Publications
2020
The growth of spontaneously twisted crystals is a common but poorly understood phenomenon. An analysis of the formation of twisted crystals of a metastable benzamide polymorph (form II) crystallizing from highly supersaturated aqueous and ethanol solutions is given here. Benzamide, the first polymorphic molecular crystal reported (1832), would have been the first helicoidal crystal observed had the original authors undertaken an analysis by light microscopy. Polymorphism and twisting frequently concur as they are both associated with high thermodynamic driving forces for crystallization. Optical and electron microscopies as well as electron and powder X-ray diffraction reveal a complex lamellar structure of benzamide form II needle-like crystals. The internal stress produced by the overgrowth of lamellae is shown to be able to create a twist moment that is responsible for the observed non-classical morphologies.
The endoplasmic reticulum (ER) is a highly dynamic network of membranes. Here, we combine live-cell microscopy with in situ cryo-electron tomography to directly visualize ER dynamics in several secretory cell types including pancreatic beta-cells and neurons under near-native conditions. Using these imaging approaches, we identify a novel, mobile form of ER, ribosome-associated vesicles (RAVs), found primarily in the cell periphery, which is conserved across different cell types and species. We show that RAVs exist as distinct, highly dynamic structures separate from the intact ER reticular architecture that interact with mitochondria via direct intermembrane contacts. These findings describe a new ER subcompartment within cells.
Protein crystallization is important in structural biology, disease research and pharmaceuticals. It has recently been recognized that nonclassical crystallization—involving initial formation of an amorphous precursor phase—occurs often in protein, organic and inorganic crystallization processes1–5. A two-step nucleation theory has thus been proposed, in which initial low-density, solvated amorphous aggregates subsequently densify, leading to nucleation4,6,7. This view differs from classical nucleation theory, which implies that crystalline nuclei forming in solution have the same density and structure as does the final crystalline state1. A protein crystallization mechanism involving this classical pathway has recently been observed directly8. However, a molecular mechanism of nonclassical protein crystallization9–15 has not been established9,11,14. To determine the nature of the amorphous precursors and whether crystallization takes place within them (and if so, how order develops at the molecular level), three-dimensional (3D) molecular-level imaging of a crystallization process is required. Here we report cryogenic scanning transmission microscopy tomography of ferritin aggregates at various stages of crystallization, followed by 3D reconstruction using simultaneous iterative reconstruction techniques to provide a 3D picture of crystallization with molecular resolution. As crystalline order gradually increased in the studied aggregates, they exhibited an increase in both order and density from their surface towards their interior. We observed no highly ordered small structures typical of a classical nucleation process, and occasionally we observed several ordered domains emerging within one amorphous aggregate, a phenomenon not predicted by either classical or two-step nucleation theories. Our molecular-level analysis hints at desolvation as the driver of the continuous order-evolution mechanism, a view that goes beyond current nucleation models, yet is consistent with a broad spectrum of protein crystallization mechanisms.
2019
Electron cryo-tomography using the scanning transmission modality (STEM)enables 3D reconstruction of unstained, vitrified specimens as thick as 1 μm or more. Contrast is related to mass/thickness and atomic number, providing quantifiable chemical characterization and mass mapping of intact prokaryotic and eukaryotic cells. Energy dispersive X-ray spectroscopy by STEM provides a simple, on-the-spot chemical identification of the elemental composition in sub-cellular organic bodies or mineral deposits. This chapter provides basic background and practical information for performing cryo-STEM tomography on vitrified biological cells.
Cells and extracellular matrix (ECM) are mutually interdependent: cells guide self-assembly of ECM precursors, and the resulting ECM architecture supports and instructs cells. Though bidirectional signaling between ECM and cells is fundamental to cell biology, it is challenging to gain high-resolution structural information on cellular responses to the matrix microenvironment. Here we used cryo-scanning transmission electron tomography (CSTET) to reveal the nanometer- to micron-scale organization of major fibroblast ECM components in a native-like context, while simultaneously visualizing internal cell ultrastructure including organelles and cytoskeleton. In addition to extending current models for collagen VI fibril organization, three-dimensional views of thick cell regions and surrounding matrix showed how ECM networks impact the structures and dynamics of intracellular organelles and how cells remodel ECM. Collagen VI and fibronectin were seen to distribute in fundamentally different ways in the cell microenvironment and perform distinct roles in supporting and interacting with cells. This work demonstrates that CSTET provides a new perspective for the study of ECM in cell biology, highlighting labeled extracellular elements against a backdrop of unlabeled but morphologically identifiable cellular features with nanometer resolution detail.
2018
STEM modality provides major advantages for electron tomography of thicker (>300 nm) biological specimens, both for plastic-embedded, heavy-metal stained samples, and for vitrified, unstained cells. With the proliferation of modern TEM microscopes that allow for switching between TEM and STEM modes with relative ease, we expect the use of STEM tomography to increase. The concepts for STEM imaging are significantly different than for TEM, and therefore we will describe in detail the STEM imaging modality, followed by STEM tomography concepts and applications.
2017
Communication between microorganisms in the marine environment has immense ecological impact by mediating trophic-level interactions and thus determining community structure(1). Extracellular vesicles (EVs) are produced by bacteria(2,3), archaea(4), protists(5) and metazoans, and can mediate pathogenicity(6) or act as vectors for intercellular communication. However, little is known about the involvement of EVs in microbial interactions in the marine environment(7). Here we investigated the signalling role of EVs produced during interactions between the cosmopolitan alga Emiliania huxleyi and its specific virus (EhV, Phycodnaviridae)(8), which leads to the demise of these large-scale oceanic blooms(9,10). We found that EVs are highly produced during viral infection or when bystander cells are exposed to infochemicals derived from infected cells. These vesicles have a unique lipid composition that differs from that of viruses and their infected host cells, and their cargo is composed of specific small RNAs that are predicted to target sphingolipid metabolism and cell-cycle pathways. EVs can be internalized by E. huxleyi cells, which consequently leads to a faster viral infection dynamic. EVs can also prolong EhV half-life in the extracellular milieu. We propose that EVs are exploited by viruses to sustain efficient infectivity and propagation across E. huxleyi blooms. As these algal blooms have an immense impact on the cycling of carbon and other nutrients(11,12), this mode of cell-cell communication may influence the fate of the blooms and, consequently, the composition and flow of nutrients in marine microbial food webs.
The entry of calcium into mitochondria is central to metabolism, inter-organelle communication, and cell life/death decisions. Long-sought transporters involved in mitochondrial calcium influx and efflux have recently been identified. To obtain a unified picture of mitochondrial calcium utilization, a parallel advance in understanding the forms and quantities of mitochondrial calcium stores is needed. We present here the direct 3D visualization of mitochondrial calcium in intact mammalian cells using cryo-scanning transmission electron tomography (CSTET). Amorphous solid granules containing calcium and phosphorus were pervasive in the mitochondrial matrices of a variety of mammalian cell types. Analysis based on quantitative electron scattering revealed that these repositories are equivalent to molar concentrations of dissolved ions. These results demonstrate conclusively that calcium buffering in the mitochondrial matrix in live cells occurs by phase separation, and that solid-phase stores provide a major ion reservoir that can be mobilized for bioenergetics and signaling.
How molecules in solution form crystal nuclei, which then grow into large crystals, is a poorly understood phenomenon. The classical mechanism of homogeneous crystal nucleation proceeds via the spontaneous random aggregation of species from liquid or solution. However, a non-classical mechanism suggests the formation of an amorphous dense phase that reorders to form stable crystal nuclei. So far it has remained an experimental challenge to observe the formation of crystal nuclei from five to thirty molecules. Here, using polyoxometallates, we show that the formation of small crystal nuclei is observable by cryogenic transmission electron microscopy. We observe both classical and non-classical nucleation processes, depending on the identity of the cation present. The experiments verify theoretical studies that suggest non-classical nucleation is the lower of the two energy pathways. The arrangement in just a seven-molecule proto-crystal matches the order found by X-ray diffraction of a single bulk crystal, which demonstrates that the same structure was formed in each case.
2016
It is well established that the expression profiles of multiple and possibly redundant matrix-remodeling proteases (e.g., collagenases) differ strongly in health, disease, and development. Although enzymatic redundancy might be inferred from their close similarity in structure, their in vivo activity can lead to extremely diverse tissue-remodeling outcomes. We observed that proteolysis of collagen-rich natural extracellular matrix (ECM), performed uniquely by individual homologous proteases, leads to distinct events that eventually affect overall ECM morphology, viscoelastic properties, and molecular composition. We revealed striking differences in the motility and signaling patterns, morphology, and gene-expression profiles of cells interacting with natural collagen-rich ECM degraded by different collagenases. Thus, in contrast to previous notions, matrix-remodeling systems are not redundant and give rise to precise ECM-cell crosstalk. Because ECM proteolysis is an abundant biochemical process that is critical for tissue homoeostasis, these results improve our fundamental understanding its complexity and its impact on cell behavior.
The electron microscope has made paramount contributions to understanding the structure of biological molecules, cells, and tissues. In general, the most faithful preservation of biological specimens and other soft-organic materials is achieved through cryogenic fixation. The embedding medium is the native aqueous environment itself, immobilized in vitrified form by rapid or pressurized cooling. Until recently, imaging of such vitrified thin specimens by electron cryo-microscopy has been nearly synonymous with wide-field transmission electron microscopy (TEM). Several new approaches have entered the cryo-microscopy field, including soft x-ray imaging, serial surface imaging using focused ion beam scanning electron microscopy, phase plates, and scanning TEM (STEM). In this article, we focus on the STEM method and its adaptation to biological cryo-microscopy. Cryogenic imaging of unstained specimens by STEM introduces specific challenges. Difficulties were long considered insurmountable, and the potential advantages were underappreciated. Future developments in experimental setup and detector technologies will allow for extension of the method to thicker specimens with improved resolution and analytic capabilities.
Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an 'aloof' electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies
We recently demonstrated that cryo-scanning transmission electron tomography (CSTET) provides tomographic reconstructions of vitrified cells with superior information transfer at high tilts and for thicker specimens than defocus phase contrast (Wolf et al., 2014). In cryoSTEM, there are no image-forming lenses after the electron beam passes through the sample; detection is incoherent and inelastically scattered electrons provide usable contrast information. By obviating the need for zero-loss energy filtration, the STEM modality provides efficient use of electron dose, thereby minimizing specimen damage. Here we demonstrate the use of CSTET for obtaining highly detailed 3D architectures of organelles and macromolecular complexes in unstained, unfixed, and unsectioned cultured fibroblasts while simultaneously collecting analytical information from high-angle, incoherently scattered electrons. As a case in point, cryoSTEM tomograms revealed characteristic patterns of dense deposits sequestered in mitochondria. Energy-dispersive X-ray (EDX) spectroscopy of these deposits revealed calcium and phosphorus. Once the elemental identification was made, the STEM scattering signal could be interpreted quantitatively as a three-dimensional map of mitochondrial calcium deposition. This approach can be extended to identify and map other concentrations of elements in the cell heavier than the pervasive carbon, nitrogen, and oxygen, as we demonstrated for phosphorus in bacterial cells (Wolf et al., 2015). This study provides an example of how imaging with sensitivity to atomic number in whole cells will provide a new dimension in structural cell biology by correlating elemental composition to organelle morphology.
2015
Bacterial cells often contain dense granules. Among these, polyphosphate bodies (PPBs) store inorganic phosphate for a variety of essential functions. Identification of PPBs has until now been accomplished by analytical methods that required drying or chemically fixing the cells. These methods entail large electron doses that are incompatible with low-dose imaging of cryogenic specimens. We show here that Scanning Transmission Electron Microscopy (STEM) of fully hydrated, intact, vitrified bacteria provides a simple means for mapping of phosphorus-containing dense granules based on quantitative sensitivity of the electron scattering to atomic number. A coarse resolution of the scattering angles distinguishes phosphorus from the abundant lighter atoms: carbon, nitrogen and oxygen. The theoretical basis is similar to Z contrast of materials science. EDX provides a positive identification of phosphorus, but importantly, the method need not involve a more severe electron dose than that required for imaging. The approach should prove useful in general for mapping of heavy elements in cryopreserved specimens when the element identity is known from the biological context. Lay Description Biological cells consist primarily of the light elements: hydrogen, carbon, nitrogen, and oxygen. Heavier elements are also present in smaller quantities, e.g., calcium, magnesium, phosphorous, and iron. In certain contexts these may accumulate in specific cellular bodies or granules. While imaging in the electron microscope reveals the morphology, analytical tools are required in order to determine the elemental composition. These tools put severe constraints on sample preservation and are generally incompatible with cryogenically fixed specimens due to excessive irradiation by the electron beam. In this work we analyze phosphate-rich granules in intact, cryogenically-fixed bacteria using scanning transmission electron microscopy (STEM). Focused electrons are scattered to a range of an
Manganese(IV,V)-hydroxo and oxo complexes are often implicated in both catalytic oxygenation and water oxidation reactions. Much of the research in this area is designed to structurally and/or functionally mimic enzymes. On the other hand, the tendency of such mimics to decompose under strong oxidizing conditions makes the use of molecular inorganic oxide clusters an enticing alternative for practical applications. In this context it is important to understand the reactivity of conceivable reactive intermediates in such an oxide-based chemical environment. Herein, a polyfluoroxometalate (PFOM) monosubstituted with manganese, [NaH2(Mn-L)W17F6O55](q-), has allowed the isolation of a series of compounds, Mn(II, III, IV and V), within the PFOM framework. Magnetic susceptibility measurements show that all the compounds are high spin. XPS and XANES measurements confirmed the assigned oxidation states. EXAFS measurements indicate that Mn(II)PFOM and Mn(III)PFOM have terminal aqua ligands and Mn(V)PFOM has a terminal hydroxo ligand. The data are more ambiguous for Mn(IV)PFOM where both terminal aqua and hydroxo ligands can be rationalized, but the reactivity observed more likely supports a formulation of Mn(IV)PFOM as having a terminal hydroxo ligand. Reactivity studies in water showed unexpectedly that both Mn(IV)-OH-PFOM and Mn(V)-OH-PFOM are very poor oxygen-atom donors; however, both are highly reactive in electron transfer oxidations such as the oxidation of 3-mercaptopropionic acid to the corresponding disulfide. The Mn(IV)-OH-PFOM compound reacted in water to form O-2, while Mn(V)-OH-PFOM was surprisingly indefinitely stable. It was observed that addition of alkali cations (K+, Rb+, and Cs+) led to the aggregation of Mn(IV)-OH-PFOM as analyzed by electron microscopy and DOSY NMR, while addition of Li+ and Na+ did not lead to aggregates. Aggregation leads to a lowering of the entropic barrier of the reaction without changing the free energy barrier. The observation
Cryo-tomography of intact, vitrified cells provides a three dimensional view of their structure and organization in a snapshot of the living state. Lacking heavy metal stains, tilt series images are typically produced by defocus phase contrast. Recently, a number of other methods have been introduced for 3D cryo-imaging. These include phase plate imaging, soft X-ray tomography, serial surface imaging using the focused ion beam-scanning electron microscope, and cryo-STEM tomography (CSTET). Here we explain the basis of the STEM setup and demonstrate the capabilities of CSTET to study unfixed, fully hydrated mammalian cells. Numerous cellular features are recognized in CSTET reconstructions, including membranes, vesicles, cytoskeleton, extracellular matrix, coated pits, and ribosomes. STEM signal acquisition configuration is more flexible than defocus phase contrast, and it imposes a much less severe spatial filter on the original images. Because low spatial frequency information is retained, the STEM tomographic reconstruction more faithfully represents the mass density distribution in the specimen.
Atherosclerosis is the major precursor of cardiovascular disease. The formation of cholesterol crystals in atherosclerotic plaques is associated with the onset of acute pathology. The cholesterol crystals induce physical injury in the plaque core, promoting cell apoptosis and triggering an increased inflammatory response. Herein we address the question of how cholesterol crystal formation occurs in atherosclerosis. We demonstrate that three-dimensional (3D) cholesterol crystals can undergo directed nucleation from bilayer membranes containing two-dimensional (2D) cholesterol crystalline domains. We studied crystal formation on supported lipid bilayers loaded with exogenous cholesterol and labeled using a monoclonal antibody that specifically recognizes ordered cholesterol arrays. Our findings show that 3D crystals are formed exclusively on the bilayer regions where there are segregated 2D cholesterol crystalline domains and that they form on the domains. This study has potentially significant implications for our understanding of the crucial step in the mechanism by which atherosclerotic lesions form.
2014
Marine photosynthetic microorganisms are the basis of marine food webs and are responsible for nearly 50% of the global primary production. Emiliania huxleyi forms massive oceanic blooms that are routinely terminated by large double-stranded DNA coccolithoviruses. The cellular mechanisms that govern the replication cycle of these giant viruses are largely unknown. We used diverse techniques, including fluorescence microscopy, transmission electron microscopy, cryoelectron tomography, immunolabeling and biochemical methodologies to investigate the role of autophagy in host-virus interactions. Hallmarks of autophagy are induced during the lytic phase of E.huxleyi viral infection, concomitant with up-regulation of autophagy-related genes (ATG genes). Pretreatment of the infected cells with an autophagy inhibitor causes a major reduction in the production of extracellular viral particles, without reducing viral DNA replication within the cell. The host-encoded Atg8 protein was detected within purified virions, demonstrating the pivotal role of the autophagy-like process in viral assembly and egress. We show that autophagy, which is classically considered as a defense mechanism, is essential for viral propagation and for facilitating a high burst size. This cellular mechanism may have a major impact on the fate of the viral-infected blooms, and therefore on the cycling of nutrients within the marine ecosystem. 10.1111/(ISSN)1469-8137
A large number of inorganic materials form crystals with chiral symmetry groups. Enantioselectively synthesizing nanostructures of such materials should lead to interesting optical activity effects. Here we report the synthesis of colloidal tellurium and selenium nanostructures using thiolated chiral biomolecules. The synthesis conditions are tuned to obtain tellurium nanostructures with chiral shapes and large optical activity. These nanostructures exhibit visible optical and chiroptical responses that shift with size and are successfully simulated by an electromagnetic model. The model shows that they behave as chiral optical resonators. The chiral tellurium nanostructures are transformed into chiral gold and silver telluride nanostructures with very large chiroptical activity, demonstrating a simple colloidal chemistry path to chiral plasmonic and semiconductor metamaterials. These materials are natural candidates for studies related to interactions of chiral (bio)molecules with chiral inorganic surfaces, with relevance to asymmetric catalysis, chiral crystallization and the evolution of homochirality in biomolecules.
Cryo-electron tomography (CET) of fully hydrated, vitrified biological specimens has emerged as a vital tool for biological research. For cellular studies, the conventional imaging modality of transmission electron microscopy places stringent constraints on sample thickness because of its dependence on phase coherence for contrast generation. Here we demonstrate the feasibility of using scanning transmission electron microscopy for cryo-tomography of unstained vitrified specimens (CSTET). We compare CSTET and CET for the imaging of whole bacteria and human tissue culture cells, finding favorable contrast and detail in the CSTET reconstructions. Particularly at high sample tilts, the CSTET signals contain more informative data than energy-filtered CET phase contrast images, resulting in improved depth resolution. Careful control over dose delivery permits relatively high cumulative exposures before the onset of observable beam damage. The increase in acceptable specimen thickness broadens the applicability of electron cryo-tomography.
2013
Nitroxide spin-labelled lipid analogues are often used to study model membrane properties using EPR spectroscopy. Whereas in liquid phase membranes the spin label assumes, on average, its putative location, in gel phases and frozen membrane, depending on its position along the acyl chain, it may exhibit a different average location. Here we used H-2 three-pulse Electron Spin Echo Envelope Modulation (ESEEM) of phospholipid spin probes, combined with various deuteration schemes to detect the effect of the model membrane curvature and cholesterol on vertical migrations of the spin label. We compared large and small unilamellar 1,2-Dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) vesicles with and without cholesterol (10%). The vertical displacement of the spin label was manifested as an apparently flat trans-membrane profile of water concentration and of label proximity to the head group choline. The spin-label propensity to migrate was found to increase with vesicle curvature and decrease in the presence of cholesterol. This in turn reflects the effect of packing and ordering of the membrane lipids. The results show that in curved vesicles lacking cholesterol, the label attached to carbon 16 may travel as far high along the membrane normal as the location of the label on carbon 5, due to the presence of U-shaped lipid conformations. This phenomenon must be taken into account when using spin-labelled lipids as membrane depth markers or to trace trans-membrane profiles.
Agrobacterium is known for gene transfer to plants. In addition to a linear ssDNA oligonucleotide, Agrobacterium tumefaciens secretes an abundant ssDNA-binding effector, VirE2. In many ways VirE2 adapts the conjugation mechanism to transform the eukaryotic host. The crystal structure of VirE2 shows two compact domains joined by a flexible linker. Bound to ssDNA, VirE2 forms an ordered solenoidal shell, or capsid known as the T-complex. Here, we present a three-dimensional reconstruction of the VirE2-ssDNA complex using cryo-electron microscopy and iterative helical real-space reconstruction. High-resolution refinement was not possible due to inherent heterogeneity in the protein structure. By a combination of computational modeling, chemical modifications, mass spectroscopy, and electron paramagnetic resonance, we found that the N-terminal domain is tightly constrained by both tangential and longitudinal links, while the C terminus is weakly constrained. The quaternary structure is thus rigidly assembled while remaining locally flexible. This flexibility may be important in accommodating substrates without sequence specificity.
2012
Biologically active complexes such as ribosomes and bacteriophages are formed through the self-assembly of proteins and nucleic acids(1,2). Recapitulating these biological self-assembly processes in a cell-free environment offers a way to develop synthetic biodevices(3-6). To visualize and understand the assembly process, a platform is required that enables simultaneous synthesis, assembly and imaging at the nanoscale. Here, we show that a silicon dioxide grid, used to support samples in transmission electron microscopy, can be modified into a biochip to combine in situ protein synthesis, assembly and imaging. Light is used to pattern the biochip surface with genes that encode specific proteins, and antibody traps that bind and assemble the nascent proteins. Using transmission electron microscopy imaging we show that protein nanotubes synthesized on the biochip surface in the presence of antibody traps efficiently assembled on these traps, but pre-assembled nanotubes were not effectively captured. Moreover, synthesis of green fluorescent protein from its immobilized gene generated a gradient of captured proteins decreasing in concentration away from the gene source. This biochip could be used to create spatial patterns of proteins assembled on surfaces.
Studies of membrane peptide interactions at the molecular level are important for understanding essential processes such as membrane disruption or fusion by membrane active peptides. In a previous study, we combined several electron paramagnetic resonance (EPR) techniques, particularly continuous wave (CW) EPR, electron spin echo envelope modulation (ESEEM), and double electron-electron resonance (DEER) with Monte Carlo (MC) simulations to probe the conformation, insertion depth, and orientation with respect to the membrane of the membrane active peptide melittin. Here, we combined these EPR techniques with cryogenic transmission electron microscopy (cryo-TEM) to examine the effect of the peptide/phospholipid (P/PL) molar ratio, in the range of 1:400 to 1:25, on the membrane shape, lipids packing, and peptide orientation and penetration. Large unilamellar vesicles (LUVs) of DPPC/PG (7:3 dipalmitoylphosphatidylcholine/egg phosphatidylglycerol) were used as model membranes. Spin-labeled peptides were used to probe the peptide behavior whereas spin-labeled phspholipids were used to examine the membrane properties. The cryo-TEM results showed that melittin causes vesicle rupture and fusion into new vesicles with ill-defined structures. This new state was investigated by the EPR methods. In terms of the peptide, CW EPR showed decreased mobility, and ESEEM revealed increased insertion depth as the P/PL ratio was raised. DEER measurements did not reveal specific aggregates of melittin, thus excluding the presence of stable, well-defined pore structures. In terms of membrane properties, the CW EPR reported reduced mobility in both polar head and alkyl chain regions with increasing P/PL. ESEEM measurements showed that, as the P/PL ratio increased, a small increase in water content in the PL headgroup region took place and no change was observed in the alkyl chains part close to the hydrophilic region. In terms of lipid local density, opposite behavior was observed for the
Nanoparticles (NPs) may be exploited to make practical materials that are capable of the selective detection of (bio)molecules.[1–7] Sensing with NPs often depends on the ability to selectively form aggregates. For instance, Mirkin et al. introduced a bio-barcode amplification method for ultrasensitive protein detection.[8] Another important study involves the detection of copper ions by hybrid AuNP assemblies in click chemistry.[9, 10] The structures of AuNPbased assemblies can also be controlled electrochemically or by light.[11–13] However, despite these successes, controlling the properties and structure of NP-based assemblies with organic cross-linkers (CLs) still remains a challenge.[14] We have previously shown that the molecular geometry of CLs and the number of possible NP binding sites are related to the formation of hybrid AuNP assemblies and their associated optical properties.[15]
2011
Most molecular self-assembly strategies involve equilibrium systems, leading to a single thermodynamic product as a result of weak, reversible non-covalent interactions. Yet, strong non-covalent interactions may result in non-equilibrium self-assembly, in which structural diversity is achieved by forming several kinetic products based on a single covalent building block. We demonstrate that well-defined amphiphilic molecular systems based on perylene diimide/peptide conjugates exhibit kinetically controlled self-assembly in aqueous medium, enabling pathway-dependent assembly sequences, in which different organic nanostructures are evolved in a stepwise manner. The self-assembly process was characterized using UV/Vis circular dichroism (CD) spectroscopy, and cryogenic transmission electron microscopy (cryo-TEM). Our findings show that pathway-controlled self-assembly may significantly broaden the methodology of non-covalent synthesis.
2010
Elucidating the structure of the immature HIV-1 Gag core is an important aspect of understanding the biology of this virus. In doing so, preservation of the fragile Gag lattice is essential. In this study, the effects of purification methods on the structural and mechanical integrity of immature HIV-1 are examined. The results show that the morphological and mechanical properties of the virion are preserved to a significantly higher degree by lodixanol (OptiPrep) purification compared to the standard sucrose method. In conclusion, these results indicate that OptiPrep instead of sucrose purification should be employed when conducting structural studies on the HIV-1 virion. (C) 2010 Elsevier B.V. All rights reserved.
Amyloids are pathological fibrillar aggregates of proteins related to over 20 diseases. Amyloid fibers are characterized by the cross-beta motif, which is minimally defined as a series of beta-strands extended perpendicular to the fiber axis, joined by hydrogen bonds parallel to the fiber direction. Several structures, all in agreement with the cross-beta definition, have been proposed for specific amyloids. We study the correlation among the suprastructural chirality, molecular structure, and molecular chirality of amyloids. Here we investigate the suprastructure chirality of different (all-S) serum amyloid A (SAA) truncated peptides. We found that the suprastructure chirality of amyloid fibers from segments SAA(2-6), SAA(1-11) and the majority of those from SAA(2-9) is left-handed, which is consistent with the beta-sheet protofilament model. In contrast, SAA(1-12) and SAA(2-12) as well as SAA(1-12), where the C-terminal aspartic acid was point mutated to either leucine or alanine, form right-handed helical amyloid fibers. Such a suprastructure switch indicates a molecular change in the protofilament structure. This is supported by the behavior observed in the FTIR spectra, where the amide I peak of all of the right-handed fibers is red shifted relative to the left-handed amyloid fibers. This work is a case study where isolated short fragments of SAA containing the same amyloidogenic core sequence fold into different amyloid structures. We show that core sequences, supposed to start the misfolding aggregation of the full-length amyloid peptides, may have structures different from those assumed by the isolated segments.
Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS(2) or MoS(2) fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.
2009
Design of an extensive supramolecular three-dimensional network that is both robust and adaptive represents a significant challenge. The molecular system PP2b based on a perylene diimide chromophore (PDI) decorated with polyethylene glycol groups self-assembles in aqueous media into extended supramolecular fibers that form a robust three-dimensional network resulting in gelation. The self-assembled systems were characterized by cryo-TEM, cryo-SEM, and rheological measurements. The gel possesses exceptional robustness and multiple stimuli-responsiveness. Reversible charging of PP2b allows for switching between the gel state and fluid solution that is accompanied by switching on and off the material's birefringence. Temperature triggered deswelling of the gel leads to the (reversible) expulsion of a large fraction of the aqueous solvent. The dual sensibility toward chemical reduction and temperature with a distinct and interrelated response to each of these stimuli is pertinent to applications in the area of adaptive functional materials. The gel also shows strong absorption of visible light and good exciton mobility (elucidated using femtosecond transient absorption), representing an advantageous light harvesting system.
Amalgam, a multi-domain member of the immunoglobulin superfamily, possesses homophilic and heterophilic cell adhesion properties. It is required for axon guidance during Drosophila development in which it interacts with the extracellular domain of the transmembrame protein, neurotactin, to promote adhesion. Amalgam was heterologously expressed in Pichia pastoris, and the secreted protein product, bearing an NH(2)-terminal His(6)Tag, was purified from the growth medium by metal affinity chromatography. Size exclusion chromatography separated the purified protein into two fractions: a major, multimeric fraction and a minor, dimeric one. Two protocols to reduce the percentage of multimers were tested. In one, protein induction was performed in the presence of the zwitterionic detergent CHAPS, yielding primarily the dimeric form of amalgam. in a second protocol, agitation was gradually reduced during the course of the induction and antifoam was added daily to reduce the airiliquid interfacial foam area. This latter protocol lowered the percentage of multimer 2-fold, compared to constant agitation. Circular dichroism measurements showed that the dimeric fraction had a high beta-sheet content, as expected for a protein with an immunoglobulin fold. Dynamic light scattering and sedimentation velocity measurements showed that the multimeric fraction displays a monodisperse distribution, with R(H) = 16 nm. When co-expressed together with amalgam the ectodomain of neurotactin copurified with it. Furthermore, both purified fractions of amalgam were shown to interact with Torpedo californica acetylcholinesterase, a structural homolog of neurotactin. (C) 2008 Elsevier Inc. All rights reserved.
2008
Self-assembling systems, whose structure and function can be reversibly controlled in situ are of primary importance for creating multifunctional supramolecular arrays and mimicking the complexity of natural systems. Herein we report on photofunctional fibers self-assembled from perylene diimide cromophores, in which interactions between aromatic monomers can be attenuated through their reduction to anionic species that causes fiber fission. Oxidation with air restores the fibers. The sequence represents reversible supramolecular depolymerization-polymerization in situ and is accompanied by a reversible switching of photofunction.
Agrobacterium tumefaciens infects its plant hosts by a mechanism of horizontal gene transfer. This capability has led to its widespread use in artificial genetic transformation. In addition to DNA, the bacterium delivers an abundant ssDNA binding protein, VirE2, whose roles in the host include protection from cytoplasmic nucleases and adaptation for nuclear import. In Agrobacterium, VirE2 is bound to its acidic chaperone VirE1. When expressed in vitro in the absence of VirE1, VirE2 is prone to oligomerization and forms disordered filamentous aggregates. These filaments adopt an ordered solenoidal form in the presence of ssDNA, which was characterized previously by electron microscopy and three-dimensional image processing. VirE2 coexpressed in vitro with VirE1 forms a soluble heterodimer. VirE1 thus prevents VirE2 oligomerization and competes with its binding to ssDNA. We present here a crystal structure of VirE2 in complex with VirE1, showing that VirE2 is composed of two independent domains presenting a novel fold, joined by a flexible linker. Electrostatic interactions with VirE1 cement the two domains of VirE2 into a locked form. Comparison with the electron microscopy structure indicates that the VirE2 domains adopt different relative orientations. We suggest that the flexible linker between the domains enables VirE2 to accommodate its different binding partners.
We present the advancement of electron tomography for three-dimensional structure reconstruction of fullerene-like particles toward atomicscale resolution. The three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is achieved by the combination of low voltage operation of the electron microscope with aberration-corrected phase contrast imaging. The method enables the study of defects and irregularities in the three-dimensional structure of individual fullerene-like particles on the scale of 2 - 3 angstrom. Control over shape, size, and atomic architecture is a key issue in synthesis and design of functional nanoparticles. Transmission electron microscopy (TEM) is the primary technique to characterize materials down to the atomic level, albeit the images are two-dimensional projections of the studied objects. Recent advancements in aberration-corrected TEM have demonstrated single atom sensitivity for light elements at subangstrom resolution. Yet, the resolution of tomographic schemes for three-dimensional structure reconstruction has not surpassed 1 nm(3), preventing it from becoming a powerful tool for characterization in the physical sciences on the atomic scale. Here we demonstrate that negative spherical aberration imaging at low acceleration voltage enables tomography down to the atomic scald at reduced radiation damage. First experimental data on the three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is presented. The method is applicable to the analysis of the atomic architecture of a wide range of nanostructures where strong electron channeling is absent, in particular to carbon fullerenes and inorganic fullerenes.
Controlled formation of complex nanostructures is one of the main goals of nanoscience and nanotechnology. Stable Protein 1 (SP1) is a boiling-stable ring protein complex, 11 nm in diameter, which self-assembles from 12 identical monomers. SP1 can be utilized to form large ordered arrays; it can be easily modified by genetic engineering to produce various mutants; it is also capable of binding gold nanoparticles (GNPs) and thus forming protein-GNP chains made of alternating SP1s and GNPs. We report the formation and the protocols leading to the formation of those nanostructures and their characterization by transmission electron microscopy, atomic force microscopy, and electrostatic force microscopy. Further control over the GNP interdistances within the protein-GNP chains may lead to the formation of nanowires and structures that may be useful for nanoelectronics.
2007
MdfA is a 410-residue-long secondary multidrug transporter from E. coli. Cells expressing MdfA from a multicopy plasmid exhibit resistance against a diverse group of toxic compounds, including neutral and cationic ones, because of active multidrug export. As a prerequisite for high-resolution structural studies and a better understanding of the mechanism of substrate recognition and translocation by MdfA, we investigated its biochemical properties and overall structural characteristics. To this end, we purified the beta-dodecyl maltopyranoside (DDM)-solubilized protein using a 6-His tag and metal affinity chromatography, and size exclusion chromatography (SE-HPLC). Purified MdfA was analyzed for its DDM and phospholipid (PL) content, and tetraphenylphosphonium (TPP+)-binding activity. The results are consistent with MdfA being an active monomer in DDM solution. Furthermore, an investigation of two-dimensional crystals by electron crystallography and 3D reconstruction lent support to the notion that MdfA may also be monomeric in reconstituted proteoliposomes.
Agrobacterium tumefaciens infects plant cells by the transfer of DNA. A key factor in this process is the bacterial virulence protein VirE2, which associates stoichiometrically with the transported single-stranded (ss) DNA molecule (T-strand). As observed in vitro by transmission electron microscopy, VirE2-ssDNA readily forms an extended helical complex with a structure well suited to the tasks of DNA protection and nuclear import. Here we have elucidated the role of the specific molecular chaperone VirE1 in regulating VireE2-VirE2 and VirE2-ssDNA interactions. VirE2 alone formed functional filamentous aggregates capable of ssDNA binding. In contrast, co-expression with VirE1 yielded monodisperse VirE1-VirE2 complexes. Cooperative binding of VirE2 to ssDNA released VirE1, resulting in a controlled formation mechanism for the helical complex that is further promoted by macromolecular crowding. Based on this in vitro evidence, we suggest that the constrained volume of the VirB channel provides a natural site for the exchange of VirE2 binding from VirE1 to the T-strand.
2006
In a newly isolated temperature-sensitive lethal Escherichia coli mutant affecting the chaperonin GroEL, we observed wholesale aggregation of newly translated proteins. After temperature shift, transcription, translation, and growth slowed over two to three generations, accompanied by filamentation and accretion (in approximate to 2% of cells) of paracrystalline arrays containing mutant chaperonin complex. A biochemically isolated inclusion body fraction contained the collective of abundant proteins of the bacterial cytoplasm as determined by SDS/PAGE and proteolysis/MS analyses. Pulse-chase experiments revealed that newly made proteins, but not preexistent ones, were recruited to this insoluble fraction. Although aggregation of "stringent" GroEL/GroES-dependent substrates may secondarily produce an "avalanche" of aggregation, the observations raise the possibility, supported by in vitro refolding experiments, that the widespread aggregation reflects that GroEL function supports the proper folding of a majority of newly translated polypeptides, not just the limited number indicated by interaction studies and in vitro experiments.
Stable protein 1 (SP1) is a homo-oligomeric protein isolated from aspen (Populus tremula aspen) plants which forms a ring-shape dodecameric particle with a central cavity. The oligomeric form of SP1 is an exceptionally stable structure that is resistant to proteases (e.g., trypsin, V8, and proteinase K), high temperatures, organic solvents, and high levels of ionic detergent. Analytical ultra-centrifugation, chemical cross-linking, matrix-assisted laser-desorption time-of-flight mass spectrometry (MALDI-TOF-MS), and transmission electron microscopy were used to further characterize the SP1 dodecamer. Introduction of a single cysteine at the N-terminus of SP1 enabled the formation of disulfide bridges within the SP1 dodecamer, concurrent with increased melting point. A six-histidine tag was introduced at the N-terminus of SP1 to generate 6HSP1, and the Delta NSP1 mutant was generated by a deletion of amino acids 2-6 at the N-terminus. Both 6HSP1 and ANSP1 maintained their ability to assemble a stable dodecamer. Remarkably, these SP1 homo-dodecamers were able to re-assemble into stable hetero-dodecamers following co-electro-elution from SDS-PAGE. The exceptional stability of the SP1-nano ring and its ability to self-assemble hetero-complexes paves the way to further research in utilizing this unique protein in nano-biotechnology. (c) 2006 Wiley Periodicals, Inc.
The doublecortin-like (DCX) domains serve as protein-interaction platforms. DCX tandem domains appear in the product of the X-linked doublecortin (DCX) gene, in retinitis pigmentosa-1 (RP1), as well as in other gene products. Mutations in the human DCX gene are associated with abnormal neuronal migration, epilepsy, and mental retardation; mutations in RP1 are associated with a form of inherited blindness, while DCDC2 has been associated with dyslectic reading disabilities. Motivated by the possible importance of this gene family, a thorough analysis to detect all family members in the mouse was conducted. The DCX-repeat gene superfamily is composed of eleven paralogs, and we cloned the DCX domains from nine different genes. Our study questioned which functions attributed to the DCX domain, are conserved among the different members. Our results suggest that the proteins with the DCX-domain have conserved and unique roles in microtubule regulation and signal transduction. All the tested proteins stimulated microtubule assembly in vitro. Proteins with tandem repeats stabilized the microtubule cytoskeleton in transfected cells, while those with single repeats localized to actin-rich subcellular structures, or the nucleus. All tested proteins interacted with components of the JNK/MAP-kinase pathway, while only a subset interacted with Neurabin 2, and a nonoverlapping group demonstrated actin association. The sub-specialization of some members due to confined intracellular localization, and protein interactions may explain the success of this superfamily.
Adaptation of the halotolerant alga Dunaliella salina to iron deprivation involves extensive changes of chloroplast morphology, photosynthetic activities, and induction of a major 45-kDa chloroplast protein termed Tidi. Partial amino acid sequencing of proteolytic peptides suggested that Tidi resembles chlorophyll a/b-binding proteins which compose light-harvesting antenna complexes (LHC) ( Varsano, T., Kaftan, D., and Pick, U. ( 2003) J. Plant Nutr. 26, 2197 - 2210). Here we show that Tidi shares the highest amino acid sequence similarity with light-harvesting I chlorophyll a/b-binding proteins from higher plants but has an extended proline-rich N-terminal domain. The accumulation of Tidi is reversed by iron supplementation, and its level is inversely correlated with photosystem I(PS-I) reaction center proteins. In native gel electrophoresis, Tidi co-migrates with enlarged PS-I-LHC-I super-complexes. Single particle electron microscopy analysis revealed that PS-I units from iron-deficient cells are larger ( 31 and 37 nm in diameter) than PS-I units from control cells ( 22 nm). The 77 K chlorophyll fluorescence emission spectra of isolated complexes suggest that the Tidi-LHC-I antenna are functionally coupled to the reaction centers of PS-I. These findings indicate that Tidi acts as an accessory antenna of PS-I. The enlargement of PS-I antenna in algae and in cyanobacteria under iron deprivation suggests a common limitation that requires rebalancing of the energy distribution between the two photosystems.
2005
Type IV secretion systems (T4SSs) are used by various bacteria to deliver protein and DNA molecules to a wide range of target cells. These include systems that are directly involved in pathogenesis, such as the secretion of pertussis toxin by Bordetella pertussis into human cells and the delivery of single-stranded DNA (ssDNA) into plants by Agrobacterium. These complex systems are composed of proteins that span the bacterial cytoplasm. The Agrobacterium T4SS is composed of 12 virulence proteins and delivers its transferred ssDNA and several virulence protein substrates to a variety of eukaryotic cells. Recent studies on the Agrobacterium T4SS have revealed new information on the localization and structure of its proteins in the bacteria, the biochemical properties of its transport signal, the route of a DNA substrate through the secretion system, and the initial point of contact of the system with its host. These findings have expanded our knowledge and understanding of the still mostly obscure structure and function of the T4SSs.
The eukaryotic cytoplasmic chaperonin containing TCP-1 (CCT) is a hetero-oligomeric complex that assists the folding of actins, tubulins and other proteins in an ATP- dependent manner. To understand the allosteric transitions that occur during the functional cycle of CCT, we imaged the chaperonin complex in the presence of different ATP concentrations. Labeling by monoclonal antibodies that bind specifically to the CCT and CCT subunits enabled alignment of all the CCT subunits of a given type in different particles. The analysis shows that the apo state of CCT has considerable apparent conformational heterogeneity that decreases with increasing ATP concentration. In contrast with the concerted allosteric switch of GroEL, ATP- induced conformational changes in CCT are found to spread around the ring in a sequential fashion that may facilitate domain- by-domain substrate folding. The approach described here can be used to unravel the allosteric mechanisms of other ring-shaped molecular machines.
2004
We previously reported on a new boiling stable protein isolated from aspen plants ( Populus tremula), which we named SP1. SP1 is a stress-related protein with no significant sequence homology to other stress-related proteins. It is a 108-amino-acid hydrophilic polypeptide with a molecular mass of 12.4 kDa (Wang, W. X., Pelah, D., Alergand, T., Shoseyov, O., and Altman, A. ( 2002) Plant Physiol. 130, 865 - 875) and is found in an oligomeric form. Preliminary electron microscopy studies and matrix-assisted laser desorption ionization time-of-flight mass spectrometry experiments showed that SP1 is a dodecamer composed of two stacking hexamers. We performed a SDS-PAGE analysis, a differential scanning calorimetric study, and crystal structure determination to further characterize SP1. SDS-PAGE indicated a spontaneous assembly of SP1 to one stable oligomeric form, a dodecamer. Differential scanning calorimetric showed that SP1 has high thermostability i.e. T(m) of 107 degreesC (at pH 7.8). The crystal structure of SP1 was initially determined to 2.4 Angstrom resolution by multi-wavelength anomalous dispersion method from a crystal belonging to the space group I422. The phases were extended to 1.8 Angstrom resolution using data from a different crystal form (P21). The final refined molecule includes 106 of the 108 residues and 132 water molecules ( on average for each chain). The R-free is 20.1%. The crystal structure indicated that the SP1 molecule has a ferredoxin-like fold. Strong interactions between each two molecules create a stable dimer. Six dimers associate to form a ring-like-shaped dodecamer strongly resembling the particle visualized in the electron microscopy studies. No structural similarity was found between the crystal structure of SP1 and the crystal structure of other stress-related proteins such as small heat shock proteins, whose structure has been already determined. This structural study further supports our previous report that SP1 may represent
Splicing of pre-mRNA occurs in a multicomponent macromolecular machine-the spliceosome. The spliceosome can be assembled in vitro by a stepwise assembly of a number of snRNPs and additional proteins on exogenously added pre-mRNA. In contrast, splicing in vivo occurs in preformed particles where endogenous pre-mRNAs are packaged with all five spliceosomal U snRNPs (penta-snRNP) together with other splicing factors. Here we present a three-dimensional image reconstruction by cryo-electron microscopy of native spliceosomes, derived from cell nuclei, at a resolution of 20 Angstrom. The structure revealed an elongated globular particle made up of two distinct subunits connected to each other leaving a tunnel in between. We show here that the larger subunit is a suitable candidate to accommodate the penta-snRNP, and that the tunnel could accommodate the pre-mRNA component of the spliceosome. The features this structure reveals provide new insight into the global architecture of the native splicing machine.
Agrobacterium tumefaciens infects plant cells by a unique mechanism involving an interkingdom genetic transfer. A single-stranded DNA substrate is transported across the two cell walls along with the bacterial virulence proteins VirD2 and VirE2. A single VirD2 molecule covalently binds to the 5'-end of the single-stranded DNA, while the VirE2 protein binds stoichiometrically along the length of the DNA, without sequence specificity. An earlier transmission/scanning transmission electron microscopy study indicated a solenoidal ("telephone coil") organization of the VirE2-DNA complex. Here we report a three-dimensional reconstruction of this complex using electron microscopy and single-particle image-processing methods. We find a hollow helical structure of 15.7-nm outer diameter, with a helical rise of 51.5 nm and 4.25 VirE2 proteins/turn. The inner face of the protein units contains a continuous wall and an inward protruding shelf. These structures appear to accommodate the DNA binding. Such a quaternary arrangement naturally sequesters the DNA from cytoplasmic nucleases and suggests a mechanism for its nuclear import by decoration with host cell factors. Coexisting with the helices, we also found VirE2 tetrameric ring structures. A two-dimensional average of the latter confirms the major features of the three-dimensional reconstruction.
Bacterial spores have long been recognized as the sturdiest known life forms on earth, revealing extraordinary resistance to a broad range of environmental assaults. A family of highly conserved spore-specific DNA-binding proteins, termed alpha/beta-type small, acid-soluble spore proteins (SASP), plays a major role in mediating spore resistance. The mechanism by which these proteins exert their protective activity remains poorly understood, in part due to the lack of structural data on the DNA-SASP complex. By using cryoelectron microscopy, we have determined the structure of the helical complex formed between DNA and SspC, a characteristic member of the alpha/beta-type SASP family. The protein is found to fully coat the DNA, forming distinct protruding domains, and to modify DNA structure such that it adopts a 3.2-nm pitch. The protruding SspC motifs allow for interdigitation of adjacent DNA-SspC filaments into a tightly packed assembly of nucleoprotein helices. By effectively sequestering DNA molecules, this dense assembly of filaments is proposed to enhance and complement DNA protection obtained by DNA saturation with the alpha/beta-type SASP.
The textbook view of the bacterial cytoplasm as an unstructured environment has been overturned recently by studies that highlighted the extent to which non-random organization and coherent motion of intracellular components are central for bacterial life-sustaining activities. Because such a dynamic order critically depends on continuous consumption of energy, it cannot be perpetuated in starved, and hence energy-depleted, stationary-state bacteria. Here, we show that, at the onset of the stationary state, bacterial chromatin undergoes a massive reorganization into ordered toroidal structures through a process that is dictated by the intrinsic properties of DNA and by the ubiquitous starvation-induced DNA-binding protein Dps. As starvation proceeds, the toroidal morphology acts as a structural template that promotes the formation of DNA-Dps crystalline assemblies through epitaxial growth. Within the resulting condensed assemblies, DNA is effectively protected by means of structural sequestration. We thus conclude that the transition from bacterial active growth to stationary phase entails a co-ordinated process, in which the energy-dependent dynamic order of the chromatin is sequentially substituted with an equilibrium crystalline order.
2003
The reaction cycle of the double-ring chaperonin GroEL is driven by ATP binding that takes place with positive cooperativity within each seven-membered ring and negative cooperativity between rings. The positive cooperativity within rings is due to ATP binding-induced conformational changes that are fully concerted. Herein, it is shown that the mutation Asp-155 --> Ala leads to an ATP-induced break in intra-ring and inter-ring symmetry. Electron microscopy analysis of single-ring GroEL particles containing the Asp-155 Ala mutation shows that the break in intra-ring symmetry is due to stabilization of allosteric intermediates such as one in which three subunits have switched their conformation while the other four have not. Our results show that eliminating an intra-subunit interaction between Asp-155 and Arg-395 results in conversion of the allosteric switch of GroEL from concerted to sequential, thus demonstrating that its allosteric behavior arises from coupled tertiary conformational changes.
2001
The enhanced stress resistance exhibited by starved bacteria represents a central facet of virulence, since nutrient depletion is regularly encountered by pathogens in their natural in vivo and ex vivo environments. Here we explore the notion that the regular stress responses, which are mediated by enzymatically catalyzed chemical transactions and promote endurance during the logarithmic growth phase, can no longer be effectively induced during starvation, We show that survival of bacteria in nutrient-depleted habitats is promoted by a novel strategy: finely tuned and fully reversible intracellular phase transitions. These nonenzymatic transactions, detected and studied in bacteria as well as in defined in vitro systems, result in DNA sequestration and generic protection within tightly packed and highly ordered assemblies. Since this physical mode of defense is uniquely independent of enzymatic activity or de novo protein synthesis, and consequently does not require energy consumption, it promotes virulence by enabling long-term bacterial endurance and enhancing antibiotic resistance in adverse habitats.
2000
The inducible SOS response increases the ability of bacteria to cope with DNA damage through various DNA repair processes in which the RecA protein plays a central role. Here we present the first study of the morphological aspects that accompany the SOS response in Escherichia coil. We find that induction of the SOS system in wild-type bacteria results in a fast and massive intracellular coaggregation of RecA and DNA into a lateral macroscopic assembly. The coaggregates comprise substantial portions of both the cellular RecA and the DNA complement. The structural features of the coaggregates and their relation to in vitro RecA-DNA networks, as well as morphological studies of strains carrying RecA mutants, are all consistent with the possibility that the intracellular assemblies represent a functional entity in which RecA-mediated DNA repair and protection activities occur.
Mutations in the X-linked gene doublecortin (DCX) result in lissencephaly in males or subcortical laminar heterotopia ('double cortex') in females, Various types of mutation were identified and the sequence differences included nonsense, splice site and missense mutations throughout the gene. Recently, we and others have demonstrated that DCX interacts and stabilizes microtubules, Here, we performed a detailed sequence analysis of DCX and DCX-like proteins from various organisms and defined an evolutionarily conserved Doublecortin (DC) domain. The domain typically appears in the N-terminus of proteins and consists of two tandemly repeated 80 amino acid regions, In the large majority of patients, missense mutations in DCX fall within the conserved regions. We hypothesized that these repeats may be important for microtubule binding, We expressed DCX or DCLK (KIAA0369) repeats in vitro and in vivo. Our results suggest that the first repeat binds tubulin but not microtubules and enhances microtubule polymerization. To study the functional consequences of DCX mutations, we overexpressed seven of the reported mutations in COS7 cells and examined their effect on the microtubule cytoskeleton. The results demonstrate that some of the mutations disrupt microtubules. The most severe effect was observed with a tyrosine to histidine mutation at amino acid 125 (Y125H). Produced as a recombinant protein, this mutation disrupts microtubules in vitro at high molar concentration. The positions of the different mutations are discussed according to the evolutionarily defined DC-repeat motif. The results from this study emphasize the importance of DCX-microtubule interaction during normal and abnormal brain development.
1999
X-linked lissencephaly is a severe brain malformation affecting males. Recently it has been demonstrated that the doublecortin gene is implicated in this disorder. In order to study the function of Doublecortin, we analyzed the protein upon transfection of COS cells. Doublecortin was found to bind to the microtubule cytoskeleton, In vitro assays (using biochemical methods, DIC microscopy and electron microscopy) demonstrate that Doublecortin binds microtubules directly, stabilizes them and causes bundling. In vivo assays also show that Doublecortin stabilizes microtubules and causes bundling. Doublecortin is a basic protein with an isoelectric point of 10, typical of microtubule-binding proteins. However, its sequence contains no known microtubule-binding domain(s). The results obtained in this study with Doublecortin and our previous work on another lissencephaly gene (LIS1) emphasize the central role of regulation of microtubule dynamics and stability during neuronal morphogenesis.
The crystalline state is considered to be incompatible with life. However, in living systems exposed to severe environmental assaults, the sequestration of vital macromolecules in intracellular crystalline assemblies may provide an efficient means for protection. Here we report a generic defence strategy found in Escherichia coli, involving co-crystallization of its DNA with the stress-induced protein Dps(1,2). We show that when purified Dps and DNA interact, extremely stable crystals form almost instantaneously, within which DNA is sequestered and effectively protected against varied assaults. Crystalline structures with similar lattice spacings are formed in E. coli in which Dps is slightly over expressed, as well as in starved wild-type bacteria. Hence, DNA-Dps co-crystallization is proposed to represent a binding mode that provides wide-range protection of DNA by sequestration. The rapid induction and large-scale production of Dps in response to stress, as well as the presence of Dps homologues in many distantly related bacteria, indicate that DNA protection by biocrystallization may be crucial and widespread in prokaryotes.
1998
The alpha beta tubulin heterodimer is the structural subunit of microtubules, which are cytoskeletal elements that are essential for intracellular transport and cell division in all eukaryotes. Each tubulin monomer binds a guanine nucleotide, which is non-exchangeable when it is bound in the alpha subunit, or N site, and exchangeable when bound in the beta subunit, or E site. The alpha- and beta-tubulins share 40% amino-acid sequence identity, both exist in several isotype forms, and both undergo a variety of posttranslational modifications'. Limited sequence homology has been found with the proteins FtsZ(2) and Misato(3), which are involved in cell division in bacteria and Drosophila, respectively. Here we present an atomic model of the alpha beta tubulin dimer fitted to a 3.7-Angstrom density map obtained by electron crystallography of zinc-induced tubulin sheets. The structures of alpha- and beta-tubulin are basically identical: each monomer is formed by a core of two beta-sheets surrounded by alpha-helices. The monomer structure is very compact, but can be divided into three functional domains: the amino-terminal domain containing the nucleotide-binding region, an intermediate domain containing the Taxol-binding site, and the carboxy-terminal domain, which probably constitutes the binding surface for motor proteins.
1997
We are in the process of determining the structure of tubulin using electron crystallography of zinc-induced, crystalline sheets. We have now extended the resolution to 4 A, and there are many features in the map that appear to show details of the secondary structure. X-ray crystallographers are well aware of the problems of interpreting maps with such limited resolution, and the additional problem of the missing cone of data inherent in electron crystallography may make interpretation even more difficult. To investigate how reliably these maps can be interpreted, we have calculated density maps of a known structure, actin, under conditions similar to those of the tubulin map. Results of these simulations support the limited interpretations we made previously in the 6.5-A maps and the more extensive interpretations we make here in the 4-A map. Most of the secondary structure of the tubulin dimer can now be identified.
1996
We previously used electron crystallography of zinc-induced two-dimensional crystalline sheets of tubulin to construct a medium-resolution three dimensional (3-D) reconstruction (at 6.5 Angstrom) of this protein. Here we present an improved model, and extend the interpretation to correlate it to microtubule structure. Secondary sequence predictions and projection density maps of subtilisin-cleaved tubulin provide information on the location of the C-terminal portion, which has been suggested to be involved in the binding of microtubule-associated proteins. The zinc-sheet tubulin model is compared to microtubules in two ways; comparison of electron diffraction from the zinc-sheets to electron diffraction from microtubules, and by docking the zinc-sheet protofilament 3-D model into a helical reconstruction from ice-embedded microtubules. By correlating the zinc-sheet protofilament to a reconstruction of axonemal protofilaments, we assigned polarity to the protofilament in our model. The polarity assignment, together with our model for dimer boundaries and the assignment of alpha- and beta-monomers in our reconstruction, provides a microtubule model where the alpha-monomer crowns the plus- (or fast-growing) end of the microtubule and contact is made in the centrosome with gamma-tubulin via the beta-monomer. (C) 1996 Academic Press Limited
1995
Zinc-induced sheets of tubulin are two-dimensional crystalline polymers that constitute an ideal sample for high resolution studies of tubulin by electron crystallography. We show that these 2-dimensional tubulin crystals can be stabilized by taxol against low-temperature depolymerization and degradation with time, easing the way for the preparation of electron microscopy samples. The preservation of the crystals to high resolution has been tested with different embedding media. While glucose-embedded samples diffract poorly, samples embedded in tannin consistently diffract to a resolution of at least 3.5 A. Even better results are obtained by embedding with a combination of tannin and glucose, which improves the flatness of the crystals and allows the collection of isotropic high-resolution data from tilted specimens.
Tubulin, the major component of microtubules, is a heterodimer of two chains, alpha and beta, both of relative molecular mass 50,000 (Mr50K) and with 40-50% identity. The isotypic variety and conformational flexibility of tubulin have so far made it impossible to obtain crystals for X-ray work. Structural knowledge of tubulin has been limited to about 20 A from X-ray diffraction of oriented microtubules, and from electron microscopy of microtubules and zinc-induced crystalline sheets in negative stain. The sheets consist of protofilaments similar to those in microtubules but associated in an antiparallel arrangement, and their two-dimensional character is ideal for high-resolution electron microscopy. Here we present a three-dimensional reconstruction of tubulin to 6.5 A resolution, obtained by electron crystallography of zinc-induced two-dimensional crystals of the protein. The alpha- and beta-subunits appear topologically similar, in agreement with their sequence homology. Several features can be defined in terms of secondary structure. An apparent alpha-helical portion, adjacent to both interdimer and inter-protofilament contacts, is tentatively attributed to a segment near the carboxy terminus of the protein. We can assign the alpha- and beta-subunits on the basis of projection studies of the binding of taxol, which show one taxol site per tubulin heterodimer, in agreement with the known stoichiometry of taxol in microtubules. These studies indicate that taxol affects the interaction between protofilaments; to our knowledge, this is the first time that a ligand-binding site has been visualized in the tubulin molecule.
Moving along a microtubule, kinesin follows a course parallel to the protofilaments; but it is not known whether kinesin binds exclusively on a single protofilament. The presence of zinc during tubulin polymerization induces sheets where neighboring protofilaments are antiparallel. If kinesin could support the motility of these zinc-sheets, then the binding site for a kinesin molecule would be limited to a single protofilament. Kamimura and Mandelkow [1992: J. Cell Biol. 118:865-75] reported that kinesin moves along zinc-sheets. We found that zinc-sheets grown under their conditions often had a microtubule-like structure along one edge. We confirmed the possibility that the motility observed by Kamimura and Mandelkow [1992: J. Cell Biol. 118:865-75] is attributed to the microtubule-like structure rather than the zinc-sheet. To resolve the question of whether kinesin can recognize an antiparallel protofilament lattice, we investigated the kinesin-mediated motility of zinc-macrotubes. At higher free zinc concentrations, zinc-sheets roll up as macrotubes, free of edges. In the presence of 10 microM taxol and 100 nM free Zn2+ at pH 6.8, the samples were shown by electron microscopy to contain only macrotubes. Under these buffer conditions, kinesin could bind strongly to axonemal doublets in the presence of AMP-PNP, and generate motility in the presence of ATP, but kinesin did not bind to nor move the macrotubes. This shows that kinesin cannot bind efficiently to nor move on the anti-parallel lattice; it is possible (though not necessary) that the groove between two parallel protofilaments is required for kinesin's motility.
1994
Imperfect specimen flatness can be a significant limitation in the application of electron crystallography to high-resolution structure analysis of biological macromolecules. We now report that the choice of solid carbon stock that is used to make evaporated carbon films can have a very great effect on the preparation of flat specimens of glucose-embedded purple membrane. The degree of purity of the carbon does not seem to be the controlling factor, and other likely factors such as the type of mica used as a substrate, the evaporation apparatus used (and its limiting vacuum), and the use of a continuous versus an interrupted evaporation protocol do not have a discernible influence. The physical or chemical basis for the observed differences in specimen flatness is still unknown; however, the important conclusion that we can communicate at this point is that the choice of evaporating material does have a major effect on the flatness of purple membrane, the specimen used here. The implication is that different sources of carbon stock should be tried whenever difficulty is encountered in the preparation of suitably flat specimens of biological macromolecules.
1993
The protein tubulin is the main constituent of microtubules. Previous studies have shown that zinc ions induce the formation of crystalline sheets and macrotubes of tubulin. Both crystal types are suitable for structural studies by electron crystallography. However, crystallographic structural analysis of tubulin has been hampered by limited crystal size and quality and the inability to control crystal polymorphism. We can obtain well-ordered crystals which are grown upon prolonged incubations (up to 24 hr). The presence of NaCl delays the degradation of the crystals, and addition of the protease inhibitor pepstatin improves crystal quality. The crystal form (sheet or macrotube) can be controlled with incubation conditions. The size of the crystals can reach up to 2 microns in width for the sheets and up to 0.5 microns in diameter for the macrotubes. Both crystal types can reach several micrometers in length. Comparison of the projection maps of the two crystal structures shows that adjacent protofilaments in the macrotubes are shifted by about 6 A relative to their positions in the sheets. Observable changes of monomer shape appear to allow close interprotofilament contacts to be maintained in both crystal forms. Images of glucose-embedded specimens obtained under these conditions give structural information beyond 4 A resolution. Merging of high- and low-resolution data allows for unambiguous assignment of monomer boundaries to high-resolution features.
1992
Recently, grazing-incidence X-ray diffraction studies of insoluble amphiphilic molecules have shown that molecules possessing fluorocarbon chains crystallize more efficiently on the surface of water that those possessing hydrocarbon chains. Here, we perform lattice energy calculations involving atomic electrostatic and van der Waals parameters on model two-dimensional crystals of hydrocarbon chains and fluorocarbon chains which possess crystalline arrangements similar to those of the corresponding amphiphilic films on water. The electrostatic parameters of CF2 groups were determined from an X-ray study of the deformation electron density of perfluoroglutaramide, using single-crystal low-temperature (approximately 100 K) X-ray diffraction data. The net charge on the fluorine atoms q = -0.14 e is almost twice that on hydrogen atoms q = +0.06 e, suggesting that intramolecular repulsion between fluorines will limit the possibility for conformational disorder in fluorocarbon chains. The calculated lattice energy of the model 2-D crystalline films of vertical fluorocarbon chains containing 20 carbons is lower by about 3.0 kcal per CF2 group than the lattice energy of the model 2-D crystalline films of vertical hydrocarbon chains with the same number of carbons. We conclude that the crystallization behavior of amphiphilic molecules with fluorocarbon chains is determined by a higher backbone stiffness and higher interchain attractive van der Waals forces than for molecules with hydrocarbon chains. In addition, we show that it is possible to simply correlate the calculated lattice energies and the observed crystalline self-assembly at the air-water interface in various amphiphilic systems, in particular the homologous series of carboxylic acid molecules CnH2n+1CO2H (n = 13, 19, 20, 21, 29): for more attractive lattice energies, the extent of crystalline order is larger.
The advent of well-collimated, high-intensity synchrotron X-ray sources and the consequent development of surface-specific X-ray diffraction and fluorescence techniques have recently revolutionized the study of Langmuir monolayers at the air-liquid interface. These methods allowed for the first time the determination of the in-plane and vertical structure of such monolayers with a resolution approaching the atomic level. We briefly describe these methods, including grazing incidence X-ray diffraction, specular reflectivity, Bragg rods, standing waves, and surface fluorescence techniques, and review recent results obtained from them for Langmuir films. The methods have been successfully applied in the elucidation of the structure of crystalline aggregates of amphiphilic molecules such as alcohols, carboxylic acids and their salts, alpha-amino acids, and phospholipids at the water surface. In addition, it became possible to monitor by diffraction the growth and dissolution of the crystalline self-aggregates as well as structural changes occurring by phase transitions. Furthermore, the surface X-ray methods shed new light on the structure of the underlying ionic layer of attached solvent or solute species. Examples are given where singly or doubly charged ions bound to the two-dimensional (2D) crystal form either an ordered or diffuse counterionic layer. Finally, the surface diffraction methods provide data on transfer of structural information from 2D clusters to 3D single crystals, which had been successfully accomplished by epitaxial-like crystallization both in organic and inorganic crystals.
1990
In order to provide, on the molecular level, information on crystal nucleation of monolayers at air-water interfaces, the self-aggregation of lH,lH,2H,2H-perfiuorododecyl aspartate CF3(CF2)9(CH2)20COCH2CH(NH3+)C02~ (PFA) over water subphases at various pH values was studied using synchrotron X-ray grazing incidence diffraction (GID), including Bragg rods (BR) and reflectivity (XR) measurements. Two-dimensional crystalline domains with coherence lengths exceeding 1 500 A were detected for low surfactant surface densities and zero surface pressure. GID measurements reveal structural changes with subphase pH and composition. Structural models are proposed at high, neutral, and low pH. For water subphases containing KOH at pH > 11.2, the diffraction is consistent with molecules arranged in a hexagonal net and vertically aligned. Over pure water and acidic subphases containing HC1 at pH = 1.5, the molecules pack in a distorted hexagonal net with the fluorocarbon chains tilted from the vertical. The growth in time of the uncompressed crystallites over aqueous glycine solutions was directly monitored by GID. Compression and subsequent decompression of the monolayers over pure water and HC1 (pH = 1.5) subphases, for which the fluorocarbon chains are originally tilted, were found to reduce the crystallinity of the system considerably. By contrast, over KOH at pH > 11.2, the hexagonal net with vertically aligned molecules is preserved at all surface pressures and the crystalline order of the system is reduced upon compression but increases again upon release of pressure. Estimates of the degree of crystallinity of the monolayer were made over water for various states of compression and over KOH at pH >11.2 in the uncompressed state. The packing characteristics and the dynamics involved in the formation and partial destruction of the crystallites can be understood in terms of interaction between the hydrophilic ionic head groups of the monolayer and, if present, the attached molecules or ions (water, K+ or Cl"). Additional support for the packing arrangements proposed at high, neutral, and low pH was obtained from studies of the oriented growth of sodium chloride under PFA monolayers.
The packing disorder in racemic valine is characterized by techniques previously used to control nucleation, growth, and dissolution of crystals. R,S-valine crystals were grown and dissolved in the presence of other racemic α-amino acid additives. We inferred the presence of disorder in R,S-valine crystals from the lack of enantiomeric segregation of the additives occluded inside growing crystals, and from the non-specific etch-pit formation on the faces of dissolving crystals. Subsequent X-ray diffraction studies showed the disorder to arise from “flipping” of hydrogen-bonded bilayers across interfaces which are linked by relatively weak hydrophobic interactions. Possible mechanisms for the disorder are discussed.
1989
Monolayers of PFA, a fluorinated surfactant, on water were studied using synchrotron X-ray grazing incidence diffraction (GID) and reflectivity measurements (XR). The uncompressed monolayer is found to self-assemble into crystalline domains giving a strong GID peak. Upon compression and decompression a surface pressure driven solid-solid phase transition takes place. A hexagonal lattice with vertical molecules at high pressure undergoes a distortion due to a rigid molecular tilt as the pressure is decreased. Bragg rod scans provide conclusive evidence for a tilt of about 20 " at 10 mN/m and show the tilt to be towards nearest neighbours. The uncompressed monolayer has a molecular tilt of about 25 '.
Crystal nucleation of glycine and sodium chloride has been studied under floating Langmuir monolayers at air/solution interfaces, and at glass slides coated with Langmuir-Blodgett films. The packing arrangements of the polar head groups of the monolayers were varied in a controlled manner by introducing different groups in the hydrophobic tails. The structures of some of these monolayers were independently elucidated by grazing incidence X-ray diffraction and reflectivity measurements using synchrotron light. It was found that the crystals nucleated at the interface exposed a top layer of molecules with an arrangement similar or complementary to that of the polar head groups of the monolayer. These results imply that the packing of the polar head groups determines the morphology and the nucleation rate of the attached crystal.
In a stereochemical approach aimed at the understanding of crystal nucleation on a molecular level, the oriented crystallization of glycine at air-solution interfaces covered with monolayers 1-12 of resolved a-amino acids has been studied. Three types of monolayers with different packing motifs of the polar head groups have been used. Coverage of a supersaturated aqueous glycine solution with monolayers 1 and 2 did not lead to crystallization at the interface; on the other hand, coverage with monolayers 3-8 yielded a fast crystallization with only partial orientation. Finally, monolayers 9-12 yielded a fast nucleation of glycine with complete orientation of the crystals. These results imply that the packing of the polar head groups determines the nucleation rate and the degree of orientation of the attached growing crystals. This conclusion is strongly substantiated by the assignment of the structures of monolayers 3 and 9 using grazing-angle X-ray diffraction and reflectivity measurements from a synchrotron light source. Crystallization experiments were performed on solid hydrophobic glass supports coated with Langmuir-Blodgett films of monolayers of 1, 3, 4, 6, 9, and 11; in all cases the results were similar to those observed with the corresponding Langmuir monolayers
1988
A measurement and interpretation on a molecular level of a phase transition in an ordered Langmuir monolayer is reported. The diagram of surface pressure (π) versus molecular area of a monolayer of chiral (S)-[CF3-(CF2)9-(CH2)2-OCO-CH2-CH (NH3+)CO2-] over water shows a change in slope at about πs= 25 millinewtons per meter. Grazing-incidence x-ray diffraction and specular reflectivity measurements indicate a solid-solid phase transition at πs. The diffraction pattren at low pressures reveals two diffraction peaks of equal intensities, with lattice spacings d of 5.11 and 5.00 angstroms; these coalesce for π ≥πs. Structural models that fit the diffraction data show that at π> πs the molecules pack in a two-dimensional crystal with the molecules aligned vertically. At π < πs there is a molecular tilt of 16 ° ± 7 °. Independent x-ray reflectivity data yield a tilt of 26 ° ± 7°. Concomitant with the tilt, the diffraction data indicate a transition from a hexagonal to a distorted-hexagonal lattice. The hexagonal arrangement is favored because the -(CF2)9CF3 moiety adopts a helical conformation. Compression to 70 millinewtons per meter yields a unit cell with increased crystallinity and a coherence length exceeding 1000 angstroms.
We have determined the packing arrangement of a floating monolayer of palmitoyl-(R)-lysine at the air-water interface by grazing incidence X-ray diffraction and reflection measurements. These techniques utilize the unique properties of synchrotron radiation: high intensity within a small natural collimation. In the grazing angle diffraction experiment two peaks were detected in the "twodimensional powder" pattern from a monolayer of palmitoyl-(R)-lysine. Their widths indicated coherence lengths of 500 J~. The positions and intensities of these peaks allowed us to choose between various models and to determine the monolayer structure. The packing arrangement of the Qt-amino acid headgroups in the model proved to be very similar to that found in the crystal structures of the 0t form of glycine and several hydrophobic at-amino acids, thus providing a simple explanation for the oriented crystallization of 0t-glycine at monolayer-solution interfaces. The tilt of the molecule calculated from the model is consistent with the results from reflectivity measurements and X-ray powder diffraction data of the crystalline powder material. Reflectivity measurements indicate that at surface pressures as high as 30 mN m- 1 the monolayer covers only about 90% of the surface. Reflectivity measurements of the monolayer over water and over solutions of 29/o (S)-glutamine showed significant differences, indicating binding of the solute molecules to the monolayer.
1987
Recently it has been demonstrated that a compressed monolayer of palmitoyl-(R)-lysine (Fig. 1) on the surface of water induces the orientated growth of α-glyeine crystals. This effect was inter-preted to be a structural match between the monolayer and the α-glycine. To test this hypothesis we undertook to determine the packing arrangement of the monolayer by grazing incidence X-ray diffraction and reflection. These techniques use the unique proper-ties of synchrotron radiation: high intensity within a small natural collimation. In the diffraction experiment two peaks were detect-able in the two-dimensional powder pattern from a monolayer of palmitoyl-(R)-lysine. The positions and intensities of these peaks allowed us to choose between various models and determine the monolayer structure. This is the first time that the crystal structure of a compressed surfactant monolayer at the air–water interface has been determined. The same techniques could be used for structural characterization of other monolayers of interest in fields as diverse as biological membranes and optical second harmonic generation. The packing arrangement of the α-amino acid head groups in the model proved to be very similar to that found in the crystal structures of α-glycine and several hydrophobic α-amino acids.