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Articles by Vlad Brumfeld in JoVE

 JoVE Bioengineering

High Resolution 3D Imaging of Ex-Vivo Biological Samples by Micro CT


JoVE 2688 6/21/2011

1Department of Molecular Genetics, Weizmann Institute of Science, 2Department of Biological Regulation, Weizmann Institute of Science, 3Department of Chemical Infrastructure, Weizmann Institute of Science

Non-destructive volume visualization can be achieved only by tomographic techniques, of which the most efficient is the x-ray micro computerized tomography ( CT).

Other articles by Vlad Brumfeld on PubMed

The PKA Phosphorylation of Vitronectin: Effect on Conformation and Function

Vitronectin (Vn) stabilizes the inhibitory form of plasminogen activator inhibitor-1 (PAI-1), an important modulator of fibrinolysis. We have previously reported that Vn is specifically phosphorylated by PKA (at Ser378), a kinase we have shown to be released from platelets upon their physiological activation. Here we describe the molecular consequences of this phosphorylation and show (by circular dichroism, and by phosphorylation with casein kinase II) that it acts by modulating the conformation of Vn. The PKA phosphorylation of Vn is enhanced in the presence of either PAI-1, or heparin, or both. This enhanced phosphorylation occurs exclusively on Ser378 as shown with the Vn mutants Ser378Ala and Ser378Glu. The binding of PKA phosphorylated Vn to immobilized PAI-1 and to immobilized plasminogen is shown to be lower than that of Vn. The evidence compiled here suggests that this phosphorylation of Vn can modulate plasminogen activation and consequently control fibrinolysis.

From Chloroplasts to Photosystems: in Situ Scanning Force Microscopy on Intact Thylakoid Membranes

Envelope-free chloroplasts were imaged in situ by contact and tapping mode scanning force microscopy at a lateral resolution of 3-5 nm and vertical resolution of approximately 0.3 nm. The images of the intact thylakoids revealed detailed structural features of their surface, including individual protein complexes over stroma, grana margin and grana-end membrane domains. Structural and immunogold-assisted assignment of two of these complexes, photosystem I (PS I) and ATP synthase, allowed direct determination of their surface density, which, for both, was found to be highest in grana margins. Surface rearrangements and pigment- protein complex redistribution associated with salt-induced membrane unstacking were followed on native, hydrated specimens. Unstacking was accompanied by a substantial increase in grana diameter and, eventually, led to their merging with the stroma lamellae. Concomitantly, PS IIalpha effective antenna size decreased by 21% and the mean size of membrane particles increased substantially, consistent with attachment of mobile light-harvesting complex II to PS I. The ability to image intact photosynthetic membranes at molecular resolution, as demonstrated here, opens up new vistas to investigate thylakoid structure and function.

Polyproline Type II Conformation in the C-terminal Domain of the Nuclear Pore Complex Protein Gp210

gp210 is a major constituent of the nuclear pore complex (NPC) with possible structural and regulatory roles. It interacts with components of the NPC via its C-terminal domain (CTD), which follows a transmembrane domain and a massive ( approximately 200 kDa) N-terminal region that resides in the lumen of the perinuclear space. Here, we report the solution structure of the human gp210 CTD as determined by various spectroscopic techniques. In water, the CTD adopts an extended, largely unordered conformation, which contains a significant amount of left-handed polyproline type II (PII) helical structure. The conformation of the CTD is altered by high pH, charged detergents, and the hydrogen bond-promoting reagent trifluoroethanol (TFE), which decrease the PII fraction of the fragment. TFE also induces a conformational change in a region containing an SPXX motif whose serine becomes specifically phosphorylated during mitosis. We propose that PII elements in the CTD may play a role in its interaction with the NPC and may serve as recognition sites for regulatory proteins bearing WW or other, unknown PII-binding motifs.

A Molecular Switch Between Alternative Conformational States in the Complex of Ran and Importin Beta1

Several million macromolecules are exchanged each minute between the nucleus and cytoplasm by receptor-mediated transport. Most of this traffic is controlled by the small GTPase Ran, which regulates assembly and disassembly of the receptor-cargo complexes in the appropriate cellular compartment. Here we applied dynamic force spectroscopy to study the interaction of Ran with the nuclear import receptor importin beta1 (impbeta) at the single-molecule level. We found that the complex alternates between two distinct conformational states of different adhesion strength. The application of an external mechanical force shifts equilibrium toward one of these states by decreasing the height of the interstate activation energy barrier. The other state can be stabilized by a functional Ran mutant that increases this barrier. These results support a model whereby functional control of Ran-impbeta is achieved by a population shift between pre-existing alternative conformations.

DNA Toroids: Framework for DNA Repair in Deinococcus Radiodurans and in Germinating Bacterial Spores

Direct Discrimination Between Models of Protein Activation by Single-molecule Force Measurements

The limitations imposed on the analyses of complex chemical and biological systems by ensemble averaging can be overcome by single-molecule experiments. Here, we used a single-molecule technique to discriminate between two generally accepted mechanisms of a key biological process--the activation of proteins by molecular effectors. The two mechanisms, namely induced-fit and population-shift, are normally difficult to discriminate by ensemble approaches. As a model, we focused on the interaction between the nuclear transport effector, RanBP1, and two related complexes consisting of the nuclear import receptor, importin beta, and the GDP- or GppNHp-bound forms of the small GTPase, Ran. We found that recognition by the effector proceeds through either an induced-fit or a population-shift mechanism, depending on the substrate, and that the two mechanisms can be differentiated by the data.

Enhanced Intracellular Mobility and Nuclear Accumulation of DNA Plasmids Associated with a Karyophilic Protein

The use of synthetic gene delivery systems in human gene transfer is hampered by poor transfection efficiencies, largely because of the inability of DNA to translocate across the nuclear pore complex. A means to overcome this barrier is to bind the DNA to nuclear localization signals (NLSs), which are recognized by shuttling receptors of the nuclear import machinery. Here, we studied the intracellular transport of plasmid DNA microinjected into HeLa cell cytoplasm, alone or as a complex with intact or NLS-deleted NFkappaB p50, using confocal microscopy imaging. We found that association of NLS-carrying p50 with DNA facilitated not only nuclear entry of the DNA but also its migration through the cytoplasm toward the nucleus. Facilitated transport of p50-DNA complexes in the cytoplasm proceeded along microtubules in a dynein-dependent manner and is mediated by the heterodimeric nuclear transport receptor that recognizes the p50-born NLS.

The Microenvironment Effect on the Generation of Reactive Oxygen Species by Pd-bacteriopheophorbide

Generation of reactive oxygen species (ROS) is the hallmark of important biological processes and photodynamic therapy (PDT), where ROS production results from in situ illumination of certain dyes. Here we test the hypothesis that the yield, fate, and efficacy of the species evolved highly depend on the dye's environment. We show that Pd-bacteriopheophorbide (Pd-Bpheid), a useful reagent for vascular targeted PDT (VTP) of solid tumors, which has recently entered into phase II clinical trials under the code name WST09 (trade name TOOKAD), forms appreciable amounts of hydroxyl radicals, superoxide radicals, and probably hydrogen peroxide in aqueous medium but not in organic solvents where singlet oxygen almost exclusively forms. Evidence is provided by pico- and nanosecond time-resolved spectroscopies, ESR spectroscopy with spin-traps, time-resolved singlet oxygen phosphorescence, and chemical product analysis. The quantum yield for singlet oxygen formation falls from approximately 1 in organic solvents to approximately 0.5 in membrane-like systems (micelles or liposomes), where superoxide and hydroxyl radicals form at a minimal quantum yield of 0.1%. Analysis of photochemical products suggests that the formation of oxygen radicals involves both electron and proton transfer from (3)Pd-Bpheid at the membrane/water interface to a colliding oxygen molecule, consequently forming superoxide, then hydrogen peroxide, and finally hydroxyl radicals, with no need for metal catalysis. The ability of bacteriochlorophyll (Bchl) derivatives to form such radicals upon excitation at the near infrared (NIR) domain opens new avenues in PDT and research of redox regulation in animals and plants.

Direct Measurement of Protein Energy Landscape Roughness

The energy landscape of proteins is thought to have an intricate, corrugated structure. Such roughness should have important consequences on the folding and binding kinetics of proteins, as well as on their equilibrium fluctuations. So far, no direct measurement of protein energy landscape roughness has been made. Here, we combined a recent theory with single-molecule dynamic force spectroscopy experiments to extract the overall energy scale of roughness epsilon for a complex consisting of the small GTPase Ran and the nuclear transport receptor importin-beta. The results gave epsilon > 5k(B)T, indicating a bumpy energy surface, which is consistent with the ability of importin-beta to accommodate multiple conformations and to interact with different, structurally distinct ligands.

Three-dimensional Organization of Higher-plant Chloroplast Thylakoid Membranes Revealed by Electron Tomography

The light-harvesting and energy-transducing functions of the chloroplast are performed within an intricate lamellar system of membranes, called thylakoid membranes, which are differentiated into granum and stroma lamellar domains. Using dual-axis electron microscope tomography, we determined the three-dimensional organization of the chloroplast thylakoid membranes within cryo-immobilized, freeze-substituted lettuce (Lactuca sativa) leaves. We found that the grana are built of repeating units that consist of paired layers formed by bifurcations of stroma lamellar sheets, which fuse within the granum body. These units are rotated relative to each other around the axis of the granum cylinder. One of the layers that makes up the pair bends upwards at its edge and fuses with the layer above it, whereas the other layer bends in the opposite direction and merges with the layer below. As a result, each unit in the granum is directly connected to its neighbors as well as to the surrounding stroma lamellae. This highly connected morphology has important consequences for the formation and function of the thylakoid membranes as well as for their stacking/unstacking response to variations in light conditions.

Effect of Anions on the Photocycle of Halorhodopsin. Substitution of Chloride with Formate Anion

Halorhodopsin from Natronomonas pharaonis is a light-driven chloride pump which transports a chloride anion across the plasma membrane following light absorption by a retinal chromophore which initiates a photocycle. It was shown that the chloride anion bound in the vicinity of retinal PSB can be replaced by several inorganic anions, including azide which converts the chloride pump into a proton pump and induces formation of an M-like intermediate detected in the bR photocycle but not in native halorhodopsin. Here we have studied the possibility of replacing the chloride anion with organic anions and have followed the photocycle under several conditions. It is revealed that the chloride can be replaced with a formate anion but not with larger organic anions such as acetate. Flash photolysis experiments detected in the formate pigment an M-like intermediate characterized by a lifetime much longer than that of the O intermediate. The lifetime of the M-like intermediate depends on the pH, and its decay is significantly accelerated at low pH. The decay rate exhibited a titration-like curve, suggesting that the protonation of a protein residue controls the rate of M decay. Similar behavior was detected in N. pharaonis pigments in which the chloride anion was replaced with NO(2)(-) and OCN(-) anions. It is suggested that the formation of the M-like intermediate indicates branching pathways from the L intermediate or basic heterogeneity in the original pigment.

Inactivation of Photosynthetic Electron Flow During Desiccation of Desert Biological Sand Crusts and Microcoleus Sp.-enriched Isolates

Filamentous cyanobacteria, the main primary producers in biological sand crusts, survive harsh environmental conditions including diurnal desiccation/rehydration cycles. Here we describe the inactivation of photosystem II during dehydration of native crusts (NC) and Microcoleus sp. isolates grown on nitrocellulose filters (NCF). The morphology of NCF cells, visualized by scanning-transmission and atomic-force microscopy, disclosed long bacterial filaments encapsulated in extracellular polysaccharides (EPS) tubes consisting of parallel fibrils (100-400 nm wide and 50-100 nm high) oriented mostly perpendicular to the tube length. Presence of empty EPS tubes indicated a gliding capability of the cells. Desiccation of NC resulted in a rapid decline of F(o) and complete loss of F(v). These changes were accompanied by a decrease of 77 K PSII fluorescence emission relative to that of PSI, when excited at 430 nm, and a significant decrease of energy transfer from phycobilisomes to PSII. Lowering the turgor pressure through the addition of 1.5 M trehalose to natural crusts, reduced F(v)/F(m) by over 50% and was accompanied by a decrease of 77 K PSI fluorescence induced by chlorophyll excitation. Excitation of phycobilisomes resulted in a downshift of the PSI emission wavelength by 8 nm, indicative of reduced energy transfer from LHCI to the core PSI. Decline of F(v)/F(m) in trehalose-incubated NCF cells did not induce significant changes in 77 K fluorescence emission. These results suggest that alterations in energy transfer from antennae to reaction centers may be part of the survival strategy of Microcoleus.

The Protonated Schiff Base of Halorhodopsin from Natronobacterium Pharaonis is Hydrolyzed at Elevated Temperatures

Halorhodopsin from Natronobacterium pharaonis (pHR) is a light-driven chloride pump in which photoisomerzation of a retinal chromophore triggers a photocycle which leads to a chloride anion transport across the plasma membrane. Similarly to other retinal proteins the protonated Schiff base (PSB), which covalently links the retinal to the protein, does not experience hydrolysis reaction at room temperature even though several water molecules are located in the protonated Schiff base (PSB) vicinity. In the present studies we have revealed that in contrast to other studied archaeal rhodopsins, temperature increase to about 70 degrees C hydrolyses the PSB linkage of pHR. The rate of the reaction is affected by Cl-concentration and reveals an anion binding site (in addition to the Cl- in the SB vicinity) with a binding constant of 100mM (measured at 70 degrees C). We suggest that this binding site is located on the extracellular side and its possible role in the Cl-pumping mechanism is discussed. The rate of the hydrolysis reaction is affected by the nature of the anion bound to pHR. Substitution of the Cl- anion by Br-, I- and SCN- exhibits similar behavior to that of CI- in the region of 100mM but higher concentrations are needed for N3-, HCOO- and NO2-to achieve similar behavior. Steady state pigment illumination accelerates the reaction and reduces the energy of activation and the frequency factor. Adjusting the sample temperature to 25 degrees C following the hydrolysis reaction led to about 80% pigment recovery. However, the newly reformed pigment is different from the mother pigment and has different characteristics. It is concluded that the apo-membrane adopts a modified conformation and/or aggregated state which rebinds the retinal to give a new conformation of the pHR pigment.

A Micellar Model System for the Role of Zeaxanthin in the Non-photochemical Quenching Process of Photosynthesis--chlorophyll Fluorescence Quenching by the Xanthophylls

To get an insight to the mechanism of the zeaxanthin-dependent non-photochemical quenching in photosystem II of photosynthesis, we probed the interaction of some xanthophylls with excited chlorophyll-a by trapping both pigments in micelles of triton X-100. Optimal distribution of pigments among micelles was obtained by proper control of the micelle concentration, using formamide in the reaction mixture, which varies the micellar aggregation number over three orders of magnitude. The optimal reaction mixture was obtained around 40% (v/v) formamide in 0.2-0.4% (v/v) triton X-100 in water. Zeaxanthin in the micellar solution exhibited initially absorption and circular dichroism spectral features corresponding to a J-type aggregate. The spectrum was transformed over time (half-time values vary-an average characteristic figure is roughly 20 min) to give features representing an H-type aggregate. The isosbestic point in the series of spectral curves favors the supposition of a rather simple reaction between two pure J and H-types dimeric species. Violaxanthin exhibited immediately stable spectral features corresponding to a mixture of J-type and more predominately H-type dimers. Lutein, neoxanthin and beta-carotene did not show any aggregated spectral forms in micelles. The spectral features in micelles were compared to spectra in aqueous acetone, where the assignment to various aggregated types was established previously. The specific tendency of zeaxanthin to form the J-type dimer (or aggregate) could be important for its function in photosynthesis. The abilities of five carotenoids (zeaxanthin, violaxanthin, lutein, neoxanthin and beta-carotene) to quench chlorophyll-a fluorescence were compared. Zeaxanthin, in its two micellar dimeric forms, and beta-carotene were comparable good quenchers of chlorophyll-a fluorescence. Violaxanthin was a much weaker quencher, if at all. Lutein and neoxanthin rather enhanced the fluorescence. The implications to non-photochemical quenching process in photosynthesis are discussed.

Passive and Facilitated Transport in Nuclear Pore Complexes is Largely Uncoupled

Nuclear pore complexes provide the sole gateway for the exchange of material between nucleus and cytoplasm of interphase eukaryotic cells. They support two modes of transport: passive diffusion of ions, metabolites, and intermediate-sized macromolecules and facilitated, receptor-mediated translocation of proteins, RNA, and ribonucleoprotein complexes. It is generally assumed that both modes of transport occur through a single diffusion channel located within the central pore of the nuclear pore complex. To test this hypothesis, we studied the mutual effects between transporting molecules utilizing either the same or different modes of translocation. We find that the two modes of transport do not interfere with each other, but molecules utilizing a particular mode of transport do hinder motion of others utilizing the same pathway. We therefore conclude that the two modes of transport are largely segregated.

Thylakoid Membrane Remodeling During State Transitions in Arabidopsis

Adaptability of oxygenic photosynthetic organisms to fluctuations in light spectral composition and intensity is conferred by state transitions, short-term regulatory processes that enable the photosynthetic apparatus to rapidly adjust to variations in light quality. In green algae and higher plants, these processes are accompanied by reversible structural rearrangements in the thylakoid membranes. We studied these structural changes in the thylakoid membranes of Arabidopsis thaliana chloroplasts using atomic force microscopy, scanning and transmission electron microscopy, and confocal imaging. Based on our results and on the recently determined three-dimensional structure of higher-plant thylakoids trapped in one of the two major light-adapted states, we propose a model for the transitions in membrane architecture. The model suggests that reorganization of the membranes involves fission and fusion events that occur at the interface between the appressed (granal) and nonappressed (stroma lamellar) domains of the thylakoid membranes. Vertical and lateral displacements of the grana layers presumably follow these localized events, eventually leading to macroscopic rearrangements of the entire membrane network.

A Note on Three-dimensional Models of Higher-plant Thylakoid Networks

Photosynthetic System in Blastochloris Viridis Revisited

The bacterium Blastochloris viridis carries one of the simplest photosynthetic systems, which includes a single light-harvesting complex that surrounds the reaction center, membrane soluble quinones, and a soluble periplasmic protein cytochrome c(2) that shuttle between the reaction center and the bc(1) complex and act as electron carriers, as well as the ATP synthase. The close arrangement of the photosynthetic membranes in Bl. viridis, along with the extremely tight arrangement of the photosystems within these membranes, raises a fundamental question about the diffusion of the electron carriers. To address this issue, we analyzed the structure and response of the Bl. viridis photosynthetic system to various light conditions, by using a combination of electron microscopy, whole-cell cryotomography, and spectroscopic methods. We demonstrate that in response to high light intensities, the ratio of both cytochrome c(2) and bc(1) complexes to the reaction centers is increased. The shorter membrane stacks, along with the notion that the bc(1) complex is located at the highly curved edges of these stacks, result in a smaller average distance between the reaction centers and the bc(1) complexes, leading to shorter pathways of cytochrome c(2) between the two complexes. Under anaerobic conditions, the slow diffusion rate is further mitigated by keeping most of the quinone pool reduced, resulting in a concentration gradient of quinols that allows for a constant supply of theses electron carriers to the bc(1) complex.

A C-terminal Lobe of the Beta Subunit of Na,K-ATPase and H,K-ATPase Resembles Cell Adhesion Molecules

The beta subunit of Na,K-ATPase is required for stabilization and maturation of the catalytic alpha subunits and is also involved in cell adhesion and establishing epithelial cell polarity. However, the mechanism of cell adhesion effects and protein partners of beta are unknown. We have applied fold recognition methods to predict that a C-terminal domain of the beta subunits of Na,K-ATPase and H,K-ATPase has an immunoglobulin-like fold, which resembles cell adhesion molecules. Comparison of the predicted C-terminal domain with a recently published structure of shark rectal gland Na,K-ATPase at 2.4 A in which alpha, beta, and FXYD subunits were resolved confirms that the beta subunit ectodomain contains an immunoglobulin-like structure. Expression in Escherichia coli of a sequence corresponding to the C-terminal domain, followed by its purification, refolding, and circular dichroism analysis, shows that the domain is independently stable with prominent beta sheet secondary structure, as predicted. Proteolytic digestion of the purified detergent-soluble recombinant Na,K-ATPase (alpha1beta1) is also indicative of a stable C-terminal domain of beta in the native complex. The major conclusion of this work is consistent with prior evidence for a role of the beta subunit in cell-cell adhesion, and it attributes that function largely to the C-terminal lobe of the beta ectodomain. In the light of these findings, we discuss its role in cell adhesion and recognition of the beta subunits of Na,K-ATPase, including potential protein partners.

Binding of Anions to Proteorhodopsin Affects the Asp97 PK(a)

Proteorhodopsin (PR), a retinal protein of marine proteobacteria, is a light-driven proton pump. Light excitation of PR initiates a photocycle that triggers the translocation of a proton from the cytoplasmic to the extracellular side. Asp97 is located near the retinal-protonated Schiff base and serves as the proton acceptor during the photocycle. The pK(a) of Asp97 is unusually high ( approximately 7.0), especially in comparison with that of its bR equivalent residue Asp85 ( approximately 2.6). We have studied possible anions binding to PR (produced from gene vector eBAC31A08 and expressed in Escherichia coli) and their effect on its absorption maxima, Asp97 pK(a), and the photocycle. We found that chloride, sulfate, trifluoroacetate, trichloroacetate, and tribromoacetate anions bind to PR and regulate Asp97 pK(a). Asp97 has a pK(a) of approximately 7.8 in water, but the value decreases to approximately 7.0 in the presence of sulfate and chloride anions. Halogeno-acetate anions elevated Asp97 pK(a) and compete with chloride anions. The most significant effect was detected with tribromoacetate anions that increase the Asp97 pK(a) to a value of >9.5. The possibility that PR has at least two binding sites for these anions is discussed. In addition, we have demonstrated that these anions bind to PR also at high pH (above Asp97 pK(a)) because they affect the rate of growth and thermal decay of the M intermediate in the photocycle of PR.

Tooth Movements Are Guided by Specific Contact Areas Between the Tooth Root and the Jaw Bone: A Dynamic 3D MicroCT Study of the Rat Molar

Teeth sustain high loads over a lifetime and yet intact tooth failure is rare. The different structures of the tooth, jaw bone and the intervening soft periodontal ligament enable the tooth to endure repeated loading during mastication. Although mechanical and functional properties of the different components are thoroughly investigated, the manner in which the whole tooth functions under load is still enigmatic. A custom-made loading system inside a microCT scanner was used to directly visualize the root movements in relation to the jaw bone as the rat molar tooth was loaded. At low loads no contact was observed between the root surface and the bone, whereas at higher loads three specific contact areas between the root surface and the jaw bone were observed. These contact areas restrict tooth movement in the buccal-lingual direction, but enable the tooth to rock in a "seesaw" like manner in the distal-mesial direction. The contact areas appear to play a role in determining tooth motion and in turn define the manner in which the whole tooth moves when loaded. These observations are important for understanding basic structure-function relations of the tooth-PDL-bone system, and have direct implications for better understanding pathological and therapeutic processes in orthodontics, periodontics and jaw bone regeneration.

Certain Biominerals in Leaves Function As Light Scatterers

Cystoliths are amorphous calcium carbonate bodies that form in the leaves of some plant families. Cystoliths are regularly distributed in the epidermis and protrude into the photosynthetic tissue, the mesophyll. The photosynthetic pigments generate a steep light gradient in the leaf. Under most illumination regimes the outer mesophyll is light saturated, thus the photosynthetic apparatus is kinetically unable to use the excess light for photochemistry. Here we use micro-scale modulated fluorometry to demonstrate that light scattered by the cystoliths is distributed from the photosynthetically inefficient upper tissue to the efficient, but light deprived, lower tissue. The results prove that the presence of light scatterers reduces the steep light gradient, thus enabling the leaf to use the incoming light flux more efficiently. MicroCT and electron microscopy confirm that the spatial distribution of the minerals is compatible with their optical function. During the study we encountered large calcium oxalate druses in the same anatomical location as the cystoliths. These druses proved to have similar light scattering functions as the cystoliths. This study shows that certain minerals in the leaves of different plants distribute the light flux more evenly inside the leaf.

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