| 1. |
- Albeck, S, et al.
(författare)
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New trends in protein expression
- 2010
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Ingår i: Journal of structural biology. - : Elsevier BV. - 1095-8657 .- 1047-8477. ; 172:1, s. 1-2
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 2. |
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| 3. |
- Caddeo, Andrea, et al.
(författare)
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MBOAT7 is anchored to endomembranes by six transmembrane domains.
- 2019
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Ingår i: Journal of structural biology. - : Elsevier BV. - 1095-8657 .- 1047-8477. ; 206:3, s. 349-360
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Tidskriftsartikel (refereegranskat)abstract
- Membrane bound O-acyltransferase domain- containing 7 (MBOAT7, also known as LPIAT1) is a protein involved in the acyl chain remodeling of phospholipids via the Lands' cycle. The MBOAT7 is a susceptibility risk genetic locus for non-alcoholic fatty liver disease (NAFLD) and mental retardation. Although it has been shown that MBOAT7 is associated to membranes, the MBOAT7 topology remains unknown. To solve the topological organization of MBOAT7, we performed: A) solubilization of the total membrane fraction of cells overexpressing the recombinant MBOAT7-V5, which revealed MBOAT7 is an integral protein strongly attached to endomembranes; B) in silico analysis by using 22 computational methods, which predicted the number and localization of transmembrane domains of MBOAT7 with a range between 5 and 12; C) in vitro analysis of living cells transfected with GFP-tagged MBOAT7 full length and truncated forms, using a combination of Western Blotting, co-immunofluorescence and Fluorescence Protease Protection (FPP) assay; D) in vitro analysis of living cells transfected with FLAG-tagged MBOAT7 full length forms, using a combination of Western Blotting, selective membrane permeabilization followed by indirect immunofluorescence. All together, these data revealed that MBOAT7 is a multispanning transmembrane protein with six transmembrane domains. Based on our model, the predicted catalytic dyad of the protein, composed of the conserved asparagine in position 321 (Asn-321) and the preserved histidine in position 356 (His-356), has a lumenal localization. These data are compatible with the role of MBOAT7 in remodeling the acyl chain composition of endomembranes.
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| 4. |
- Cheng, Kimberley, et al.
(författare)
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tmRNA-SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes
- 2010
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Ingår i: Journal of Structural Biology. - : Elsevier BV. - 1047-8477 .- 1095-8657. ; 169:3, s. 342-348
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial ribosomes stalled on faulty, often truncated, mRNAs lacking stop codons are rescued by trans-translation. It relies on an RNA molecule (tmRNA) capable of replacing the faulty mRNA with its own open reading frame (ORF). Translation of tmRNA ORF results in the tagging of faulty protein for degradation and its release from the ribosome. We used single-particle cryo-electron microscopy to visualize tmRNA together with its helper protein SmpB on the 70S Escherichia coli ribosome in states subsequent to GTP hydrolysis on elongation factor Tu (EF-Tu). Three-dimensional reconstruction and heterogeneity analysis resulted in a 15 A resolution structure of the tmRNA-SmpB complex accommodated in the A site of the ribosome, which shows that SmpB mimics the anticodon- and D-stem of native tRNAs missing in the tRNA-like domain of tmRNA. We conclude that the tmRNA-SmpB complex accommodates in the ribosomal A site very much like an aminoacyl-tRNA during protein elongation.
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| 5. |
- Cisneros, David A., et al.
(författare)
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Observing growth steps of collagen self-assembly by time-lapse high-resolution atomic force microscopy
- 2006
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Ingår i: Journal of Structural Biology. - : Elsevier BV. - 1047-8477 .- 1095-8657. ; 154:3, s. 232-245
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Tidskriftsartikel (refereegranskat)abstract
- Insights into molecular mechanisms of collagen assembly are important for understanding countless biological processes and at the same time a prerequisite for many biotechnological and medical applications. In this work, the self-assembly of collagen type I molecules into fibrils could be directly observed using time-lapse atomic force microscopy (AFM). The smallest isolated fibrillar structures initiating fibril growth showed a thickness of approximately 1.5 nm corresponding to that of a single collagen molecule. Fibrils assembled in vitro established an axial D-periodicity of approximately 67 nm such as typically observed for in vivo assembled collagen fibrils from tendon. At given collagen concentrations of the buffer solution the fibrils showed constant lateral and longitudinal growth rates. Single fibrils continuously grew and fused with each other until the supporting surface was completely covered by a nanoscopically well-defined collagen matrix. Their thickness of approximately 3 nm suggests that the fibrils were build from laterally assembled collagen microfibrils. Laterally the fibrils grew in steps of approximately 4 nm, indicating microfibril formation and incorporation. Thus, we suggest collagen fibrils assembling in a two-step process. In a first step, collagen molecules assemble with each other. In the second step, these molecules then rearrange into microfibrils which form the building blocks of collagen fibrils. High-resolution AFM topographs revealed substructural details of the D-band architecture of the fibrils forming the collagen matrix. These substructures correlated well with those revealed from positively stained collagen fibers imaged by transmission electron microscopy.
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| 6. |
- Cusack, Maggie, et al.
(författare)
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Biomineral repair of abalone shell apertures
- 2013
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Ingår i: Journal of Structural Biology. - : Elsevier. - 1047-8477 .- 1095-8657. ; 183:2, s. 165-171
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Tidskriftsartikel (refereegranskat)abstract
- The shell of the gastropod mollusc, abalone, is comprised of nacre with an outer prismatic layer that is composed of either calcite or aragonite or both, depending on the species. A striking characteristic of the abalone shell is the row of apertures along the dorsal margin. As the organism and shell grow, new apertures are formed and the preceding ones are filled in. Detailed investigations, using electron backscatter diffraction, of the infill in three species of abalone: Haliotis asinina, Haliotis gigantea and Haliotis rufescens reveals that, like the shell, the infill is composed mainly of nacre with an outer prismatic layer. The infill prismatic layer has identical mineralogy as the original shell prismatic layer. In H. asinina and H. gigantea, the prismatic layer of the shell and infill are made of aragonite while in H. rufescens both are composed of calcite. Abalone builds the infill material with the same high level of biological control, replicating the structure, mineralogy and crystallographic orientation as for the shell. The infill of abalone apertures presents us with insight into what is, effectively, shell repair.
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| 7. |
- Das, Anuska, et al.
(författare)
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Structural principles of CRISPR-Cas enzymes used in nucleic acid detection
- 2022
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Ingår i: JOURNAL OF STRUCTURAL BIOLOGY. - : Elsevier BV. - 1047-8477 .- 1095-8657. ; 214:1
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Tidskriftsartikel (refereegranskat)abstract
- Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-based technology has revolutionized the field of biomedicine with broad applications in genome editing, therapeutics and diagnostics. While a majority of applications involve the RNA-guided site-specific DNA or RNA cleavage by CRISPR enzymes, recent successes in nucleic acid detection rely on their collateral and non-specific cleavage activated by viral DNA or RNA. Ranging in enzyme composition, the mechanism for distinguishing self-from foreign-nucleic acids, the usage of second messengers, and enzymology, the CRISPR enzymes provide a diverse set of diagnosis tools in further innovations. Structural biology plays an important role in elucidating the mechanisms of these CRISPR enzymes. Here we summarize and compare structures of three types of CRISPR enzymes used in nucleic acid detection captured in their respective functional forms and illustrate the current understanding of their activation mechanism.
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| 8. |
- de Borst, Karin, et al.
(författare)
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Microstructure-€“stiffness relationships of ten European and tropical hardwood species
- 2012
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Ingår i: Journal of Structural Biology. - : Elsevier BV. - 1047-8477 .- 1095-8657. ; 177:2, s. 532-542
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Tidskriftsartikel (refereegranskat)abstract
- Hardwood species exhibit a huge anatomical variability. This makes them perfect study objects for exploring relations between structural features at different length scales and corresponding stiffness properties of wood. We carry out microscopic analysis, nanoindentation tests, as well as macroscale ultrasonic and quasi-static tension tests and build a complete set of microstructural and corresponding micromechanical data of ten different (European and tropical) hardwood species. In addition, we apply micromechanical modeling to further elucidate the individual influences of particular structural features, which might appear only in a superimposed manner in experiments. The test results confirm the dominant influences of the microfibril angle on the stiffness at cell wall level and of density at the macroscopic scale. Vessels and ray cells affect the macroscopic stiffness of the wood tissue not only through their content, but also through their arrangement and shape: A ring-porous structure results in comparably higher longitudinal but lower radial stiffness than a diffuse-porous one. As for ray cells, large and particularly compactly shaped bundles might reduce the stiffness in tangential direction because of the fiber deviations they cause. Moreover, vessel and ray content might affect the relation between nanoindentation modulus and density-corrected macroscopic longitudinal stiffness.
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| 9. |
- El-Schich, Zahra, et al.
(författare)
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Induction of morphological changes in death-induced cancer cells monitored by holographic microscopy
- 2015
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Ingår i: Journal of Structural Biology. - : Elsevier. - 1047-8477 .- 1095-8657. ; 189:3, s. 207-212
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Tidskriftsartikel (refereegranskat)abstract
- We are using the label-free technique of holographic microscopy to analyze cellular parameters including cell number, confluence, cellular volume and area directly in the cell culture environment. We show that death-induced cells can be distinguished from untreated counterparts by the use of holographic microscopy, and we demonstrate its capability for cell death assessment. Morphological analysis of two representative cell lines (L929 and DU145) was performed in the culture flasks without any prior cell detachment. The two cell lines were treated with the anti-tumour agent etoposide for one to three days. Measurements by holographic microscopy showed significant differences in average cell number, confluence, volume and area when comparing etoposide-treated with untreated cells. The cell volume of the treated cell lines was initially increased at early time-points. By time, cells decreased in volume, especially when treated with high doses of etoposide. In conclusion, we have shown that holographic microscopy allows label-free and completely non-invasive morphological measurements of cell growth, viability and death. Future applications could include real-time monitoring of these holographic microscopy parameters in cells in response to clinically relevant compounds.
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| 10. |
- Elmlund, Dominika, 1981-, et al.
(författare)
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High-resolution single-particle orientation refinement based on spectrally self-adapting common lines
- 2009
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Ingår i: Journal of Structural Biology. - : Elsevier BV. - 1047-8477 .- 1095-8657. ; 167:1, s. 83-94
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Tidskriftsartikel (refereegranskat)abstract
- Three-dimensional (3D) structure determination from electron microscopic images of single molecules can be difficult for particles with low or no internal symmetry, and for images with low signal-to-noise ratio (SNR), due to the existence of false maxima in the scoring function used for orientation search. In attempt to improve robustness of orientation parameter refinement towards noise and poor starting reconstruction quality, we have developed a method for common lines-based orientation search in Fourier space. The Fourier-space formulation enables inclusion of resolution (spatial frequency of the low-pass limit) as a variable that is adjusted in a particle-dependent, self-adaptive manner. The method allows for the underlying 3D structure to be estimated to high resolution, and requires only a crude, low-resolution reconstruction as starting-point for refinement. Benchmarking of the method is performed on experimental and synthetic data.
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