Change search
Link to record
Permanent link

Direct link
BETA
Publications (10 of 69) Show all publications
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
Show others...
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
Show others...
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
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
Show others...
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
Show others...
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)
Note

QC 20170929

Available from: 2017-09-29 Created: 2017-09-29 Last updated: 2017-09-29Bibliographically 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
Show others...
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
Zhu, L., Petrlova, J., Gysbers, P., Hebert, H., Wallin, S., Jegerschöld, C. & Lagerstedt, J. O. (2017). Structures of apolipoprotein A-I in high density lipoprotein generated by electron microscopy and biased simulations. Biochimica et Biophysica Acta - General Subjects, 1861(11), 2726-2738
Open this publication in new window or tab >>Structures of apolipoprotein A-I in high density lipoprotein generated by electron microscopy and biased simulations
Show others...
2017 (English)In: Biochimica et Biophysica Acta - General Subjects, ISSN 0304-4165, E-ISSN 1872-8006, Vol. 1861, no 11, p. 2726-2738Article in journal (Refereed) Published
Abstract [en]

Background: Apolipoprotein A-I (apoA-I) in high-density lipoprotein (HDL) is a key protein for the transport of cholesterol from the vascular wall to the liver. The formation and structure of nascent HDL, composed of apoA-I and phospholipids, is critical to this process. Methods: The HDL was assembled in vitro from apoA-I, cholesterol and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) at a 1:4:50 molar ratio. The structure of HDL was investigated in vitreous samples, frozen at cryogenic temperatures, as well as in negatively stained samples by transmission electron microscopy. Low resolution electron density maps were next used as restraints in biased Monte Carlo simulations of apolipoprotein A-I dimers, with an initial structure derived from atomic resolution X-ray structures. Results: Two final apoA-I structure models for the full-length structure of apoA-I dimer in the lipid bound conformation were generated, showing a nearly circular, flat particle with an uneven particle thickness. Conclusions: The generated structures provide evidence for the discoidal, antiparallel arrangement of apoA-I in nascent HDL, and propose two preferred conformations of the flexible N-termini.

Place, publisher, year, edition, pages
Elsevier, 2017
Keywords
Apolipoprotein A-I, Biased simulations, Cryo-EM, HDL, Negative stain electron microscopy, 2 oleoyl 1 palmitoylphosphatidylcholine, apolipoprotein A1, cholesterol, dimer, high density lipoprotein, amino terminal sequence, Article, disorders of lipoprotein metabolism, electron, electron microscopy, image analysis, in vitro study, priority journal, protein analysis, protein lipid interaction, protein modification, protein structure, simulation, temperature, transmission electron microscopy
National Category
Structural Biology
Identifiers
urn:nbn:se:kth:diva-218631 (URN)10.1016/j.bbagen.2017.07.017 (DOI)000415768500022 ()28754383 (PubMedID)2-s2.0-85026642644 (Scopus ID)
Funder
Swedish Research Council, K2014-54X-22426-01-3The Wenner-Gren Foundation
Note

QC 20171130

Available from: 2017-11-30 Created: 2017-11-30 Last updated: 2017-12-07Bibliographically approved
Ermund, A., Meiss, L. N., Rodriguez-Pineiro, A. M., Baehr, A., Nilsson, H. E., Trillo-Muyo, S., . . . Hansson, G. C. (2017). The normal trachea is cleaned by MUC5B mucin bundles from the submucosal glands coated with the MUC5AC mucin. Biochemical and Biophysical Research Communications - BBRC, 492(3), 331-337
Open this publication in new window or tab >>The normal trachea is cleaned by MUC5B mucin bundles from the submucosal glands coated with the MUC5AC mucin
Show others...
2017 (English)In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 492, no 3, p. 331-337Article in journal (Refereed) Published
Abstract [en]

To understand the mucociliary clearance system, mucins were visualized by light, confocal and electron microscopy, and mucus was stained by Alcian blue and tracked by video microscopy on tracheal explants of newborn piglets. We observed long linear mucus bundles that appeared at the submucosal gland openings and were transported cephalically. The mucus bundles were shown by mass spectrometry and immunostaining to have a core made of MUC5B mucin and were coated with MUC5AC mucin produced by surface goblet cells. The transport speed of the bundles was slower than the airway surface liquid flow. We suggest that the goblet cell MUC5AC mucin anchors the mucus bundles and thus controls their transport. Normal clearance of the respiratory tree of pigs and humans, both rich in submucosal glands, is performed by thick and long mucus bundles. 

Place, publisher, year, edition, pages
ACADEMIC PRESS INC ELSEVIER SCIENCE, 2017
Keywords
Respiratory tract, Mucus, MUC5AC, Airway surface liquid, Lung
National Category
Medical Biotechnology
Identifiers
urn:nbn:se:kth:diva-215783 (URN)10.1016/j.bbrc.2017.08.113 (DOI)000411424300008 ()28859985 (PubMedID)2-s2.0-85028533537 (Scopus ID)
Note

QC 20171023

Available from: 2017-10-23 Created: 2017-10-23 Last updated: 2017-10-23Bibliographically approved
Vijayvargia, R., Epand, R., Leitner, A., Jung, T., Shin, B., Jung, R., . . . Seong, I. S. (2016). Huntingtin's spherical solenoid structure enables polyglutamine tract-dependent modulation of its structure and function. eLIFE, 5, Article ID e11184.
Open this publication in new window or tab >>Huntingtin's spherical solenoid structure enables polyglutamine tract-dependent modulation of its structure and function
Show others...
2016 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 5, article id e11184Article in journal (Refereed) Published
Abstract [en]

The polyglutamine expansion in huntingtin protein causes Huntington's disease. Here, we investigated structural and biochemical properties of huntingtin and the effect of the polyglutamine expansion using various biophysical experiments including circular dichroism, single particle electron microscopy and cross-linking mass spectrometry. Huntingtin is likely composed of five distinct domains and adopts a spherical alpha-helical solenoid where the amino-terminal and carboxyl-terminal regions fold to contain a circumscribed central cavity. Interestingly, we showed that the polyglutamine expansion increases alpha-helical properties of huntingtin and affects the intramolecular interactions among the domains. Our work delineates the structural characteristics of full-length huntingtin, which are affected by the polyglutamine expansion, and provides an elegant solution to the apparent conundrum of how the extreme amino-terminal polyglutamine tract confers a novel property on huntingtin, causing the disease.

Place, publisher, year, edition, pages
ELIFE SCIENCES PUBLICATIONS, 2016
National Category
Structural Biology
Identifiers
urn:nbn:se:kth:diva-185632 (URN)10.7554/eLife.11184 (DOI)000373331100001 ()2-s2.0-84964285135 (Scopus ID)
Note

QC 20160429

Available from: 2016-04-29 Created: 2016-04-25 Last updated: 2017-11-30Bibliographically approved
Härmark, J., Hebert, H. & Koeck, P. J. (2016). Shell thickness determination of polymer-shelled microbubbles using transmission electron microscopy. Micron, 85, 39-43
Open this publication in new window or tab >>Shell thickness determination of polymer-shelled microbubbles using transmission electron microscopy
2016 (English)In: Micron, ISSN 0968-4328, E-ISSN 1878-4291, Vol. 85, p. 39-43Article in journal (Refereed) Published
Abstract [en]

Intravenously injected microbubbles (MBs) can be utilized as ultrasound contrast agent (CA) resulting in enhanced image quality. A novel CA, consisting of air filled MBs stabilized with a shell of polyvinyl alcohol (PVA) has been developed. These spherical MBs have been decorated with superparamagnetic iron oxide nanoparticles (SPIONs) in order to serve as both ultrasound and magnetic resonance imaging (MRI) CA. In this study, a mathematical model was introduced that determined the shell thickness of two types of SPIONs decorated MBs (Type A and Type B). The shell thickness of MBs is important to determine, as it affects the acoustical properties. In order to investigate the shell thickness, thin sections of plastic embedded MBs were prepared and imaged using transmission electron microscopy (TEM). However, the sections were cut at random distances from the MB center, which affected the observed shell thickness. Hence, the model determined the average shell thickness of the MBs from corrected mean values of the outer and inner radii observed in the TEM sections. The model was validated using simulated slices of MBs with known shell thickness and radius. The average shell thickness of Type A and Type B MBs were 651nm and 637nm, respectively.

Place, publisher, year, edition, pages
Elsevier, 2016
Keywords
Shell thickness, Contrast agent, Transmission electron microscopy
National Category
Medical Engineering
Research subject
Medical Technology
Identifiers
urn:nbn:se:kth:diva-186876 (URN)10.1016/j.micron.2016.03.009 (DOI)000376217400006 ()27077316 (PubMedID)2-s2.0-84962835270 (Scopus ID)
Funder
EU, FP7, Seventh Framework Programme, 245572
Note

QC 20160516

Available from: 2016-05-16 Created: 2016-05-16 Last updated: 2017-11-30Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-3220-9402

Search in DiVA

Show all publications