SPRING - an image processing package for single-particle based helical reconstruction from electron cryomicrographs.
Desfosses, A., Ciuffa, R., Gutsche, I. & Sachse, C.
J Struct Biol. 2013 Nov 20. pii: S1047-8477(13)00302-X. doi:10.1016/j.jsb.2013.11.003.
Helical reconstruction from electron cryomicrographs has become a routine technique for macromolecular structure determination of helical assemblies since the first days of Fourier-based three-dimensional image reconstruction. In the past decade, the single-particle technique has had an important impact on the advancement of helical reconstruction. Here, we present the software package SPRING that combines Fourier based symmetry analysis and real-space helical processing into a single workflow. One of the most time-consuming steps in helical reconstruction is the determination of the initial symmetry parameters. First, we propose a class-based helical reconstruction approach that enables the simultaneous exploration and evaluation of many symmetry combinations at low resolution. Second, multiple symmetry solutions can be further assessed and refined by single-particle based helical reconstruction using the correlation of simulated and experimental power spectra. Finally, the 3D structure can be determined to high resolution. In order to validate the procedure, we use the reference specimen Tobacco Mosaic Virus (TMV). After refinement of the helical symmetry, a total of 50,000 asymmetric units from two micrographs are sufficient to reconstruct a subnanometer 3D structure of TMV at 6.4 Aresolution. Furthermore, we introduce the individual programs of the software and discuss enhancements of the helical reconstruction workflow. Thanks to its user-friendly interface and documentation, SPRING can be utilized by the novice as well as the expert user. In addition to the study of well-ordered helical structures, the development of a streamlined workflow for single-particle based helical reconstruction opens new possibilities to analyze specimens that are heterogeneous in symmetries.
GTP regulates the microtubule nucleation activity of gamma-tubulin.
Gombos, L., Neuner, A., Berynskyy, M., Fava, L.L., Wade, R.C., Sachse, C. & Schiebel, E.
Nat Cell Biol. 2013 Nov;15(11):1317-27. doi: 10.1038/ncb2863. Epub 2013 Oct 27.
Both subunits of alphabeta-tubulin that comprise the core components of microtubules bind GTP. GTP binding to alpha-tubulin has a structural role, whereas beta-tubulin binds and hydrolyses GTP to regulate microtubule dynamics. gamma-tubulin, another member of the tubulin superfamily that seeds microtubule nucleation at microtubule-organizing centres, also binds GTP; however, the importance of this association remains elusive. To address the role of GTP binding to gamma-tubulin, we systematically mutagenized the GTP contact residues in the yeast gamma-tubulin Tub4. Tub4(GTP)-mutant proteins that exhibited greatly reduced GTP affinity still assembled into the small gamma-tubulin complex. However, tub4(GTP) mutants were no longer viable, and had defects in interaction between gamma-tubulin and alphabeta-tubulin, decreased microtubule nucleation and defects in microtubule organization. In vitro and in vivo data show that only gamma-tubulin loaded with GTP nucleates microtubules. Our results suggest that GTP recruitment to gamma-tubulin enhances its interaction with alphabeta-tubulin similarly to GTP recruitment to beta-tubulin.
Cartwheel architecture of Trichonympha basal body.
Guichard, P., Desfosses, A., Maheshwari, A., Hachet, V., Dietrich, C., Brune, A., Ishikawa, T., Sachse, C. & Gonczy, P.
Science. 2012 Aug 3;337(6094):553. Epub 2012 Jul 12.
Centrioles and basal bodies are essential for the formation of cilia, flagella, and centrosomes. They exhibit a characteristic ninefold symmetry imparted by a cartwheel thought to contain rings of SAS-6 proteins. We used cryoelectron tomography to investigate the architecture of the exceptionally long cartwheel of the flagellate Trichonympha. We found that the cartwheel is a stack of central rings that exhibit a vertical periodicity of 8.5 nanometers and is able to accommodate nine SAS-6 homodimers. The spokes that emanate from two such rings associate into a layer, with a vertical periodicity of 17 nanometers on the cartwheel margin. Thus, by using the power of biodiversity, we unveiled the architecture of the cartwheel at the root of the ninefold symmetry of centrioles and basal bodies.
Structure of the immature retroviral capsid at 8 A resolution by cryo-electron microscopy.
Bharat, T.A., Davey, N.E., Ulbrich, P., Riches, J.D., de Marco, A., Rumlova, M., Sachse, C., Ruml, T. & Briggs, J.A.
Nature. 2012 Jul 19;487(7407):385-9.
The assembly of retroviruses such as HIV-1 is driven by oligomerization of their major structural protein, Gag. Gag is a multidomain polyprotein including three conserved folded domains: MA (matrix), CA (capsid) and NC (nucleocapsid). Assembly of an infectious virion proceeds in two stages. In the first stage, Gag oligomerization into a hexameric protein lattice leads to the formation of an incomplete, roughly spherical protein shell that buds through the plasma membrane of the infected cell to release an enveloped immature virus particle. In the second stage, cleavage of Gag by the viral protease leads to rearrangement of the particle interior, converting the non-infectious immature virus particle into a mature infectious virion. The immature Gag shell acts as the pivotal intermediate in assembly and is a potential target for anti-retroviral drugs both in inhibiting virus assembly and in disrupting virus maturation. However, detailed structural information on the immature Gag shell has not previously been available. For this reason it is unclear what protein conformations and interfaces mediate the interactions between domains and therefore the assembly of retrovirus particles, and what structural transitions are associated with retrovirus maturation. Here we solve the structure of the immature retroviral Gag shell from Mason-Pfizer monkey virus by combining cryo-electron microscopy and tomography. The 8-A resolution structure permits the derivation of a pseudo-atomic model of CA in the immature retrovirus, which defines the protein interfaces mediating retrovirus assembly. We show that transition of an immature retrovirus into its mature infectious form involves marked rotations and translations of CA domains, that the roles of the amino-terminal and carboxy-terminal domains of CA in assembling the immature and mature hexameric lattices are exchanged, and that the CA interactions that stabilize the immature and mature viruses are almost completely distinct.
Three-dimensional structure of TspO by electron cryomicroscopy of helical crystals.
Korkhov, V.M., Sachse, C., Short, J.M. & Tate, C.G.
Structure. 2010 Jun 9;18(6):677-87.
The 18 kDa TSPO protein is a polytopic mitochondrial outer membrane protein involved in a wide range of physiological functions and pathologies, including neurodegeneration and cancer. The pharmacology of TSPO has been extensively studied, but little is known about its biochemistry, oligomeric state, and structure. We have expressed, purified, and characterized a homologous protein, TspO from Rhodobacter sphaeroides, and reconstituted it as helical crystals. Using electron cryomicroscopy and single-particle helical reconstruction, we have determined a three-dimensional structure of TspO at 10 A resolution. The structure suggests that monomeric TspO comprises five transmembrane alpha helices that form a homodimer, which is consistent with the dimeric state observed in detergent solution. Furthermore, the arrangement of transmembrane domains of individual TspO subunits indicates a possibility of two substrate translocation pathways per dimer. The structure provides the first insight into the molecular architecture of TSPO/PBR protein family that will serve as a framework for future studies.
Nanoscale flexibility parameters of Alzheimer amyloid fibrils determined by electron cryo-microscopy.
Sachse, C., Grigorieff, N. & Fandrich, M.
Angew Chem Int Ed Engl. 2010 Feb 8;49(7):1321-3. Europe PMC
Structure of a bacterial dynamin-like protein lipid tube provides a mechanism for assembly and membrane curving.
Low, H.H., Sachse, C., Amos, L.A. & Lowe, J.
Cell. 2009 Dec 24;139(7):1342-52.
Proteins of the dynamin superfamily mediate membrane fission, fusion, and restructuring events by polymerizing upon lipid bilayers and forcing regions of high curvature. In this work, we show the electron cryomicroscopy reconstruction of a bacterial dynamin-like protein (BDLP) helical filament decorating a lipid tube at approximately 11 A resolution. We fitted the BDLP crystal structure and produced a molecular model for the entire filament. The BDLP GTPase domain dimerizes and forms the tube surface, the GTPase effector domain (GED) mediates self-assembly, and the paddle region contacts the lipids and promotes curvature. Association of BDLP with GMPPNP and lipid induces radical, large-scale conformational changes affecting polymerization. Nucleotide hydrolysis seems therefore to be coupled to polymer disassembly and dissociation from lipid, rather than membrane restructuring. Observed structural similarities with rat dynamin 1 suggest that our results have broad implication for other dynamin family members.
Comparison of Alzheimer Abeta(1-40) and Abeta(1-42) amyloid fibrils reveals similar protofilament structures.
Schmidt, M., Sachse, C., Richter, W., Xu, C., Fandrich, M. & Grigorieff, N.
Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19813-8. Epub 2009 Oct 20.
We performed mass-per-length (MPL) measurements and electron cryomicroscopy (cryo-EM) with 3D reconstruction on an Abeta(1-42) amyloid fibril morphology formed under physiological pH conditions. The data show that the examined Abeta(1-42) fibril morphology has only one protofilament, although two protofilaments were observed with a previously studied Abeta(1-40) fibril. The latter fibril was resolved at 8 A resolution showing pairs of beta-sheets at the cores of the two protofilaments making up a fibril. Detailed comparison of the Abeta(1-42) and Abeta(1-40) fibril structures reveals that they share an axial twofold symmetry and a similar protofilament structure. Furthermore, the MPL data indicate that the protofilaments of the examined Abeta(1-40) and Abeta(1-42) fibrils have the same number of Abeta molecules per cross-beta repeat. Based on this data and the previously studied Abeta(1-40) fibril structure, we describe a model for the arrangement of peptides within the Abeta(1-42) fibril.
Abeta(1-40) fibril polymorphism implies diverse interaction patterns in amyloid fibrils.
Meinhardt, J., Sachse, C., Hortschansky, P., Grigorieff, N. & Fandrich, M.
J Mol Biol. 2009 Feb 27;386(3):869-77. Epub 2008 Nov 14.
Amyloid fibrils characterize a diverse group of human diseases that includes Alzheimer's disease, Creutzfeldt-Jakob and type II diabetes. Alzheimer's amyloid fibrils consist of amyloid-beta (Abeta) peptide and occur in a range of structurally different fibril morphologies. The structural characteristics of 12 single Abeta(1-40) amyloid fibrils, all formed under the same solution conditions, were determined by electron cryo-microscopy and three-dimensional reconstruction. The majority of analyzed fibrils form a range of morphologies that show almost continuously altering structural properties. The observed fibril polymorphism implies that amyloid formation can lead, for the same polypeptide sequence, to many different patterns of inter- or intra-residue interactions. This property differs significantly from native, monomeric protein folding reactions that produce, for one protein sequence, only one ordered conformation and only one set of inter-residue interactions.
Paired beta-sheet structure of an Abeta(1-40) amyloid fibril revealed by electron microscopy.
Sachse, C., Fandrich, M. & Grigorieff, N.
Proc Natl Acad Sci U S A. 2008 May 27;105(21):7462-6. Epub 2008 May 15.
Alzheimer's disease is a neurodegenerative disorder that is characterized by the cerebral deposition of amyloid fibrils formed by Abeta peptide. Despite their prevalence in Alzheimer's and other neurodegenerative diseases, important details of the structure of amyloid fibrils remain unknown. Here, we present a three-dimensional structure of a mature amyloid fibril formed by Abeta(1-40) peptide, determined by electron cryomicroscopy at approximately 8-A resolution. The fibril consists of two protofilaments, each containing approximately 5-nm-long regions of beta-sheet structure. A local twofold symmetry within each region suggests that pairs of beta-sheets are formed from equivalent parts of two Abeta(1-40) peptides contained in each protofilament. The pairing occurs via tightly packed interfaces, reminiscent of recently reported steric zipper structures. However, unlike these previous structures, the beta-sheet pairing is observed within an amyloid fibril and includes significantly longer amino acid sequences.
A dose-rate effect in single-particle electron microscopy.
Chen, J.Z., Sachse, C., Xu, C., Mielke, T., Spahn, C.M. & Grigorieff, N.
J Struct Biol. 2008 Jan;161(1):92-100. Epub 2007 Oct 1.
A low beam intensity, low electron dose imaging method has been developed for single-particle electron cryo-microscopy (cryo-EM). Experiments indicate that the new technique can reduce beam-induced specimen movement and secondary radiolytic effects, such as "bubbling". The improvement in image quality, especially for multiple-exposure data collection, will help single-particle cryo-EM to reach higher resolution.
Directed selection of a conformational antibody domain that prevents mature amyloid fibril formation by stabilizing Abeta protofibrils.
Habicht, G., Haupt, C., Friedrich, R.P., Hortschansky, P., Sachse, C., Meinhardt, J., Wieligmann, K., Gellermann, G.P., Brodhun, M., Gotz, J., Halbhuber, K.J., Rocken, C., Horn, U. & Fandrich, M.
Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19232-7. Epub 2007 Nov 27.
The formation of amyloid fibrils is a common biochemical characteristic that occurs in Alzheimer's disease and several other amyloidoses. The unifying structural feature of amyloid fibrils is their specific type of beta-sheet conformation that differentiates these fibrils from the products of normal protein folding reactions. Here we describe the generation of an antibody domain, termed B10, that recognizes an amyloid-specific and conformationally defined epitope. This antibody domain was selected by phage-display from a recombinant library of camelid antibody domains. Surface plasmon resonance, immunoblots, and immunohistochemistry show that this antibody domain distinguishes Abeta amyloid fibrils from disaggregated Abeta peptide as well as from specific Abeta oligomers. The antibody domain possesses functional activity in preventing the formation of mature amyloid fibrils by stabilizing Abeta protofibrils. These data suggest possible applications of B10 in the detection of amyloid fibrils or in the modulation of their formation.
High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus.
Sachse, C., Chen, J.Z., Coureux, P.D., Stroupe, M.E., Fandrich, M. & Grigorieff, N.
J Mol Biol. 2007 Aug 17;371(3):812-35. Epub 2007 Jun 4.
The treatment of helical objects as a string of single particles has become an established technique to resolve their three-dimensional (3D) structure using electron cryo-microscopy. It can be applied to a wide range of helical particles such as viruses, microtubules and helical filaments. We have made improvements to this approach using Tobacco Mosaic Virus (TMV) as a test specimen and obtained a map from 210,000 asymmetric units at a resolution better than 5 A. This was made possible by performing a full correction of the contrast transfer function of the microscope. Alignment of helical segments was helped by constraints derived from the helical symmetry of the virus. Furthermore, symmetrization was implemented by multiple inclusions of symmetry-related views in the 3D reconstruction. We used the density map to build an atomic model of TMV. The model was refined using a real-space refinement strategy that accommodates multiple conformers. The atomic model shows significant deviations from the deposited model for the helical form of TMV at the lower-radius region (residues 88 to 109). This region appears more ordered with well-defined secondary structure, compared with the earlier helical structure. The RNA phosphate backbone is sandwiched between two arginine side-chains, stabilizing the interaction between RNA and coat protein. A cluster of two or three carboxylates is buried in a hydrophobic environment isolating it from neighboring subunits. These carboxylates may represent the so-called Caspar carboxylates that form a metastable switch for viral disassembly. Overall, the observed differences suggest that the new model represents a different, more stable state of the virus, compared with the earlier published model.
Quaternary structure of a mature amyloid fibril from Alzheimer's Abeta(1-40) peptide.
Sachse, C., Xu, C., Wieligmann, K., Diekmann, S., Grigorieff, N. & Fandrich, M.
J Mol Biol. 2006 Sep 15;362(2):347-54.
Amyloid fibrils are fibrous polypeptide aggregates that can be formed in vitro and under pathologic conditions, such as in type II diabetes, Alzheimer's and Creutzfeldt-Jakob diseases. Using a range of biophysical techniques including electron microscopy we have analysed the quaternary structure of a mature amyloid fibril formed from the Abeta(1-40) peptide from Alzheimer's disease. We find that the analysed fibril is discernibly polar and represents a left-handed helix consisting of two or three protofilaments. These are organised in a manner so that the cross-section is, under the present resolution conditions (2.6 nm), S-shaped. In the cross-section, each protofilament can accommodate two beta-strands, suggesting that each protofilament contains two cross-beta-sheets. These data shed new light on the way in which Abeta(1-40) and the protofilaments formed from this peptide are organised within the mature fibril.
Concentration-dependent realignment of the antimicrobial peptide PGLa in lipid membranes observed by solid-state 19F-NMR.
Glaser, R.W., Sachse, C., Durr, U.H., Wadhwani, P., Afonin, S., Strandberg, E. & Ulrich, A.S.
Biophys J. 2005 May;88(5):3392-7. Epub 2005 Feb 4.
The membrane-disruptive antimicrobial peptide PGLa is found to change its orientation in a dimyristoyl-phosphatidylcholine bilayer when its concentration is increased to biologically active levels. The alignment of the alpha-helix was determined by highly sensitive solid-state NMR measurements of (19)F dipolar couplings on CF(3)-labeled side chains, and supported by a nonperturbing (15)N label. At a low peptide/lipid ratio of 1:200 the amphiphilic peptide resides on the membrane surface in the so-called S-state, as expected. However, at high peptide concentration (>/=1:50 molar ratio) the helix axis changes its tilt angle from approximately 90 degrees to approximately 120 degrees , with the C-terminus pointing toward the bilayer interior. This tilted "T-state" represents a novel feature of antimicrobial peptides, which is distinct from a membrane-inserted I-state. At intermediate concentration, PGLa is in exchange between the S- and T-state in the timescale of the NMR experiment. In both states the peptide molecules undergo fast rotation around the membrane normal in liquid crystalline bilayers; hence, large peptide aggregates do not form. Very likely the obliquely tilted T-state represents an antiparallel dimer of PGLa that is formed in the membrane at increasing concentration.
Orientation of the antimicrobial peptide PGLa in lipid membranes determined from 19F-NMR dipolar couplings of 4-CF3-phenylglycine labels.
Glaser, R.W., Sachse, C., Durr, U.H., Wadhwani, P. & Ulrich, A.S.
J Magn Reson. 2004 May;168(1):153-63.
A highly sensitive solid state (19)F-NMR strategy is described to determine the orientation and dynamics of membrane-associated peptides from specific fluorine labels. Several analogues of the antimicrobial peptide PGLa were synthesized with the non-natural amino acid 4-trifluoromethyl-phenylglycine (CF(3)-Phg) at different positions throughout the alpha-helical peptide chain. A simple 1-pulse (19)F experiment allows the simultaneous measurement of both the anisotropic chemical shift and the homonuclear dipolar coupling within the rotating CF(3)-group in a macroscopically oriented membrane sample. The value and sign of the dipolar splitting determines the tilt of the CF(3)-rotational axis, which is rigidly attached to the peptide backbone, with respect to the external magnetic field direction. Using four CF(3)-labeled peptide analogues (with L-CF(3)-Phg at Ile9, Ala10, Ile13, and Ala14) we confirmed that PGLa is aligned at the surface of lipid membranes with its helix axis perpendicular to the bilayer normal at a peptide:lipid ratio of 1:200. We also determined the azimuthal rotation angle of the helix, which agrees well with the orientation expected from its amphiphilic character. Peptide analogues with a D-CF(3)-Phg label resulting from racemization of the amino acid during synthesis were separately collected by HPLC. Their spectra provide additional information about the PGLa structure and orientation but allow only to discriminate qualitatively between multiple solutions. The structural and functional characterization of the individual CF(3)-labeled peptides by circular dichroism and antimicrobial assays showed only small effects for our four substitutions on the hydrophobic face of the helix, but a significant disturbance was observed in a fifth analogue where Ala8 on the hydrophilic face had been replaced. Even though the hydrophobic CF(3)-Phg side chain cannot be utilized in all positions, it allows highly sensitive NMR measurements over a wide range of experimental conditions and dynamic regimes of the peptide.