibility and Function of Distal Substrate-Binding Tryptophans in the Blue Mussel β-Mannanase MeMan5A and Their Role in Hydrolysis and Transglycosylation

Birgersson, S., Morrill, J., Stenström, O., Wiemann, M., Weininger, U., Söderhjelm, P., Akke, M. & Stålbrand, H., 2023 Sept, In: Catalysts. 13, 9, 1281.

Research output: Contribution to journal › Article › peer-review

Open Access

Conformational Dynamics of Phytoglobin BvPgb1.2 from Beta vulgaris ssp. vulgaris

Christensen, S., Stenström, O., Akke, M. & Bülow, L., 2023 Feb, In: International Journal of Molecular Sciences. 24, 4, 3973.

Research output: Contribution to journal › Article › peer-review

Open Access

Cosolvent Dimethyl Sulfoxide Influences Protein-Ligand Binding Kinetics via Solvent Viscosity Effects: Revealing the Success Rate of Complex Formation Following Diffusive Protein-Ligand Encounter

Wernersson, S., Birgersson, S. & Akke, M., 2023 Jan 3, In: Biochemistry. 62, 1, p. 44-52 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2022

Bromodomain Interactions with Acetylated Histone 4 Peptides in the BRD4 Tandem Domain: Effects on Domain Dynamics and Internal Flexibility

Wernersson, S., Bobby, R., Flavell, L., Milbradt, A. G., Holdgate, G. A., Embrey, K. J. & Akke, M., 2022 Nov 1, In: Biochemistry. 61, 21, p. 2303-2318 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Characterizing Fast Conformational Exchange of Aromatic Rings Using Residual Dipolar Couplings: Distinguishing Jumplike Flips from Other Exchange Mechanisms

Dreydoppel, M., Akke, M. & Weininger, U., 2022 Oct 13, In: Journal of Physical Chemistry B. 126, 40, p. 7950-7956 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2021

Transition-State Compressibility and Activation Volume of Transient Protein Conformational Fluctuations

Dreydoppel, M., Dorn, B., Modig, K., Akke, M. & Weininger, U., 2021 Jun 3, In: JACS Au. 1, 6, p. 833-842 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

¹H R_1ρ relaxation dispersion experiments in aromatic side chains

Dreydoppel, M., Lichtenecker, R. J., Akke, M. & Weininger, U., 2021, In: Journal of Biomolecular NMR. 75, 44846, p. 383-392

Research output: Contribution to journal › Article › peer-review

Open Access

Entropy–Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C

Wallerstein, J., Ekberg, V., Misini Ignjatović, M., Kumar, R., Caldararu, O., Peterson, K., Wernersson, S., Brath, U., Leffler, H., Oksanen, E., Logan, D. T., Nilsson, U. J., Ryde, U. & Akke, M., 2021, In: Journal of the American Chemical Society. 1, 4, p. 484–500 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Mapping the energy landscape of protein-ligand binding via linear free energy relationships determined by protein NMR relaxation dispersion

Stenström, O., Diehl, C., Modig, K., Nilsson, U. J. & Akke, M., 2021, In: RSC Chemical Biology. 2, 1, p. 259-265 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Rapid measurement of heteronuclear transverse relaxation rates using non-uniformly sampled R_1ρ accordion experiments

Wernersson, S., Carlström, G., Jakobsson, A. & Akke, M., 2021, In: Magnetic Resonance. 2, 2, p. 571-587 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Structural characterization of the microbial enzyme urocanate reductase mediating imidazole propionate production

Venskutonytė, R., Koh, A., Stenström, O., Khan, M. T., Lundqvist, A., Akke, M., Bäckhed, F. & Lindkvist-Petersson, K., 2021, In: Nature Communications. 12, 1, p. 1347

Research output: Contribution to journal › Article › peer-review

Open Access

2020

Accurate Backbone ¹³C and ¹⁵N Chemical Shift Tensors in Galectin-3 Determined by MAS NMR and QM/MM: Details of Structure and Environment Matter

Kraus, J., Gupta, R., Lu, M., Gronenborn, A. M., Akke, M. & Polenova, T., 2020 Jul 2, In: ChemPhysChem. 21, 13, p. 1436-1443 8 p.

Research output: Contribution to journal › Article › peer-review

Dynamic allosteric communication pathway directing differential activation of the glucocorticoid receptor

Köhler, C., Carlström, G., Gunnarsson, A., Weininger, U., Tångefjord, S., Ullah, V., Lepistö, M., Karlsson, U., Papavoine, T., Edman, K. & Akke, M., 2020 Jul 1, In: Science Advances. 6, 29, eabb5277.

Research output: Contribution to journal › Article › peer-review

Open Access

Ultrastructural evidence for self-replication of alzheimer-associated Aβ42 amyloid along the sides of fibrils

Tornquist, M., Cukalevski, R., Weininger, U., Meisl, G., Knowles, T. P. J., Leiding, T., Malmendal, A., Akke, M. & Linse, S., 2020 May 26, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 21, p. 11265-11273 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2019

Revealing Well-Defined Soluble States during Amyloid Fibril Formation by Multilinear Analysis of NMR Diffusion Data

Jensen, K. S., Linse, S., Nilsson, M., Akke, M. & Malmendal, A., 2019 Nov 27, In: Journal of the American Chemical Society. 141, 47, p. 18649−18652 4 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Rotamer jumps, proton exchange, and amine inversion dynamics of dimethylated lysine residues in proteins resolved by ph-dependent ¹h and ¹³c nmr relaxation dispersion

Weininger, U., Modig, K., Ishida, H., Vogel, H. J. & Akke, M., 2019 Nov 21, In: Journal of Physical Chemistry B. 123, 46, p. 9742−9750 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Rapid NMR Relaxation Rate Measurements Using Optimal Non-Uniform Sampling of Multi-Dimensional Accordion Data Analyzed by a Sparse Reconstruction Method

Carlström, G., Elvander, F., Swärd, J., Jakobsson, A. & Akke, M., 2019 Jun 13, In: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. 123, 27, p. 5718-5723 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Adsorption of unfolded Cu/Zn superoxide dismutase onto hydrophobic surfaces catalyzes its formation of amyloid fibrils

Khan, A., Weininger, U., Kjellström, S., Deep, S. & Akke, M., 2019, In: Protein Engineering Design & Selection. 32, 2, p. 77–85

Research output: Contribution to journal › Article › peer-review

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Backbone ¹ H, ¹³ C, and ¹⁵ N resonance assignments of BoMan26A, a β-mannanase of the glycoside hydrolase family 26 from the human gut bacterium Bacteroides ovatus

Wernersson, S., Bågenholm, V., Persson, C., Upadhyay, S. K., Stålbrand, H. & Akke, M., 2019, In: Biomolecular NMR Assignments. 13, 1, p. 213-218

Research output: Contribution to journal › Article › peer-review

Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding

Verteramo, M. L., Stenström, O., Ignjatović, M. M., Caldararu, O., Olsson, M. A., Manzoni, F., Leffler, H., Oksanen, E., Logan, D. T., Nilsson, U. J., Ryde, U. & Akke, M., 2019, In: Journal of the American Chemical Society. 141, 5, p. 2012–2026

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Open Access

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Minute Additions of DMSO Affect Protein Dynamics Measurements by NMR Relaxation Experiments through Significant Changes in Solvent Viscosity

Wallerstein, J. & Akke, M., 2019, In: ChemPhysChem. 20, 2, p. 326-332

Research output: Contribution to journal › Article › peer-review

Stability and Local Unfolding of SOD1 in the Presence of Protein Crowders

Bille, A., Jensen, K. S., Mohanty, S., Akke, M. & Irbäck, A., 2019, In: Journal of Physical Chemistry B. 123, 9, p. 1920-1930 11 p.

Research output: Contribution to journal › Article › peer-review

2018

Elucidation of Hydrogen Bonding Patterns in Ligand-Free, Lactose- and Glycerol-Bound Galectin-3C by Neutron Crystallography to Guide Drug Design

Manzoni, F., Wallerstein, J., Schrader, T. E., Ostermann, A., Coates, L., Akke, M., Blakeley, M. P., Oksanen, E. & Logan, D. T., 2018 May 24, In: Journal of Medicinal Chemistry. 61, 10, p. 4412-4420 9 p.

Research output: Contribution to journal › Article › peer-review

Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations

Kraus, J., Gupta, R., Yehl, J., Lu, M., Case, D. A., Gronenborn, A. M., Akke, M. & Polenova, T., 2018 Mar 22, In: Journal of Physical Chemistry B. 122, 11, p. 2931-2939 9 p.

Research output: Contribution to journal › Article › peer-review

Conformational Entropy of FK506 Binding to FKBP12 Determined by Nuclear Magnetic Resonance Relaxation and Molecular Dynamics Simulations

Solomentsev, G., Diehl, C. & Akke, M., 2018 Mar 6, In: Biochemistry. 57, 9, p. 1451-1461 11 p.

Research output: Contribution to journal › Article › peer-review

Systematic Tuning of Fluoro-galectin-3 Interactions Provides Thiodigalactoside Derivatives with Single-Digit nM Affinity and High Selectivity

Peterson, K., Kumar, R., Stenström, O., Verma, P., Verma, P. R., Håkansson, M., Kahl-Knutsson, B., Zetterberg, F., Leffler, H., Akke, M., Logan, D. T. & Nilsson, U. J., 2018 Feb 8, In: Journal of Medicinal Chemistry. 61, 3, p. 1164-1175 12 p.

Research output: Contribution to journal › Article › peer-review

Backbone ¹H, ¹³C, and ¹⁵N resonance assignments of the ligand binding domain of the human wildtype glucocorticoid receptor and the F602S mutant variant

Köhler, C., Carlström, G., Tångefjord, S., Papavoine, T., Lepistö, M., Edman, K. & Akke, M., 2018, In: Biomolecular NMR Assignments. 12, 2, p. 263-268

Research output: Contribution to journal › Article › peer-review

Open Access

Designing interactions by control of protein-ligand complex conformation: Tuning arginine-arene interaction geometry for enhanced electrostatic protein-ligand interactions

Noresson, A. L., Aurelius, O., Öberg, C. T., Engström, O., Sundin, A. P., Håkansson, M., Stenström, O., Akke, M., Logan, D. T., Leffler, H. & Nilsson, U. J., 2018, In: Chemical Science. 9, 4, p. 1014-1021 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2017

Cu/Zn Superoxide Dismutase Forms Amyloid Fibrils under Near-Physiological Quiescent Conditions: The Roles of Disulfide Bonds and Effects of Denaturant

Khan, A., Respondek, M., Kjellström, S., Deep, S., Linse, S. & Akke, M., 2017 Sept 20, In: ACS Chemical Neuroscience. 8, 9, p. 2019-2026 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

Structural model of dodecameric heat-shock protein Hsp21: Flexible N-terminal arms interact with client proteins while C-terminal tails maintain the dodecamer and chaperone activity

Rutsdottir, G., Härmark, J., Weide, Y., Hebert, H., Ib Rasmussen, M., Wernersson, S., Respondek, M., Akke, M., Højrup, P., Koeck, P. J. B., Söderberg, C. A. G. & Emanuelsson, C., 2017 May 12, In: Journal of Biological Chemistry. 292, 19, p. 8103-8121 19 p.

Research output: Contribution to journal › Article › peer-review

Open Access

The Dynameomics Entropy Dictionary: A Large-Scale Assessment of Conformational Entropy across Protein Fold Space

Towse, C. L., Akke, M. & Daggett, V., 2017 Apr 27, In: Journal of Physical Chemistry B. 121, 16, p. 3933-3945 13 p.

Research output: Contribution to journal › Article › peer-review

Dynamics of Aromatic Side Chains in the Active Site of FKBP12

Weininger, U., Modig, K., Geitner, A. J., Schmidpeter, P. A. M., Koch, J. R. & Akke, M., 2017 Jan 10, In: Biochemistry. 56, 1, p. 334-343 10 p.

Research output: Contribution to journal › Article › peer-review

2016

Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD

Quistgaard, E. M., Weininger, U., Ural-Blimke, Y., Modig, K., Nordlund, P., Akke, M. & Löw, C., 2016 Sept 23, In: BMC Biology. 14, 1, 82.

Research output: Contribution to journal › Article › peer-review

Open Access

Structural analysis of a complex between small ubiquitin-like modifier 1 (SUMO1) and the ZZ domain of CREB-binding protein (CBP/p300) reveals a new interaction surface on SUMO

Diehl, C., Akke, M., Bekker-Jensen, S., Mailand, N., Streicher, W. & Wikström, M., 2016 Jun 10, In: Journal of Biological Chemistry. 291, 24, p. 12658-12672 15 p.

Research output: Contribution to journal › Article › peer-review

A de Novo Designed Coiled-Coil Peptide with a Reversible pH-Induced Oligomerization Switch

LIZATOVIC, ROBERT., Aurelius, O., Stenström, O., Drakenberg, T., Akke, M., Logan, D. T. & André, I., 2016 Jun 7, In: Structure. 24, 6, p. 946-955 10 p.

Research output: Contribution to journal › Article › peer-review

Structural Insights into the Calcium-Mediated Allosteric Transition in the C-Terminal Domain of Calmodulin from Nuclear Magnetic Resonance Measurements.

Kukic, P., Lundström, P., Camilloni, C., Evenäs, J., Akke, M. & Vendruscolo, M., 2016, In: Biochemistry. 55, 1, p. 19-28

Research output: Contribution to journal › Article › peer-review

2015

Site-Specific Protonation Kinetics of Acidic Side Chains in Proteins Determined by pH-Dependent Carboxyl (13)C NMR Relaxation.

Wallerstein, J., Weininger, U., Khan, A., Linse, S. & Akke, M., 2015, In: Journal of the American Chemical Society. 137, 8, p. 3093-3101

Research output: Contribution to journal › Article › peer-review

Open Access

2014

Computational design of a leucine-rich repeat protein with a predefined geometry.

Rämisch, S., Weininger, U., Martinsson, J., Akke, M. & André, I., 2014, In: Proceedings of the National Academy of Sciences. 111, 50, p. 17875-17880

Research output: Contribution to journal › Article › peer-review

Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability

Genheden, S., Akke, M. & Ryde, U., 2014, In: Journal of Chemical Theory and Computation. 10, 1, p. 432-438

Research output: Contribution to journal › Article › peer-review

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Off-resonance rotating-frame relaxation dispersion experiment for (13)C in aromatic side chains using L-optimized TROSY-selection.

Weininger, U., Brath, U., Modig, K., Teilum, K. & Akke, M., 2014, In: Journal of Biomolecular NMR. 59, 1, p. 23-29

Research output: Contribution to journal › Article › peer-review

Open Access

Ring Flips Revisited: C-13 Relaxation Dispersion Measurements of Aromatic Side Chain Dynamics and Activation Barriers in Basic Pancreatic Trypsin Inhibitor

Weininger, U., Modig, K. & Akke, M., 2014, In: Biochemistry. 53, 28, p. 4519-4525

Research output: Contribution to journal › Article › peer-review

2013

2012

(13)C relaxation experiments for aromatic side chains employing longitudinal- and transverse-relaxation optimized NMR spectroscopy.

Weininger, U., Diehl, C. & Akke, M., 2012, In: Journal of Biomolecular NMR. 53, 3, p. 181-190

Research output: Contribution to journal › Article › peer-review

Conformational dynamics and thermodynamics of protein-ligand binding studied by NMR relaxation.

Akke, M., 2012, In: Biochemical Society Transactions. 40, 2, p. 419-423

Research output: Contribution to journal › Article › peer-review

Conformational exchange of aromatic side chains characterized by L-optimized TROSY-selected (13)C CPMG relaxation dispersion.

Weininger, U., Respondek, M. & Akke, M., 2012, In: Journal of Biomolecular NMR. 54, 1, p. 9-14

Research output: Contribution to journal › Article › peer-review

Specific (CD2CD2SCHD2)-C-12-D-beta-C-12-D-gamma-C-13-H-epsilon Isotopomer Labeling of Methionine To Characterize Protein Dynamics by H-1 and C-13 NMR Relaxation Dispersion

Weininger, U., Liu, Z., McIntyre, D. D., Vogel, H. J. & Akke, M., 2012, In: Journal of the American Chemical Society. 134, 45, p. 18562-18565

Research output: Contribution to journal › Article › peer-review

Mikael Akke

Research output

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