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Kim, G., Azmi, L., Jang, S., Jung, T., Hebert, H., Roe, A. J., . . . Song, J.-J. (2019). Aldehyde-alcohol dehydrogenase forms a high-order spirosome architecture critical for its activity. Nature Communications, 10(1), Article ID 4527.
Open this publication in new window or tab >>Aldehyde-alcohol dehydrogenase forms a high-order spirosome architecture critical for its activity
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2019 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, no 1, article id 4527Article in journal (Refereed) Published
Abstract [en]

Aldehyde-alcohol dehydrogenase (AdhE) is a key enzyme in bacterial fermentation, converting acetyl-CoA to ethanol, via two consecutive catalytic reactions. Here, we present a 3.5 angstrom resolution cryo-EM structure of full-length AdhE revealing a high-order spirosome architecture. The structure shows that the aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH) active sites reside at the outer surface and the inner surface of the spirosome respectively, thus topologically separating these two activities. Furthermore, mutations disrupting the helical structure abrogate enzymatic activity, implying that formation of the spirosome structure is critical for AdhE activity. In addition, we show that this spirosome structure undergoes conformational change in the presence of cofactors. This work presents the atomic resolution structure of AdhE and suggests that the high-order helical structure regulates its enzymatic activity.

Place, publisher, year, edition, pages
Nature Publishing Group, 2019
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-262952 (URN)10.1038/s41467-019-12427-8 (DOI)000489013700020 ()31586059 (PubMedID)2-s2.0-85072930837 (Scopus ID)
Note

QC 20191203

Available from: 2019-12-03 Created: 2019-12-03 Last updated: 2019-12-04Bibliographically approved
Hebert, H. (2019). CryoEM: a crystals to single particles round-trip. Current opinion in structural biology, 58, 59-67
Open this publication in new window or tab >>CryoEM: a crystals to single particles round-trip
2019 (English)In: Current opinion in structural biology, ISSN 0959-440X, E-ISSN 1879-033X, Vol. 58, p. 59-67Article in journal (Refereed) Published
Abstract [en]

In the era of intense and steadily increasing attention to cryo electron microscopy (cryoEM) as a powerful tool in structural biology, particularly with regard to randomly oriented biological macromolecules, studies of 2D and small 3D crystals using cryoEM provide added value for addressing-specific questions. Size and shape demands are not as restrictive as for single particle specimens. Crystallization may stabilize whole or partly flexible molecules. Resolutions beyond 2 A, for 3D crystals even sub-angstrom ngstrom structures, can be obtained allowing studies of chemical properties in detail. The electron dose can be kept low and reduce radiation damage for sensitive specimens. In contrast to X-ray crystallography, scattering of electrons will be directly related to the Coulomb potential and thus give information about charge distribution in biomolecules.

Place, publisher, year, edition, pages
CURRENT BIOLOGY LTD, 2019
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-264312 (URN)10.1016/j.sbi.2019.05.008 (DOI)000494891800011 ()31233976 (PubMedID)2-s2.0-85067405242 (Scopus ID)
Note

QC 20191202

Available from: 2019-12-02 Created: 2019-12-02 Last updated: 2019-12-02Bibliographically approved
Jang, S., Kang, C., Yang, H.-S., Jung, T., Hebert, H., Chung, K. Y., . . . Song, J.-J. (2019). Structural basis of recognition and destabilization of the histone H2B ubiquitinated nucleosome by the DOT1L histone H3 Lys79 methyltransferase. Genes & Development, 33(11-12), 620-625
Open this publication in new window or tab >>Structural basis of recognition and destabilization of the histone H2B ubiquitinated nucleosome by the DOT1L histone H3 Lys79 methyltransferase
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2019 (English)In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 33, no 11-12, p. 620-625Article in journal (Refereed) Published
Abstract [en]

DOT1L is a histone H3 Lys79 methyltransferase whose activity is stimulated by histone H2B Lys120 ubiquitination, suggesting cross-talk between histone H3 methylation and H2B ubiquitination. Here, we present cryo-EM structures of DOT1L complexes with unmodified or H2B ubiquitinated nucleosomes, showing that DOT1L recognizes H2B ubiquitin and the H2A/H2B acidic patch through a C-terminal hydrophobic helix and an arginine anchor in DOT1L, respectively. Furthermore, the structures combined with single-molecule FRET experiments show that H2B ubiquitination enhances a noncatalytic function of the DOT1L-destabilizing nucleosome. These results establish the molecular basis of the cross-talk between H2B ubiquitination and H3 Lys79 methylation as well as nucleosome destabilization by DOT1L.

Place, publisher, year, edition, pages
NLM (Medline), 2019
Keywords
cryo-EM, histone, nucleosome, methylation, ubiquitin
National Category
Cell Biology
Identifiers
urn:nbn:se:kth:diva-254093 (URN)10.1101/gad.323790.118 (DOI)000470071900003 ()30923167 (PubMedID)2-s2.0-85065786784 (Scopus ID)
Note

QC 20190625

Available from: 2019-06-25 Created: 2019-06-25 Last updated: 2019-06-25Bibliographically approved
Sarr, M., Kronqvist, N., Chen, G., Aleksis, R., Purhonen, P., Hebert, H., . . . Johansson, J. (2018). A spidroin-derived solubility tag enables controlled aggregation of a designed amyloid protein. The FEBS Journal, 285(10), 1873-1885
Open this publication in new window or tab >>A spidroin-derived solubility tag enables controlled aggregation of a designed amyloid protein
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2018 (English)In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 285, no 10, p. 1873-1885Article in journal (Refereed) Published
Abstract [en]

Amyloidogenesis is associated with more than 30 diseases, but the molecular mechanisms involved in cell toxicity and fibril formation remain largely unknown. The inherent tendency of amyloid-forming proteins to aggregate renders expression, purification, and experimental studies challenging. NT* is a solubility tag derived from a spider silk protein that was recently introduced for the production of several aggregation-prone peptides and proteins at high yields. Herein, we investigate whether fusion to NT* can prevent amyloid fibril formation and enable controlled aggregation for experimental studies. As an example of an amyloidogenic protein, we chose the de novo-designed polypeptide 17. The fusion protein NT*-17 was recombinantly expressed in Escherichia coli to produce high amounts of soluble and mostly monomeric protein. Structural analysis showed that 17 is kept in a largely unstructured conformation in fusion with NT*. After proteolytic release, 17 adopts a -sheet conformation in a pH- and salt-dependent manner and assembles into amyloid-like fibrils. The ability of NT* to prevent premature aggregation and to enable structural studies of prefibrillar states may facilitate investigation of proteins involved in amyloid diseases.

Place, publisher, year, edition, pages
WILEY, 2018
Keywords
amyloid disease, fibril formation, model protein, protein assembly, protein domain
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-231232 (URN)10.1111/febs.14451 (DOI)000434177700010 ()29604175 (PubMedID)2-s2.0-85045301719 (Scopus ID)
Note

QC 20180627

Available from: 2018-06-27 Created: 2018-06-27 Last updated: 2018-06-27Bibliographically approved
Yoon, J., Kim, S. J., An, S., Cho, S., Leitner, A., Jung, T., . . . Song, J.-J. (2018). Integrative Structural Investigation on the Architecture of Human Importin4_Histone H3/1-14_Asf1a Complex and Its Histone H3 Tail Binding. Journal of Molecular Biology, 430(6), 822-841
Open this publication in new window or tab >>Integrative Structural Investigation on the Architecture of Human Importin4_Histone H3/1-14_Asf1a Complex and Its Histone H3 Tail Binding
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2018 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 430, no 6, p. 822-841Article in journal (Refereed) Published
Abstract [en]

Importin4 transports histone H3/H4 in complex with Asf1a to the nucleus for chromatin assembly. Importin4 recognizes the nuclear localization sequence located at the N-terminal tail of histones. Here, we analyzed the structures and interactions of human Importin4, histones and Asf1a by cross-linking mass spectrometry, X-ray crystallography, negative-stain electron microscopy, small-angle X-ray scattering and integrative modeling. The cross-linking mass spectrometry data showed that the C-terminal region of Importin4 was extensively cross-linked with the histone H3 tail. We determined the crystal structure of the C-terminal region of Importin4 bound to the histone H3 peptide, thus revealing that the acidic patch in Importin4 accommodates the histone H3 tail, and that histone H3 Lys14 contributes to the interaction with Importin4. In addition, we show that Asf1a modulates the binding of histone H3/H4 to Importin4. Furthermore, the molecular architecture of the Importin4_histone H3/H4_Asf1a complex was produced through an integrative modeling approach. Overall, this work provides structural insights into how Importin4 recognizes histones and their chaperone complex.

Place, publisher, year, edition, pages
Academic Press, 2018
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-226795 (URN)10.1016/j.jmb.2018.01.015 (DOI)000429512800006 ()29408485 (PubMedID)2-s2.0-85042167090 (Scopus ID)
Funder
EU, European Research Council, 670821
Note

QC 20180522

Available from: 2018-05-22 Created: 2018-05-22 Last updated: 2018-05-22Bibliographically approved
von Holst, H., Purhonen, P., Lanner, D., Balakrishnan Kumar, R. & Hebert, H. (2018). White Shark Protein Metabolism may be a Model to Improve the Outcome of Cytotoxic Brain Tissue Edema and Cognitive Deficiency after Traumatic Brain Injury and Stroke. Journal of Neurology and Neurobiology, 4(2)
Open this publication in new window or tab >>White Shark Protein Metabolism may be a Model to Improve the Outcome of Cytotoxic Brain Tissue Edema and Cognitive Deficiency after Traumatic Brain Injury and Stroke
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2018 (English)In: Journal of Neurology and Neurobiology, ISSN 2379-7150, Vol. 4, no 2Article in journal (Refereed) Published
Abstract [en]

Increased intracellular water content defined as cytotoxic brain tissue edema is a serious secondary clinical complication to traumatic brain injury (TBI) and stroke and without knowledge to the etiology. Recently a hypothesis to the nervous tissue edema was presented suggesting that external dynamic and internal mechanical static impact forces caused protein unfolding resulting in an increased brain tissue water content. The hypothesis was confirmed by computer simulation tests. In this laboratory study we further evaluated the hypothesis by using the mature protein laminin LN521 upon the effects of both dynamic as well as static impact forces, respectively. Laminin was chosen as a representative protein due to it´s general and abundance presence in the cells. The treated laminin solutions were then analyzed with denatured electrophoresis and Electron Microscopy showing aggregation and fragmentation of the laminin structures. The present results confirm earlier hypothesis and computer simulation suggesting for the first time that dynamic impact force in an accident and increased mechanical static force in stroke unfold mature proteins having the potential to increase the intracellular water content defined as cytotoxic brain tissue edema. The clinical condition resembles the phenomenon when elasmobranchs including white sharks prevent their cells from too high hydrostatic pressure in the deep sea. Thus, the present laboratory study results and knowledge from marine physics may be considered to improve the clinical treatment and outcome of TBI and stroke patients.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:kth:diva-248785 (URN)10.16966/2379-7150.151 (DOI)
Note

QC 20190627

Available from: 2019-04-10 Created: 2019-04-10 Last updated: 2019-08-29Bibliographically approved
Andersson, M., Jia, Q., Abella, A., Lee, X.-Y., Landreh, M., Purhonen, P., . . . Rising, A. (2017). Biomimetic spinning of artificial spider silk from a chimeric minispidroin. Nature Chemical Biology, 13(3), 262-+
Open this publication in new window or tab >>Biomimetic spinning of artificial spider silk from a chimeric minispidroin
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2017 (English)In: Nature Chemical Biology, ISSN 1552-4450, E-ISSN 1552-4469, Vol. 13, no 3, p. 262-+Article in journal (Refereed) Published
Abstract [en]

Herein we present a chimeric recombinant spider silk protein (spidroin) whose aqueous solubility equals that of native spider silk dope and a spinning device that is based solely on aqueous buffers, shear forces and lowered pH. The process recapitulates the complex molecular mechanisms that dictate native spider silk spinning and is highly efficient; spidroin from one liter of bacterial shake-flask culture is enough to spin a kilometer of the hitherto toughest as-spun artificial spider silk fiber.

Place, publisher, year, edition, pages
Nature Publishing Group, 2017
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-204071 (URN)10.1038/NCHEMBIO.2269 (DOI)000394431500006 ()28068309 (PubMedID)2-s2.0-85008658159 (Scopus ID)
Note

QC 20170329

Available from: 2017-03-29 Created: 2017-03-29 Last updated: 2017-11-29Bibliographically approved
Kuang, Q., Purhonen, P., Alander, J., Svensson, R., Hoogland, V., Winerdal, J., . . . Hebert, H. (2017). Dead-end complex, lipid interactions and catalytic mechanism of microsomal glutathione transferase 1, an electron crystallography and mutagenesis investigation. Scientific Reports, 7, Article ID 7897.
Open this publication in new window or tab >>Dead-end complex, lipid interactions and catalytic mechanism of microsomal glutathione transferase 1, an electron crystallography and mutagenesis investigation
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2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 7897Article in journal (Refereed) Published
Abstract [en]

Microsomal glutathione transferase 1 (MGST1) is a detoxification enzyme belonging to the Membrane Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG) superfamily. Here we have used electron crystallography of two-dimensional crystals in order to determine an atomic model of rat MGST1 in a lipid environment. The model comprises 123 of the 155 amino acid residues, two structured phospholipid molecules, two aliphatic chains and one glutathione (GSH) molecule. The functional unit is a homotrimer centered on the crystallographic three-fold axes of the unit cell. The GSH substrate binds in an extended conformation at the interface between two subunits of the trimer supported by new in vitro mutagenesis data. Mutation of Arginine 130 to alanine resulted in complete loss of activity consistent with a role for Arginine 130 in stabilizing the strongly nucleophilic GSH thiolate required for catalysis. Based on the new model and an electron diffraction data set from crystals soaked with trinitrobenzene, that forms a dead-end Meisenheimer complex with GSH, a difference map was calculated. The map reveals side chain movements opening a cavity that defines the second substrate site.

Place, publisher, year, edition, pages
Nature Publishing Group, 2017
National Category
Medical Biotechnology
Identifiers
urn:nbn:se:kth:diva-214509 (URN)10.1038/s41598-017-07912-3 (DOI)000407442500037 ()28801553 (PubMedID)2-s2.0-85046007128 (Scopus ID)
Note

QC 20170929

Available from: 2017-09-29 Created: 2017-09-29 Last updated: 2018-10-16Bibliographically approved
B. Kumar, R., Zhu, L., Hebert, H. & Jegerschöld, C. (2017). Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy. Journal of Visualized Experiments (121), Article ID e55148.
Open this publication in new window or tab >>Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy
2017 (English)In: Journal of Visualized Experiments, ISSN 1940-087X, E-ISSN 1940-087X, no 121, article id e55148Article in journal (Refereed) Published
Abstract [en]

Monotopic proteins exert their function when attached to a membrane surface, and such interactions depend on the specific lipid composition and on the availability of enough area to perform the function. Nanodiscs are used to provide a membrane surface of controlled size and lipid content. In the absence of bound extrinsic proteins, sodium phosphotungstate-stained nanodiscs appear as stacks of coins when viewed from the side by transmission electron microscopy (TEM). This protocol is therefore designed to intentionally promote stacking; consequently, the prevention of stacking can be interpreted as the binding of the membrane-binding protein to the nanodisc. In a further step, the TEM images of the protein-nanodisc complexes can be processed with standard single-particle methods to yield low-resolution structures as a basis for higher resolution cryoEM work. Furthermore, the nanodiscs provide samples suitable for either TEM or non-denaturing gel electrophoresis. To illustrate the method, Ca2+-induced binding of 5-lipoxygenase on nanodiscs is presented.

Place, publisher, year, edition, pages
Journal of Visualized Experiments, 2017
Keywords
Biochemistry, Issue 121, negative staining, protein complex, TEM, lipoxygenases, visualization, non-denaturing gel electrophoresis
National Category
Other Basic Medicine
Identifiers
urn:nbn:se:kth:diva-204044 (URN)10.3791/55148 (DOI)000415744000005 ()28287545 (PubMedID)2-s2.0-85017206859 (Scopus ID)
Funder
Swedish Research Council
Note

QC 20170327

Available from: 2017-03-23 Created: 2017-03-23 Last updated: 2018-01-13Bibliographically approved
Park, K.-H., An, Y., Jung, T., Baek, I.-Y., Noh, H., Ahn, W.-C., . . . Woo, E.-J. (2017). RNA activation-independent DNA targeting of the Type III CRISPR-Cas system by a Csm complex. EMBO Reports, 18(5), 826-840
Open this publication in new window or tab >>RNA activation-independent DNA targeting of the Type III CRISPR-Cas system by a Csm complex
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2017 (English)In: EMBO Reports, ISSN 1469-221X, E-ISSN 1469-3178, Vol. 18, no 5, p. 826-840Article in journal (Refereed) Published
Abstract [en]

The CRISPR-Cas system is an adaptive and heritable immune response that destroys invading foreign nucleic acids. The effector complex of the Type III CRISPR-Cas system targets RNA and DNA in a transcription-coupled manner, but the exact mechanism of DNA targeting by this complex remains elusive. In this study, an effector Csm holocomplex derived from Thermococcus onnurineus is reconstituted with a minimalistic combination of Csm1(1)2(1)3(3)4(1)5(1), and shows RNA targeting and RNA-activated single-stranded DNA (ssDNA) targeting activities. Unexpectedly, in the absence of an RNA transcript, it cleaves ssDNA containing a sequence complementary to the bound crRNA guide region in a manner dependent on the HD domain of the Csm1 subunit. This nuclease activity is blocked by a repeat tag found in the host CRISPR loci. The specific cleavage of ssDNA without a target RNA suggests a novel ssDNA targeting mechanism of the Type III system, which could facilitate the efficient and complete degradation of foreign nucleic acids.

Place, publisher, year, edition, pages
Wiley-VCH Verlagsgesellschaft, 2017
Keywords
CRISPR, Csm complex, DNase, RNase, Thermococcus onnurineus
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-207890 (URN)10.15252/embr.201643700 (DOI)000400446100016 ()28364023 (PubMedID)2-s2.0-85017406426 (Scopus ID)
Note

QC 20170530

Available from: 2017-05-30 Created: 2017-05-30 Last updated: 2017-05-30Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-3220-9402

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