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Find video protocols related to scientific articles indexed in Pubmed.
Contact angle of sessile drops in lennard-jones systems.
Langmuir
PUBLISHED: 11-05-2014
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Molecular dynamics simulations are used for studying the contact angle of nanoscale sessile drops on a planar solid wall in a system interacting via the truncated and shifted Lennard-Jones potential. The entire range between total wetting and dewetting is investigated by varying the solid-fluid dispersive interaction energy. The temperature is varied between the triple point and the critical temperature. A correlation is obtained for the contact angle in dependence of the temperature and the dispersive interaction energy. Size effects are studied by varying the number of fluid particles at otherwise constant conditions, using up to 150?000 particles. For particle numbers below 10?000, a decrease of the contact angle is found. This is attributed to a dependence of the solid-liquid surface tension on the droplet size. A convergence to a constant contact angle is observed for larger system sizes. The influence of the wall model is studied by varying the density of the wall. The effective solid-fluid dispersive interaction energy at a contact angle of ? = 90° is found to be independent of temperature and to decrease linearly with the solid density. A correlation is developed that describes the contact angle as a function of the dispersive interaction, the temperature, and the solid density. The density profile of the sessile drop and the surrounding vapor phase is described by a correlation combining a sigmoidal function and an oscillation term.
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Interaction of the intermembrane space domain of Tim23 with mitochondrial membranes.
J. Biol. Chem.
PUBLISHED: 10-29-2014
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Tim23 mediates protein translocation into mitochondria. Although being inserted into the inner membrane, the dynamic association of its intermembrane space domain (IMS) with the outer membrane promotes protein import. However, little is known about the molecular basis of this interaction. Here, we demonstrate that the IMS domain of Tim23 tightly associates with both IMM- and OMM-like membranes through a hydrophobic anchor at its N-terminus. The structure of membrane-bound Tim23(IMS) is highly dynamic, allowing recognition of both the incoming presequence and other translocase components at the translocation contact. Cardiolipin enhances Tim23's membrane attachment, suggesting that cardiolipin can influence preprotein import.
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Long-Range Correlated Dynamics in Intrinsically Disordered Proteins.
J. Am. Chem. Soc.
PUBLISHED: 10-22-2014
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Intrinsically disordered proteins (IDPs) are involved in a wide variety of physiological and pathological processes and are best described by ensembles of rapidly interconverting conformers. Using fast field cycling relaxation measurements we here show that the IDP ?-synuclein as well as a variety of other IDPs undergoes slow reorientations at time scales comparable to folded proteins. The slow motions are not perturbed by mutations in ?-synuclein, which are related to genetic forms of Parkinson's disease, and do not depend on secondary and tertiary structural propensities. Ensemble-based hydrodynamic calculations suggest that the time scale of the underlying correlated motion is largely determined by hydrodynamic coupling between locally rigid segments. Our study indicates that long-range correlated dynamics are an intrinsic property of IDPs and offers a general physical mechanism of correlated motions in highly flexible biomolecular systems.
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Solid-state NMR, electrophysiology and molecular dynamics characterization of human VDAC2.
J. Biomol. NMR
PUBLISHED: 09-19-2014
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The voltage-dependent anion channel (VDAC) is the most abundant protein of the outer mitochondrial membrane and constitutes the major pathway for the transport of ADP, ATP, and other metabolites. In this multidisciplinary study we combined solid-state NMR, electrophysiology, and molecular dynamics simulations, to study the structure of the human VDAC isoform 2 in a lipid bilayer environment. We find that the structure of hVDAC2 is similar to the structure of hVDAC1, in line with recent investigations on zfVDAC2. However, hVDAC2 appears to exhibit an increased conformational heterogeneity compared to hVDAC1 which is reflected in broader solid-state NMR spectra and less defined electrophysiological profiles.
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Population Shuffling of Protein Conformations.
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 09-08-2014
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Motions play a vital role in the functions of many proteins. Discrete conformational transitions to excited states, happening on timescales of hundreds of microseconds, have been extensively characterized. On the other hand, the dynamics of the ground state are widely unexplored. Newly developed high-power relaxation dispersion experiments allow the detection of motions up to a one-digit microsecond timescale. These experiments showed that side chains in the hydrophobic core as well as at protein-protein interaction surfaces of both ubiquitin and the third immunoglobulin binding domain of protein G move on the microsecond timescale. Both proteins exhibit plasticity to this microsecond motion through redistribution of the populations of their side-chain rotamers, which interconvert on the picosecond to nanosecond timescale, making it likely that this "population shuffling" process is a general mechanism.
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A six-dimensional alpha proton detection-based APSY experiment for backbone assignment of intrinsically disordered proteins.
J. Biomol. NMR
PUBLISHED: 09-08-2014
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Sequence specific resonance assignment is the prerequisite for the NMR-based analysis of the conformational ensembles and their underlying dynamics of intrinsically disordered proteins. However, rapid solvent exchange in intrinsically disordered proteins often complicates assignment strategies based on HN-detection. Here we present a six-dimensional alpha proton detection-based automated projection spectroscopy (APSY) experiment for backbone assignment of intrinsically disordered proteins. The 6D HCACONCAH APSY correlates the six different chemical shifts, H?(i - 1), C?(i - 1), C'(i - 1), N(i), C?(i) and H?(i). Application to two intrinsically disordered proteins, 140-residue ?-synuclein and a 352-residue isoform of Tau, demonstrates that the chemical shift information provided by the 6D HCACONCAH APSY allows efficient backbone resonance assignment of intrinsically disordered proteins.
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Towards automatic protein backbone assignment using proton-detected 4D solid-state NMR data.
J. Biomol. NMR
PUBLISHED: 09-06-2014
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We introduce an efficient approach for sequential protein backbone assignment based on two complementary proton-detected 4D solid-state NMR experiments that correlate [Formula: see text]/Ni with CAi/COi or CAi-1/COi-1. The resulting 4D spectra exhibit excellent sensitivity and resolution and are amenable to (semi-)automatic assignment approaches. This strategy allows to obtain sequential connections with high confidence as problems related to peak overlap and multiple assignment possibilities are avoided. Non-uniform sampling schemes were implemented to allow for the acquisition of 4D spectra within a few days. Rather moderate hardware requirements enable the successful demonstration of the method on deuterated type III secretion needles using a 600 MHz spectrometer at a spinning rate of 25 kHz.
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Multiple Paramagnetic Effects through a Tagged Reporter Protein.
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 08-27-2014
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Paramagnetic effects provide unique information about the structure and dynamics of biomolecules. We developed a method in which the lanthanoid tag is not directly attached to the protein of interest, but instead to a "reporter" protein, which binds and then transmits paramagnetic information to the target. The designed method allows access to a large number of paramagnetic restraints and residual dipolar couplings produced from independent molecular alignments in high-molecular-weight proteins with unknown 3D structure.
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Macromolecular assembly of the adaptor SLP-65 at intracellular vesicles in resting B cells.
Sci Signal
PUBLISHED: 08-19-2014
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The traditional view of how intracellular effector proteins are recruited to the B cell antigen receptor (BCR) complex at the plasma membrane is based on the occurrence of direct protein-protein interactions, as exemplified by the recruitment of the tyrosine kinase Syk (spleen tyrosine kinase) to phosphorylated motifs in BCR signaling subunits. By contrast, the subcellular targeting of the cytosolic adaptor protein SLP-65 (Src homology 2 domain-containing leukocyte adaptor protein of 65 kD), which serves as a proximal Syk substrate, is unclear. We showed that SLP-65 activation required its association at vesicular compartments in resting B cells. A module of ~50 amino acid residues located at the amino terminus of SLP-65 anchored SLP-65 to the vesicles. Nuclear magnetic resonance spectroscopy showed that the SLP-65 amino terminus was structurally disordered in solution but could bind in a structured manner to noncharged lipid components of cellular membranes. Our finding that preformed vesicular signaling scaffolds are required for B cell activation indicates that vesicles may deliver preassembled signaling cargo to sites of BCR activation.
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A designed conformational shift to control protein binding specificity.
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 08-12-2014
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In a conformational selection scenario, manipulating the populations of binding-competent states should be expected to affect protein binding. We demonstrate how in silico designed point mutations within the core of ubiquitin, remote from the binding interface, change the binding specificity by shifting the conformational equilibrium of the ground-state ensemble between open and closed substates that have a similar population in the wild-type protein. Binding affinities determined by NMR titration experiments agree with the predictions, thereby showing that, indeed, a shift in the conformational equilibrium enables us to alter ubiquitin's binding specificity and hence its function. Thus, we present a novel route towards designing specific binding by a conformational shift through exploiting the fact that conformational selection depends on the concentration of binding-competent substates.
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Molecular Basis of the Dynamic Structure of the TIM23 Complex in the Mitochondrial Intermembrane Space.
Structure
PUBLISHED: 07-04-2014
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The presequence translocase TIM23 is a highly dynamic complex in which its subunits can adopt multiple conformations and undergo association-dissociation to facilitate import of proteins into mitochondria. Despite the importance of protein-protein interactions in TIM23, little is known about the molecular details of these processes. Using nuclear magnetic resonance spectroscopy, we characterized the dynamic interaction network of the intermembrane space domains of Tim23, Tim21, Tim50, and Tom22 at single-residue level. We show that Tim23(IMS) contains multiple sites to efficiently interact with the intermembrane space domain of Tim21 and to bind to Tim21, Tim50, and Tom22. In addition, we reveal the atomic details of the dynamic Tim23(IMS)-Tim21(IMS) complex. The combined data support a central role of the intermembrane space domain of Tim23 in the formation and regulation of the presequence translocase.
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High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy.
Nat Commun
PUBLISHED: 06-26-2014
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We introduce a general hybrid approach for determining the structures of supramolecular assemblies. Cryo-electron microscopy (cryo-EM) data define the overall envelope of the assembly and rigid-body orientation of the subunits while solid-state nuclear magnetic resonance (ssNMR) chemical shifts and distance constraints define the local secondary structure, protein fold and inter-subunit interactions. Finally, Rosetta structure calculations provide a general framework to integrate the different sources of structural information. Combining a 7.7-Å cryo-EM density map and 996 ssNMR distance constraints, the structure of the type-III secretion system needle of Shigella flexneri is determined to a precision of 0.4?Å. The calculated structures are cross-validated using an independent data set of 691 ssNMR constraints and scanning transmission electron microscopy measurements. The hybrid model resolves the conformation of the non-conserved N terminus, which occupies a protrusion in the cryo-EM density, and reveals conserved pore residues forming a continuous pattern of electrostatic interactions, thereby suggesting a mechanism for effector protein translocation.
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Voltage-dependent structural changes of the membrane-bound anion channel hVDAC1 probed by SEIRA and electrochemical impedance spectroscopy.
Phys Chem Chem Phys
PUBLISHED: 04-15-2014
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The voltage-dependent anion channel (VDAC) is a transmembrane protein that regulates the transfer of metabolites between the cytosol and the mitochondrium. Opening and partial closing of the channel is known to be driven by the transmembrane potential via a mechanism that is not fully understood. In this work, we employed a spectroelectrochemical approach to probe the voltage-induced molecular structure changes of human VDAC1 (hVDAC1) embedded in a tethered bilayer lipid membrane on a nanostructured Au electrode. The model membrane consisted of a mixed self-assembled monolayer of 6-mercaptohexanol and (cholesterylpolyethylenoxy)thiol, followed by the deposition of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine vesicles including hVDAC1. The stepwise assembly of the model membrane and the incorporation of hVDAC1 were monitored by surface enhanced infrared absorption and electrochemical impedance spectroscopy. Difference spectra allowed for identifying the spectral changes which may be associated with the transition from the open to the "closed" states by shifting the potential above or below the transmembrane potential determined to be ca. 0.0 V vs. the open circuit potential. These spectral changes were interpreted on the basis of the orientation- and distance-dependent IR enhancement and indicate alterations of the inclination angle of the ?-strands as crucial molecular events, reflecting an expansion or contraction of the ?-barrel pore. These protein structural changes that do not confirm nor exclude the reorientation of the ?-helix are either directly induced by the electric field or a consequence of a potential-dependent repulsion or attraction of the bilayer.
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Measuring membrane protein bond orientations in nanodiscs via residual dipolar couplings.
Protein Sci.
PUBLISHED: 04-08-2014
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Membrane proteins are involved in numerous vital biological processes. To understand membrane protein functionality, accurate structural information is required. Usually, structure determination and dynamics of membrane proteins are studied in micelles using either solution state NMR or X-ray crystallography. Even though invaluable information has been obtained by this approach, micelles are known to be far from ideal mimics of biological membranes often causing the loss or decrease of membrane protein activity. Recently, nanodiscs, which are composed of a lipid bilayer surrounded by apolipoproteins, have been introduced as a more physiological alternative than micelles for NMR investigations on membrane proteins. Here, we show that membrane protein bond orientations in nanodiscs can be obtained by measuring residual dipolar couplings (RDCs) with the outer membrane protein OmpX embedded in nanodiscs using Pf1 phage as an alignment medium. The presented collection of membrane protein RDCs in nanodiscs represents an important step toward more comprehensive structural and dynamical NMR-based investigations of membrane proteins in a natural bilayer environment.
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Toward the functional oligomerization state of tryptophan-rich sensory proteins.
Protein Sci.
PUBLISHED: 04-04-2014
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A conserved family of tryptophan-rich sensory proteins (TspO) mediates the transport of heme degradation intermediates across membranes. In eukaryotes, the homologous mitochondrial translocator protein (TSPO) binds cholesterol and radioligands as monomer. On the basis of the mammalian TSPO structure, bioinformatic analysis, and a 10 Å resolution electron microscopy map of TspO from Rhodobacter sphaeroides, we developed a model of the tertiary and quaternary structure of TspO that is in agreement with available mutagenesis data. Our study provides insight into the conformational basis for the restricted interaction of bacterial TspO with radioligands and the functional oligomerization state of bacterial TspO proteins.
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Nucleotide interactions of the human voltage-dependent anion channel.
J. Biol. Chem.
PUBLISHED: 03-25-2014
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The voltage-dependent anion channel (VDAC) mediates and gates the flux of metabolites and ions across the outer mitochondrial membrane and is a key player in cellular metabolism and apoptosis. Here we characterized the binding of nucleotides to human VDAC1 (hVDAC1) on a single-residue level using NMR spectroscopy and site-directed mutagenesis. We find that hVDAC1 possesses one major binding region for ATP, UTP, and GTP that partially overlaps with a previously determined NADH binding site. This nucleotide binding region is formed by the N-terminal ?-helix, the linker connecting the helix to the first ?-strand and adjacent barrel residues. hVDAC1 preferentially binds the charged forms of ATP, providing support for a mechanism of metabolite transport in which direct binding to the charged form exerts selectivity while at the same time permeation of the Mg(2+)-complexed ATP form is possible.
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Structure of the mitochondrial translocator protein in complex with a diagnostic ligand.
Science
PUBLISHED: 03-22-2014
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The 18-kilodalton translocator protein TSPO is found in mitochondrial membranes and mediates the import of cholesterol and porphyrins into mitochondria. In line with the role of TSPO in mitochondrial function, TSPO ligands are used for a variety of diagnostic and therapeutic applications in animals and humans. We present the three-dimensional high-resolution structure of mammalian TSPO reconstituted in detergent micelles in complex with its high-affinity ligand PK11195. The TSPO-PK11195 structure is described by a tight bundle of five transmembrane ? helices that form a hydrophobic pocket accepting PK11195. Ligand-induced stabilization of the structure of TSPO suggests a molecular mechanism for the stimulation of cholesterol transport into mitochondria.
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Turn plasticity distinguishes different modes of amyloid-? aggregation.
J. Am. Chem. Soc.
PUBLISHED: 03-21-2014
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Pathogenesis of Alzheimer's disease (AD) is associated with aggregation of the amyloid-? (A?) peptide into oligomeric and fibrillar assemblies; however, little is known about the molecular basis of aggregation of A? into distinct assembly states. Here we demonstrate that phosphorylation at serine 26 (S26) impairs A? fibrillization while stabilizing its monomers and nontoxic soluble assemblies of nonfibrillar morphology. NMR spectroscopy and replica-exchange molecular dynamics indicate that introduction of a phosphate group or phosphomimetic at position 26 diminishes A?'s propensity to form a ?-hairpin, rigidifies the region around the modification site, and interferes with formation of a fibril-specific salt bridge between aspartic acid 23 and lysine 28. The combined data demonstrate that phosphorylation of S26 prevents a distinct conformational rearrangement that is required for progression of A? aggregation toward fibrils and provide a basis for a possible role of phosphorylation at serine 26 in AD.
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Promoting business and entrepreneurial awareness in health care professionals: lessons from venture capital panels at medicine 2.0 conferences.
J. Med. Internet Res.
PUBLISHED: 03-12-2014
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There are few mechanisms that bring the academic and business worlds together in a way that would maximize the success of health technology (health tech) start-ups by increasing researchers' knowledge about how to operate in the business world. Existing solutions (eg, technology transfer offices and dual degree MD/MBA programs) are often unavailable to researchers from outside the institution or to those who have already completed their primary education, such as practicing physicians. This paper explores current solutions and offers a partial solution: include venture capital (VC) panels in medical conferences. These VC panels educate academics on 2 important and interconnected issues: how to "pitch" their ideas in the business world and what to consider when creating a company. In these sessions, academia-based start-up companies present their ideas before a VC panel composed of professional investors and receive feedback on their idea, business plan, and presentation techniques. Recent panel recommendations from Medicine 2.0 conferences fell into 7 categories: (1) the product, service, or idea you are developing into a company, (2) determine market forces and identify the target audience, (3) describe your competitive advantage, (4) the business plan, (5) current and future resources and capabilities, (6) legal aspects, and (7) general advice on the art of pitching. The academic and business literature validates many of these recommendations suggesting that VC panels may be a viable and cost-effective introduction to business and entrepreneurial education for physicians and other health care professionals. Panels benefit not only the presenting companies, but also the physicians, psychologists, and other health care professionals attending the session. Incorporating VC panels into academic conferences might also illuminate the need for incorporating relevant business training within academia.
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?-Synuclein interacts with the switch region of Rab8a in a Ser129 phosphorylation-dependent manner.
Neurobiol. Dis.
PUBLISHED: 03-05-2014
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Alpha-synuclein (?S) misfolding is associated with Parkinson's disease (PD) but little is known about the mechanisms underlying ?S toxicity. Increasing evidence suggests that defects in membrane transport play an important role in neuronal dysfunction. Here we demonstrate that the GTPase Rab8a interacts with ?S in rodent brain. NMR spectroscopy reveals that the C-terminus of ?S binds to the functionally important switch region as well as the C-terminal tail of Rab8a. In line with a direct Rab8a/?S interaction, Rab8a enhanced ?S aggregation and reduced ?S-induced cellular toxicity. In addition, Rab8 - the Drosophila ortholog of Rab8a - ameliorated ?S-oligomer specific locomotor impairment and neuron loss in fruit flies. In support of the pathogenic relevance of the ?S-Rab8a interaction, phosphorylation of ?S at S129 enhanced binding to Rab8a, increased formation of insoluble ?S aggregates and reduced cellular toxicity. Our study provides novel mechanistic insights into the interplay of the GTPase Rab8a and ?S cytotoxicity, and underscores the therapeutic potential of targeting this interaction.
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Shark Attack: High affinity binding proteins derived from shark vNAR domains by stepwise in vitro affinity maturation.
J. Biotechnol.
PUBLISHED: 02-21-2014
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A novel method for stepwise in vitro affinity maturation of antigen-specific shark vNAR domains is described that exclusively relies on semi-synthetic repertoires derived from non-immunized sharks. Target-specific molecules were selected from a CDR3-randomized bamboo shark (Chiloscyllium plagiosum) vNAR library using yeast surface display as platform technology. Various antigen-binding vNAR domains were easily isolated by screening against several therapeutically relevant antigens, including the epithelial cell adhesion molecule (EpCAM), the Ephrin type-A receptor 2 (EphA2), and the human serine protease HTRA1. Affinity maturation was demonstrated for EpCAM and HTRA1 by diversifying CDR1 of target-enriched populations which allowed for the rapid selection of nanomolar binders. EpCAM-specific vNAR molecules were produced as soluble proteins and more extensively characterized via thermal shift assays and biolayer interferometry. Essentially, we demonstrate that high-affinity binders can be generated in vitro without largely compromising the desirable high thermostability of the vNAR scaffold.
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Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins.
J. Magn. Reson.
PUBLISHED: 02-19-2014
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Proton-detected solid-state NMR was applied to a highly deuterated insoluble, non-crystalline biological assembly, the Salmonella typhimurium type iii secretion system (T3SS) needle. Spectra of very high resolution and sensitivity were obtained at a low protonation level of 10-20% at exchangeable amide positions. We developed efficient experimental protocols for resonance assignment tailored for this system and the employed experimental conditions. Using exclusively dipolar-based interspin magnetization transfers, we recorded two sets of 3D spectra allowing for an almost complete backbone resonance assignment of the needle subunit PrgI. The additional information provided by the well-resolved proton dimension revealed the presence of two sets of resonances in the N-terminal helix of PrgI, while in previous studies employing (13)C detection only a single set of resonances was observed.
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mHealth 2.0: Experiences, Possibilities, and Perspectives.
JMIR Mhealth Uhealth
PUBLISHED: 02-17-2014
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With more than 1 billion users having access to mobile broadband Internet and a rapidly growing mobile app market, all stakeholders involved have high hopes that this technology may improve health care. Expectations range from overcoming structural barriers to access in low-income countries to more effective, interactive treatment of chronic conditions. Before medical health practice supported by mobile devices ("mHealth") can scale up, a number of challenges need to be adequately addressed. From a psychological perspective, high attrition rates, digital divide of society, and intellectual capabilities of the users are key issues when implementing such technologies. Furthermore, apps addressing behavior change often lack a comprehensive concept, which is essential for an ongoing impact. From a clinical point of view, there is insufficient evidence to allow scaling up of mHealth interventions. In addition, new concepts are required to assess the efficacy and efficiency of interventions. Regarding technology interoperability, open standards and low-energy wireless protocols appear to be vital for successful implementation. There is an ongoing discussion in how far health care-related apps require a conformity assessment and how to best communicate quality standards to consumers. "Apps Peer-Review" and standard reporting via an "App synopsis" appear to be promising approaches to increase transparency for end users. With respect to development, more emphasis must be placed on context analysis to identify what generic functions of mobile information technology best meet the needs of stakeholders involved. Hence, interdisciplinary alliances and collaborative strategies are vital to achieve sustainable growth for "mHealth 2.0," the next generation mobile technology to support patient care.
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Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex.
Nat. Struct. Mol. Biol.
PUBLISHED: 02-14-2014
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The precursor mRNA (pre-mRNA) retention and splicing (RES) complex is a spliceosomal complex that is present in yeast and humans and is important for RNA splicing and retention of unspliced pre-mRNA. Here, we present the solution NMR structure of the RES core complex from Saccharomyces cerevisiae. Complex formation leads to an intricate folding of three components-Snu17p, Bud13p and Pml1p-that stabilizes the RNA-recognition motif (RRM) fold of Snu17p and increases binding affinity in tertiary interactions between the components by more than 100-fold compared to that in binary interactions. RES interacts with pre-mRNA within the spliceosome, and through the assembly of the RES core complex RNA binding efficiency is increased. The three-dimensional structure of the RES core complex highlights the importance of cooperative folding and binding in the functional organization of the spliceosome.
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Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA.
Acta Crystallogr. D Biol. Crystallogr.
PUBLISHED: 02-05-2014
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Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.
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BSH-CP based 3D solid-state NMR experiments for protein resonance assignment.
J. Biomol. NMR
PUBLISHED: 01-20-2014
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We have recently presented band-selective homonuclear cross-polarization (BSH-CP) as an efficient method for CO-CA transfer in deuterated as well as protonated solid proteins. Here we show how the BSH-CP CO-CA transfer block can be incorporated in a set of three-dimensional (3D) solid-state NMR (ssNMR) pulse schemes tailored for resonance assignment of proteins at high static magnetic fields and moderate magic-angle spinning rates. Due to the achieved excellent transfer efficiency of 33 % for BSH-CP, a complete set of 3D spectra needed for unambiguous resonance assignment could be rapidly recorded within 1 week for the model protein ubiquitin. Thus we expect that BSH-CP could replace the typically used CO-CA transfer schemes in well-established 3D ssNMR approaches for resonance assignment of solid biomolecules.
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Identification of crucial parameters in a mathematical multiscale model of glioblastoma growth.
Comput Math Methods Med
PUBLISHED: 01-16-2014
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Glioblastomas are highly malignant brain tumours. Mathematical models and their analysis provide a tool to support the understanding of the development of these tumours as well as the design of more effective treatment strategies. We have previously developed a multiscale model of glioblastoma progression that covers processes on the cellular and molecular scale. Here, we present a novel nutrient-dependent multiscale sensitivity analysis of this model that helps to identify those reaction parameters of the molecular interaction network that influence the tumour progression on the cellular scale the most. In particular, those parameters are identified that essentially determine tumour expansion and could be therefore used as potential therapy targets. As indicators for the success of a potential therapy target, a deceleration of the tumour expansion and a reduction of the tumour volume are employed. From the results, it can be concluded that no single parameter variation results in a less aggressive tumour. However, it can be shown that a few combined perturbations of two systematically selected parameters cause a slow-down of the tumour expansion velocity accompanied with a decrease of the tumour volume. Those parameters are primarily linked to the reactions that involve the microRNA-451 and the thereof regulated protein MO25.
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A general strategy for antibody library screening via conversion of transient target binding into permanent reporter deposition.
Protein Eng. Des. Sel.
PUBLISHED: 01-08-2014
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We report here a generally applicable method for the selective covalent attachment of a reporter molecule to a replicating entity that allows one to obtain specific binders from a single round of library screening. We show that selective biotinylation of phage particles displaying a binder to any given target can be achieved by application of a coupled enzyme reaction on the surface of the target-binding phage particles that includes a peroxidase, an oxidase and a catalase. Due to the covalent linkage of biotin together with the tight and stable interaction of biotin with streptavidin, very stringent wash conditions for removal of nonspecific binders can be applied. The method termed (3)CARD (triple catalytic reporter deposition) was successfully applied to single-round screening of a phage display library of camelid single-domain antibodies against three different target proteins.
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Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes.
Nat. Methods
PUBLISHED: 01-05-2014
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The quality of genetically encoded calcium indicators (GECIs) has improved dramatically in recent years, but high-performing ratiometric indicators are still rare. Here we describe a series of fluorescence resonance energy transfer (FRET)-based calcium biosensors with a reduced number of calcium binding sites per sensor. These 'Twitch' sensors are based on the C-terminal domain of Opsanus troponin C. Their FRET responses were optimized by a large-scale functional screen in bacterial colonies, refined by a secondary screen in rat hippocampal neuron cultures. We tested the in vivo performance of the most sensitive variants in the brain and lymph nodes of mice. The sensitivity of the Twitch sensors matched that of synthetic calcium dyes and allowed visualization of tonic action potential firing in neurons and high resolution functional tracking of T lymphocytes. Given their ratiometric readout, their brightness, large dynamic range and linear response properties, Twitch sensors represent versatile tools for neuroscience and immunology.
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Health information technology (IT) to improve the care of patients with chronic kidney disease (CKD).
BMC Nephrol
PUBLISHED: 01-04-2014
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Several reports show that patients with chronic disease who are empowered with information technology (IT) tools for monitoring, training and self-management have improved outcomes, however there are few such applications employed in kidney disease. This review explores the current and potential uses of health IT platforms to advance kidney disease care by offering innovative solutions to inform, engage and communicate with individuals with CKD.
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NMR-Based Detection of Hydrogen/Deuterium Exchange in Liposome-Embedded Membrane Proteins.
PLoS ONE
PUBLISHED: 01-01-2014
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Membrane proteins play key roles in biology. Determination of their structure in a membrane environment, however, is highly challenging. To address this challenge, we developed an approach that couples hydrogen/deuterium exchange of membrane proteins to rapid unfolding and detection by solution-state NMR spectroscopy. We show that the method allows analysis of the solvent protection of single residues in liposome-embedded proteins such as the 349-residue Tom40, the major protein translocation pore in the outer mitochondrial membrane, which has resisted structural analysis for many years.
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Atomic structure and handedness of the building block of a biological assembly.
J. Am. Chem. Soc.
PUBLISHED: 12-17-2013
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Noncovalent supramolecular assemblies possess in general several unique subunit-subunit interfaces.The basic building block of such an assembly consists of several subunits and contains all unique interfaces. Atomic-resolution structures of monomeric subunits are typically accessed by crystallography or solution NMR and fitted into electron microscopy density maps. However, the structure of the intact building block in the assembled state remains unknown with this hybrid approach. Here, we present the solid-state NMR atomic structure of the building block of the type III secretion system needle. The building block structure consists of a homotetrameric subunit complex with three unique supramolecular interfaces. Side-chain positions at the interfaces were solved at atomic detail. The high-resolution structure reveals unambiguously the helical handedness of the assembly, determined to be right-handed for the type III secretion system needle.Additionally, the axial rise per subunit could be extracted from the tetramer structure and independently validated by mass-per-length measurements.
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Interdomain dynamics explored by paramagnetic NMR.
J. Am. Chem. Soc.
PUBLISHED: 11-04-2013
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An ensemble-based approach is presented to explore the conformational space sampled by a multidomain protein showing moderate interdomain dynamics in terms of translational and rotational motions. The strategy was applied on a complex of calmodulin (CaM) with the IQ-recognition motif from the voltage-gated calcium channel Ca(v)1.2 (IQ), which adopts three different interdomain orientations in the crystal. The N60D mutant of calmodulin was used to collect pseudocontact shifts and paramagnetically induced residual dipolar couplings for six different lanthanide ions. Then, starting from the crystal structure, pools of conformations were generated by free MD. We found the three crystal conformations in solution, but four additional MD-derived conformations had to be included into the ensemble to fulfill all the paramagnetic data and cross-validate optimally against unused paramagnetic data. Alternative approaches led to similar ensembles. Our "ensemble" approach is a simple and efficient tool to probe and describe the interdomain dynamics and represents a general method that can be used to provide a proper ensemble description of multidomain proteins.
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Studies on the MxiH Protein in T3SS Needles Using DNP-Enhanced ssNMR Spectroscopy.
Chemphyschem
PUBLISHED: 10-28-2013
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Bacterial T3SS needles formed by the protein MxiH are studied using DNP-enhanced ssNMR spectroscopy at 14.1?T (600?MHz). This technique provides spectra of good resolution, allowing us to draw conclusions about the protein dynamics. With the obtained signal enhancement, samples of limited quantity now get within reach of ssNMR studies.
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Predictive Atomic Resolution Descriptions of Intrinsically Disordered hTau40 and ?-Synuclein in Solution from NMR and Small Angle Scattering.
Structure
PUBLISHED: 09-16-2013
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The development of molecular descriptions of intrinsically disordered proteins (IDPs) is essential for elucidating conformational transitions that characterize common neurodegenerative disorders. We use nuclear magnetic resonance, small angle scattering, and molecular ensemble approaches to characterize the IDPs Tau and ?-synuclein. Ensemble descriptions of IDPs are highly underdetermined due to the inherently large number of degrees of conformational freedom compared with available experimental measurements. Using extensive cross-validation we show that five different types of independent experimental parameters are predicted more accurately by selected ensembles than by statistical coil descriptions. The improvement increases in regions whose local sampling deviates from statistical coil, validating the derived conformational description. Using these approaches we identify enhanced polyproline II sampling in aggregation-nucleation sites, supporting suggestions that this region of conformational space is important for aggregation.
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Detection of protein interactions during virus infection by bimolecular fluorescence complementation.
Methods Mol. Biol.
PUBLISHED: 09-03-2013
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The bimolecular fluorescence complementation (BiFC) allows not only the investigation of protein interactions but also the visualization of protein complexes in living cells. This method is based on two nonfluorescent fragments of fluorescent proteins (FPs) which can reassemble into a fluorescent complex. The formation of the fluorescent complex requires association of the nonfluorescent fragments which is facilitated by their fusion to two proteins that interact with each other. It is necessary to confirm the specificity of the BiFC signal, e.g., by using proteins with a mutated interaction site. Here, we describe a BiFC protocol adapted for the investigation of protein-protein interactions during herpesvirus infection.
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Phosphorylation drives a dynamic switch in serine/arginine-rich proteins.
Structure
PUBLISHED: 08-09-2013
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Serine/arginine-rich (SR) proteins are important players in RNA metabolism and are extensively phosphorylated at serine residues in RS repeats. Here, we show that phosphorylation switches the RS domain of the serine/arginine-rich splicing factor 1 from a fully disordered state to a partially rigidified arch-like structure. Nuclear magnetic resonance spectroscopy in combination with molecular dynamics simulations revealed that the conformational switch is restricted to RS repeats, critically depends on the phosphate charge state and strongly decreases the conformational entropy of RS domains. The dynamic switch also occurs in the 100 kDa SR-related protein hPrp28, for which phosphorylation at the RS repeat is required for spliceosome assembly. Thus, a phosphorylation-induced dynamic switch is common to the class of serine/arginine-rich proteins and provides a molecular basis for the functional redundancy of serine/arginine-rich proteins and the profound influence of RS domain phosphorylation on protein-protein and protein-RNA interactions.
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Importance of lipid-pore loop interface for potassium channel structure and function.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 07-23-2013
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Potassium (i.e., K(+)) channels allow for the controlled and selective passage of potassium ions across the plasma membrane via a conserved pore domain. In voltage-gated K(+) channels, gating is the result of the coordinated action of two coupled gates: an activation gate at the intracellular entrance of the pore and an inactivation gate at the selectivity filter. By using solid-state NMR structural studies, in combination with electrophysiological experiments and molecular dynamics simulations, we show that the turret region connecting the outer transmembrane helix (transmembrane helix 1) and the pore helix behind the selectivity filter contributes to K(+) channel inactivation and exhibits a remarkable structural plasticity that correlates to K(+) channel inactivation. The transmembrane helix 1 unwinds when the K(+) channel enters the inactivated state and rewinds during the transition to the closed state. In addition to well-characterized changes at the K(+) ion coordination sites, this process is accompanied by conformational changes within the turret region and the pore helix. Further spectroscopic and computational results show that the same channel domain is critically involved in establishing functional contacts between pore domain and the cellular membrane. Taken together, our results suggest that the interaction between the K(+) channel turret region and the lipid bilayer exerts an important influence on the selective passage of potassium ions via the K(+) channel pore.
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Efficient band-selective homonuclear CO-CA cross-polarization in protonated proteins.
J. Biomol. NMR
PUBLISHED: 06-04-2013
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Previously introduced for highly deuterated proteins, band-selective magnetization transfer between CO and CA spins by dipolar-based homonuclear cross polarization is applied here to a protonated protein. Robust and efficient recoupling is achieved when the sum of effective radio-frequency fields on CO and CA resonances equals two times the spinning rate, yielding up to 33% of magnetization transfer efficiency in protonated ubiquitin. The approach is designed for moderate magic-angle spinning rates and high external magnetic fields when the isotropic chemical shift difference of CO and CA considerably exceeds the spinning rate. This method has been implemented in NiCOi-1CAi-1 and CAi(Ni)COi-1CAi-1 two-dimensional interresidual correlation experiments for fast and efficient resonance assignment of ubiquitin by solid-state NMR spectroscopy.
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Enhanced accuracy of kinetic information from CT-CPMG experiments by transverse rotating-frame spectroscopy.
J. Biomol. NMR
PUBLISHED: 04-26-2013
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Micro-to-millisecond motions of proteins transmit pivotal signals for protein function. A powerful technique for the measurement of these motions is nuclear magnetic resonance spectroscopy. One of the most widely used methodologies for this purpose is the constant-time Carr-Purcell-Meiboom-Gill (CT-CPMG) relaxation dispersion experiment where kinetic and structural information can be obtained at atomic resolution. Extraction of accurate kinetics determined from CT-CPMG data requires refocusing frequencies that are much larger than the nucleis exchange rate between states. We investigated the effect when fast processes are probed by CT-CPMG experiments via simulation and show that if the intrinsic relaxation rate (R(CT-CPMG)(2,0)) is not known a priori the extraction of accurate kinetics is hindered. Errors on the order of 50 % in the exchange rate are attained when processes become fast, but are minimized to 5 % with a priori (CT-CPMG)(2,0)) information. To alleviate this shortcoming, we developed an experimental scheme probing (CT-CPMG)(2,0)) with large amplitude spin-lock fields, which specifically contains the intrinsic proton longitudinal Eigenrelaxation rate. Our approach was validated with ubiquitin and the Oscillatoria agardhii agglutinin (OAA). For OAA, an underestimation of 66 % in the kinetic rates was observed if (CT-CPMG)(2,0)) is not included during the analysis of CT-CPMG data and result in incorrect kinetics and imprecise amplitude information. This was overcome by combining CT-CPMG with (CT-CPMG)(2,0)) measured with a high power R1? experiment. In addition, the measurement of (CT-CPMG)(2,0)) removes the ambiguities in choosing between different models that describe CT-CPMG data.
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Cross-validation and evaluation of the performance of methods for the elemental analysis of forensic glass by ?-XRF, ICP-MS, and LA-ICP-MS.
Anal Bioanal Chem
PUBLISHED: 04-09-2013
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Elemental analysis of glass was conducted by 16 forensic science laboratories, providing a direct comparison between three analytical methods [micro-x-ray fluorescence spectroscopy (?-XRF), solution analysis using inductively coupled plasma mass spectrometry (ICP-MS), and laser ablation inductively coupled plasma mass spectrometry]. Interlaboratory studies using glass standard reference materials and other glass samples were designed to (a) evaluate the analytical performance between different laboratories using the same method, (b) evaluate the analytical performance of the different methods, (c) evaluate the capabilities of the methods to correctly associate glass that originated from the same source and to correctly discriminate glass samples that do not share the same source, and (d) standardize the methods of analysis and interpretation of results. Reference materials NIST 612, NIST 1831, FGS 1, and FGS 2 were employed to cross-validate these sensitive techniques and to optimize and standardize the analytical protocols. The resulting figures of merit for the ICP-MS methods include repeatability better than 5% RSD, reproducibility between laboratories better than 10% RSD, bias better than 10%, and limits of detection between 0.03 and 9 ?g g(-1) for the majority of the elements monitored. The figures of merit for the ?-XRF methods include repeatability better than 11% RSD, reproducibility between laboratories after normalization of the data better than 16% RSD, and limits of detection between 5.8 and 7,400 ?g g(-1). The results from this study also compare the analytical performance of different forensic science laboratories conducting elemental analysis of glass evidence fragments using the three analytical methods.
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?-synuclein aggregates and induces neurodegeneration in dopaminergic neurons.
Ann. Neurol.
PUBLISHED: 03-07-2013
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Whereas the contribution of ?-synuclein to neurodegeneration in Parkinson disease is well accepted, the putative impact of its close homologue, ?-synuclein, is enigmatic. ?-Synuclein is widely expressed throughout the central nervous system, as is ?-synuclein, but the physiological functions of both proteins remain unknown. Recent findings have supported the view that ?-synuclein can act as an ameliorating regulator of ?-synuclein-induced neurotoxicity, having neuroprotective rather than neurodegenerative capabilities, and being nonaggregating due to the absence of most of the aggregation-promoting NAC domain. However, a mutation of ?-synuclein linked to dementia with Lewy bodies rendered the protein neurotoxic in transgenic mice, and fibrillation of ?-synuclein has been demonstrated in vitro.
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Influence of vortical flow structures on the glottal jet location in the supraglottal region.
J Voice
PUBLISHED: 02-14-2013
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Within the fully coupled multiphysics phonation process, the fluid flow plays an important role for sound production. This study addresses phenomena in the flow downstream of synthetic self-oscillating vocal folds. An experimental setup consisting of devices for producing and conditioning the flow including the main test channel was applied. The supraglottal channel was designed to prevent an acoustic coupling to the vocal folds. Hence, the oscillations were aerodynamically driven. The cross-section of the supraglottal channel was systematically varied by increasing the distance between the lateral channel walls. The vocal folds consisted of silicone rubber of homogenous material distribution generating self-sustained oscillations. The airflow was visualized in the immediate supraglottal region using a laser-sheet technique and a digital high-speed camera. Furthermore, the flow was studied by measuring the static pressure distributions on both lateral supraglottal channel walls. The results clearly showed different flow characteristics depending on the supraglottal configuration. In all cases with supraglottal channel, the jet was located asymmetrical and bent in medial-lateral direction. Furthermore, the side to which the jet was deflected changed in between the consecutive cycles showing a bifurcational behavior. Previously, this phenomenon was explained by the Coanda effect. However, the present data suggest that the deflection of the jet was mainly caused by large air vortices in the supraglottal channel produced by the flow field of previous oscillations. In contrast, for the case without supraglottal channel, the air jet was found totally symmetrical stabilized by the constant pressure in the ambient region. The emitted sound signal showed additional subharmonic tonal peaks for the asymmetric flow cases, which are characteristics for diplophonia.
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Efficient CO-CA transfer in highly deuterated proteins by band-selective homonuclear cross-polarization.
J. Magn. Reson.
PUBLISHED: 02-08-2013
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Robust and efficient band-selective magnetization transfer between CO and CA spins can be achieved in highly deuterated solid proteins by dipolar-based homonuclear cross polarization. The approach is designed for moderate magic-angle spinning rates and high external magnetic fields where the isotropic chemical shift difference of CO and CA considerably exceeds the spinning rate. The most efficient recoupling is achieved when the sum of effective radio-frequency fields on CO and CA resonances equals two times the spinning rate. This method can be directly implemented in proton-detected versions of inter-residual correlation experiments as needed for resonance assignment in protein solid-state NMR spectroscopy.
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The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles.
PLoS Pathog.
PUBLISHED: 01-23-2013
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The Type Three Secretion System (T3SS), or injectisome, is a macromolecular infection machinery present in many pathogenic Gram-negative bacteria. It consists of a basal body, anchored in both bacterial membranes, and a hollow needle through which effector proteins are delivered into the target host cell. Two different architectures of the T3SS needle have been previously proposed. First, an atomic model of the Salmonella typhimurium needle was generated from solid-state NMR data. The needle subunit protein, PrgI, comprises a rigid-extended N-terminal segment and a helix-loop-helix motif with the N-terminus located on the outside face of the needle. Second, a model of the Shigella flexneri needle was generated from a high-resolution 7.7-Å cryo-electron microscopy density map. The subunit protein, MxiH, contains an N-terminal ?-helix, a loop, another ?-helix, a 14-residue-long ?-hairpin (Q51-Q64) and a C-terminal ?-helix, with the N-terminus facing inward to the lumen of the needle. In the current study, we carried out solid-state NMR measurements of wild-type Shigella flexneri needles polymerized in vitro and identified the following secondary structure elements for MxiH: a rigid-extended N-terminal segment (S2-T11), an ?-helix (L12-A38), a loop (E39-P44) and a C-terminal ?-helix (Q45-R83). Using immunogold labeling in vitro and in vivo on functional needles, we located the N-terminus of MxiH subunits on the exterior of the assembly, consistent with evolutionary sequence conservation patterns and mutagenesis data. We generated a homology model of Shigella flexneri needles compatible with both experimental data: the MxiH solid-state NMR chemical shifts and the state-of-the-art cryoEM density map. These results corroborate the solid-state NMR structure previously solved for Salmonella typhimurium PrgI needles and establish that Shigella flexneri and Salmonella typhimurium subunit proteins adopt a conserved structure and orientation in their assembled state. Our study reveals a common structural architecture of T3SS needles, essential to understand T3SS-mediated infection and develop treatments.
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How do hospitalised patients with Turkish migration background estimate their language skills and their comprehension of medical information -- a prospective cross-sectional study and comparison to native patients in Germany to assess the language barrier
BMC Health Serv Res
PUBLISHED: 01-22-2013
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BACKGROUND: Today more than two million people with Turkish migration background live in Germany making them the largest ethnic minority in the country. Data concerning language skills and the perception of medical information in hospitalised patients with Turkish migration background (T) are scarce. Our study is the first to gather quantitative information on this important subject. METHODS: T and hospitalised German patients without migration background (G) of our university hospital were prospectively included into a cross-sectional study and completed a questionnaire - each group in the appropriate language (T: Turkish, G: German). RESULTS: 121 T and 121 G were included. Groups significantly differed in age (T: 44.9 +/- 17.8, G: 56.9 +/- 16.7y) and proportion of males (T: 37.2, G: 54.5%) but not regarding the proportion of college graduates (T: 19.3, G: 15.7%). The majority of T was born in Turkey (71%) and is of Turkish nationality (66%). 74% of T speak mainly Turkish at home; however, 73% speak German at work. 74.4% of T self-rated their German linguistic proficiency as "average" or better while 25.6% reported it as "very bad" or "bad". 10.7% of T need translation in order to pursue everyday activities. T were significantly less satisfied with the physicians information on disease and estimated to understand significantly less of what the physician told them: 46.3% of T estimated their reception of the physicians information to be "average" or worse. 43.3% of T had the impression that it would have helped them "much" or "very much" to be aided by an interpreter at the hospital. The information transmitted while giving informed consent to invasive medical procedure was judged to be "mostly" or "completely" sufficient by the majority of T (76%) and G (89.8%). In this setting 37 of 96 T (38.5%) reported being helped by an interpreter -- in most cases (64.9%) a family member. CONCLUSION: Although the majority of patients with Turkish migration background have spent most of their lives in Germany (28.94 +/- 10.41y) a large part of this population has limited German language skills and difficulties obtaining medical information when hospitalised.
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Cold denaturation of a protein dimer monitored at atomic resolution.
Nat. Chem. Biol.
PUBLISHED: 01-15-2013
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Protein folding and unfolding are crucial for a range of biological phenomena and human diseases. Defining the structural properties of the involved transient species is therefore of prime interest. Using a combination of cold denaturation with NMR spectroscopy, we reveal detailed insight into the unfolding of the homodimeric repressor protein CylR2. Seven three-dimensional structures of CylR2 at temperatures from 25 °C to -16 °C reveal a progressive dissociation of the dimeric protein into a native-like monomeric intermediate followed by transition into a highly dynamic, partially folded state. The core of the partially folded state seems critical for biological function and misfolding.
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A straightforward method for stereospecific assignment of val and leu prochiral methyl groups by solid-state NMR: Scrambling in the [2-13C]Glucose labeling scheme.
J. Magn. Reson.
PUBLISHED: 01-04-2013
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The unambiguous stereospecific assignment of the prochiral methyl groups in Val and Leu plays an important role in the structural investigation of proteins by NMR. Here, we present a straightforward method for their stereospecific solid-state NMR assignment based on [2-(13)C]Glucose ([2-(13)C]Glc) as the sole carbon source during protein expression. The approach is fundamentally based on the stereo-selective biosynthetic pathway of Val and Leu, and the co-presence of [2-(13)C]pyruvate produced mainly by glycolysis and [3-(13)C]/[1,3-(13)C]pyruvate most probably formed through scrambling in the pentose phosphate pathway. As a consequence, the isotope spin pairs (13)C?-(13)C?2 and (13)C?-(13)C?1 in Val, and (13)C?-(13)C?2 and (13)C?-(13)C?1 in Leu are obtained. The approach is successfully demonstrated with the stereospecific assignment of the methyl groups of Val and Leu of type 3 secretion system PrgI needles and microcrystalline ubiquitin.
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User profiles of a smartphone application to support drug adherence--experiences from the iNephro project.
PLoS ONE
PUBLISHED: 01-01-2013
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One of the key problems in the drug therapy of patients with chronic conditions is drug adherence. In 2010 the initiative iNephro was launched (www.inephro.de). A software to support regular and correct drug intake was developed for a smartphone platform (iOS). The study investigated whether and how smartphone users deployed such an application.
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Fractional deuteration applied to biomolecular solid-state NMR spectroscopy.
J. Biomol. NMR
PUBLISHED: 09-14-2011
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Solid-state Nuclear Magnetic Resonance can provide detailed insight into structural and dynamical aspects of complex biomolecules. With increasing molecular size, advanced approaches for spectral simplification and the detection of medium to long-range contacts become of critical relevance. We have analyzed the protonation pattern of a membrane-embedded ion channel that was obtained from bacterial expression using protonated precursors and D(2)O medium. We find an overall reduction of 50% in protein protonation. High levels of deuteration at H(?) and H(?) positions reduce spectral congestion in ((1)H,(13)C,(15)N) correlation experiments and generate a transfer profile in longitudinal mixing schemes that can be tuned to specific resonance frequencies. At the same time, residual protons are predominantly found at amino-acid side-chain positions enhancing the prospects for obtaining side-chain resonance assignments and for detecting medium to long-range contacts. Fractional deuteration thus provides a powerful means to aid the structural analysis of complex biomolecules by solid-state NMR.
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In vitro experimental investigation of voice production.
Curr Bioinform
PUBLISHED: 09-01-2011
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The process of human phonation involves a complex interaction between the physical domains of structural dynamics, fluid flow, and acoustic sound production and radiation. Given the high degree of nonlinearity of these processes, even small anatomical or physiological disturbances can significantly affect the voice signal. In the worst cases, patients can lose their voice and hence the normal mode of speech communication. To improve medical therapies and surgical techniques it is very important to understand better the physics of the human phonation process. Due to the limited experimental access to the human larynx, alternative strategies, including artificial vocal folds, have been developed. The following review gives an overview of experimental investigations of artificial vocal folds within the last 30 years. The models are sorted into three groups: static models, externally driven models, and self-oscillating models. The focus is on the different models of the human vocal folds and on the ways in which they have been applied.
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Weak long-range correlated motions in a surface patch of ubiquitin involved in molecular recognition.
J. Am. Chem. Soc.
PUBLISHED: 06-20-2011
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Long-range correlated motions in proteins are candidate mechanisms for processes that require information transfer across protein structures, such as allostery and signal transduction. However, the observation of backbone correlations between distant residues has remained elusive, and only local correlations have been revealed using residual dipolar couplings measured by NMR spectroscopy. In this work, we experimentally identified and characterized collective motions spanning four ?-strands separated by up to 15 Å in ubiquitin. The observed correlations link molecular recognition sites and result from concerted conformational changes that are in part mediated by the hydrogen-bonding network.
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Electron paramagnetic resonance spectroscopy measures the distance between the external ?-strands of folded ?-synuclein in amyloid fibrils.
Biophys. J.
PUBLISHED: 04-19-2011
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The misfolding of ?-synuclein (?S) to a cross-?-sheet amyloid structure is associated with pathological conditions in Parkinsons and other neurodegenerative diseases. Using pulse electron paramagnetic resonance spectroscopy combined with a cross-labeling strategy involving four double mutants, we were able to determine the intramolecular distance between the extremal ?-strands. The distance of 4.5 ± 0.5 nm is in good agreement with the dimensions of a protofilament reported by other low-resolution techniques, such as x-ray scattering and atomic force microscopy.
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Cys-Ph-TAHA: a lanthanide binding tag for RDC and PCS enhanced protein NMR.
J. Biomol. NMR
PUBLISHED: 03-29-2011
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Here we present Cys-Ph-TAHA, a new nonadentate lanthanide tag for the paramagnetic labelling of proteins. The tag can be easily synthesized and is stereochemically homogenous over a wide range of temperatures, yielding NMR spectra with a single set of peaks. Bound to ubiquitin, it induced large residual dipolar couplings and pseudocontact shifts that could be measured easily and agreed very well with the protein structure. We show that Cys-Ph-TAHA can be used to label large proteins that are biochemically challenging such as the Lac repressor in a 90 kDa ternary complex with DNA and inducer.
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13C spin dilution for simplified and complete solid-state NMR resonance assignment of insoluble biological assemblies.
J. Am. Chem. Soc.
PUBLISHED: 03-14-2011
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A strategy for simplified and complete resonance assignment of insoluble and noncrystalline proteins by solid-state NMR (ssNMR) spectroscopy is presented. Proteins produced with [1-(13)C]- or [2-(13)C]glucose are very sparsely labeled, and the resulting 2D ssNMR spectra exhibit smaller line widths (by a factor of ?2 relative to uniformly labeled proteins) and contain a reduced number of cross-peaks. This allows for an accelerated and straightforward resonance assignment without the necessity of time-consuming 3D spectroscopy or sophisticated pulse sequences. The strategy aims at complete backbone and side-chain resonance assignments based on bidirectional sequential walks. The approach was successfully demonstrated with the de novo assignment of the Type Three Secretion System PrgI needle protein. Using a limited set of simple 2D experiments, we report a 97% complete resonance assignment of the backbone and side-chain (13)C atoms.
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Effect of zinc binding on ?-amyloid structure and dynamics: implications for A? aggregation.
Biophys. J.
PUBLISHED: 02-25-2011
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Assembly of ?-amyloid (A?) peptide into toxic oligomers is widely believed to initiate Alzheimers disease pathogenesis. Under in vitro physiological conditions, zinc (Zn(II)) can bind to A? and redirect its assembly from amyloid fibrillar toward less toxic amorphous aggregation. Propensity of A? to go toward a specific form of aggregate state is determined by structural and dynamical properties of the initial monomeric as well as the aggregate state. Here we probe the structural and dynamical impact of binding of Zn(II) to monomeric A?40 using NMR spectroscopy. To obtain further support for the importance of intrinsic dynamics in the aggregation precursor, (15)N relaxation measurements were also performed for A?42, the more fibrillar aggregation-prone variant of A?. The combined data suggest that, upon Zn(II)-binding to the N-terminus of A?40, a relatively rigid turnlike structure is induced at residues Val(24)-Lys(28) whereas the residues flanking this region become more mobile on the picosecond-to-nanosecond timescale. This is in contrast to the increased rigidity of A?42 at the C-terminus, and proposed to be linked to the higher propensity of Zn(II)-bound peptide to form amorphous aggregates with less entropic penalties than their fibrillar counterparts.
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Conserved core of amyloid fibrils of wild type and A30P mutant ?-synuclein.
Protein Sci.
PUBLISHED: 02-01-2011
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The major component of neural inclusions that are the pathological hallmark of Parkinsons disease are amyloid fibrils of the protein ?-synuclein (aS). Here we investigated if the disease-related mutation A30P not only modulates the kinetics of aS aggregation, but also alters the structure of amyloid fibrils. To this end we optimized the method of quenched hydrogen/deuterium exchange coupled to NMR spectroscopy and performed two-dimensional proton-detected high-resolution magic angle spinning experiments. The combined data indicate that the A30P mutation does not cause changes in the number, location and overall arrangement of ?-strands in amyloid fibrils of aS. At the same time, several residues within the fibrillar core retain nano-second dynamics. We conclude that the increased pathogenicity related to the familial A30P mutation is unlikely to be caused by a mutation-induced change in the conformation of aS aggregates.
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Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy.
J. Biomol. NMR
PUBLISHED: 01-28-2011
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Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of globular, modular and intrinsically disordered proteins, as well as protein-protein and protein-DNA complexes. Here we characterized the conformation of a spin-label attached to the homodimeric protein CylR2 using a combination of X-ray crystallography, electron paramagnetic resonance (EPR) and NMR spectroscopy. Close agreement was found between the conformation of the spin label observed in the crystal structure with interspin distances measured by EPR and signal broadening in NMR spectra, suggesting that the conformation seen in the crystal structure is also preferred in solution. In contrast, conformations of the spin label observed in crystal structures of T4 lysozyme are not in agreement with the paramagnetic relaxation enhancement observed for spin-labeled CylR2 in solution. Our data demonstrate that accurate positioning of the paramagnetic center is essential for high-resolution structure determination.
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Functional dynamics in the voltage-dependent anion channel.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 12-10-2010
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The voltage-dependent anion channel (VDAC), located in the outer mitochondrial membrane, acts as a gatekeeper for the entry and exit of mitochondrial metabolites. Here we reveal functional dynamics of isoform one of VDAC (VDAC1) by a combination of solution NMR spectroscopy, Gaussian network model analysis, and molecular dynamics simulation. Micro- to millisecond dynamics are significantly increased for the N-terminal six ?-strands of VDAC1 in micellar solution, in agreement with increased B-factors observed in the same region in the bicellar crystal structure of VDAC1. Molecular dynamics simulations reveal that a charge on the membrane-facing glutamic acid 73 (E73) accounts for the elevation of N-terminal protein dynamics as well as a thinning of the nearby membrane. Mutation or chemical modification of E73 strongly reduces the micro- to millisecond dynamics in solution. Because E73 is necessary for hexokinase-I-induced VDAC channel closure and inhibition of apoptosis, our results imply that micro- to millisecond dynamics in the N-terminal part of the barrel are essential for VDAC interaction and gating.
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Supramolecular interactions probed by 13C-13C solid-state NMR spectroscopy.
J. Am. Chem. Soc.
PUBLISHED: 10-12-2010
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We present a robust solid-state NMR approach for the accurate determination of molecular interfaces in insoluble and noncrystalline protein-protein complexes. The method relies on the measurement of intermolecular (13)C-(13)C distances in mixtures of [1-(13)C]glucose- and [2-(13)C]glucose-labeled proteins. We have applied this method to Parkinsons disease-associated ?-synuclein fibrils and found that they are stacked in a parallel in-register arrangement. Additionally, intermolecular distance restraints for the structure determination of the fibrils at atomic resolution were measured.
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The intermembrane space domain of Tim23 is intrinsically disordered with a distinct binding region for presequences.
Protein Sci.
PUBLISHED: 08-19-2010
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Proteins targeted to the mitochondrial matrix are translocated through the outer and the inner mitochondrial membranes by two protein complexes, the translocase of the outer membrane (TOM) and one of the translocases of the inner membrane (TIM23). The protein Tim23, the core component of TIM23, consists of an N-terminal, soluble domain in the intermembrane space (IMS) and a C-terminal domain that forms the import pore across the inner membrane. Before translocation proceeds, precursor proteins are recognized by the N-terminal domain of Tim23, Tim23N (residues 1-96). By using NMR spectroscopy, we show that Tim23N is a monomeric protein belonging to the family of intrinsically disordered proteins. Titrations of Tim23N with two presequences revealed a distinct binding region of Tim23N formed by residues 71-84. In a charge-hydropathy plot containing all soluble domains of TOM and TIM23, Tim23N was found to be the only domain with more than 40 residues in the IMS that is predicted to be intrinsically disordered, suggesting that Tim23N might function as hub in the mitochondrial import machinery protein network.
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Molten globule precursor states are conformationally correlated to amyloid fibrils of human beta-2-microglobulin.
J. Am. Chem. Soc.
PUBLISHED: 06-23-2010
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Misfolding intermediates play a key role in defining aberrant protein aggregation and amyloid formation in more than 15 different human diseases. However, their experimental characterization is challenging due to the transient nature and conformational heterogeneity of the involved states. Here, we demonstrate that direct carbon-detected NMR experiments allow observation, assignment, and structural analysis of molten globule amyloid intermediates that are severely broadened by conformational exchange. The method is used to characterize the structure and dynamics of partially unfolded intermediates of the 99-residue protein beta-2-microglobulin, which is the major component of insoluble aggregates occurring in dialysis-related amyloidosis. Comparison of the conformational properties of the molten globule-like intermediates with levels of deuterium incorporation into amyloid fibrils of beta-2-microglobulin revealed a close relationship between the conformational properties of the metastable intermediates and the beta-sheet-rich insoluble aggregates of beta-2-microglobulin.
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In-silico oncology: an approximate model of brain tumor mass effect based on directly manipulated free form deformation.
Int J Comput Assist Radiol Surg
PUBLISHED: 04-30-2010
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The present work introduces a novel method for approximating mass effect of primary brain tumors.
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Tailored low-power cross-polarization under fast magic-angle spinning.
J. Magn. Reson.
PUBLISHED: 03-19-2010
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High static magnetic fields and very fast magic-angle spinning (MAS) promise to improve resolution and sensitivity of solid-state NMR experiments. The fast MAS regime has permitted the development of low-power cross-polarization schemes, such as second-order cross-polarization (SOCP), which prevent heat deposition in the sample. Those schemes are however limited in bandwidth, as weak radio-frequency (RF) fields only cover a small chemical shift range for rare nuclei (e.g. (13)C). Another consideration is that the efficiency of cross-polarization is very sensitive to magnetization decay that occurs during the spin-lock pulse on the abundant nuclei (e.g. (1)H). Having characterized this decay in glutamine at 60 kHz MAS, we propose two complementary strategies to tailor cross-polarization to desired spectral regions at low RF power. In the case of multiple sites with small chemical shift dispersion, a larger bandwidth for SOCP is obtained by slightly increasing the RF power while avoiding recoupling conditions that lead to fast spin-lock decay. In the case of two spectral regions with large chemical shift offset, an extension of the existing low-power schemes, called MOD-CP, is introduced. It consists of a spin-lock on (1)H and an amplitude-modulated spin-lock on the rare nucleus. The range of excited chemical shifts is assessed by experimental excitation profiles and numerical simulation of an I(2)S spin system. All SOCP-based schemes exhibit higher sensitivity than high-power CP schemes, as demonstrated on solid (glutamine) and semi-solid (hydrated, micro-crystalline ubiquitin) samples.
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Biomechanical modeling of the three-dimensional aspects of human vocal fold dynamics.
J. Acoust. Soc. Am.
PUBLISHED: 02-09-2010
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Human voice originates from the three-dimensional (3D) oscillations of the vocal folds. In previous studies, biomechanical properties of vocal fold tissues have been predicted by optimizing the parameters of simple two-mass-models to fit its dynamics to the high-speed imaging data from the clinic. However, only lateral and longitudinal displacements of the vocal folds were considered. To extend previous studies, a 3D mass-spring, cover-model is developed, which predicts the 3D vibrations of the entire medial surface of the vocal fold. The model consists of five mass planes arranged in vertical direction. Each plane contains five longitudinal, mass-spring, coupled oscillators. Feasibility of the model is assessed using a large body of dynamical data previously obtained from excised human larynx experiments, in vivo canine larynx experiments, physical models, and numerical models. Typical model output was found to be similar to existing findings. The resulting model enables visualization of the 3D dynamics of the human vocal folds during phonation for both symmetric and asymmetric vibrations.
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Structural properties of pore-forming oligomers of alpha-synuclein.
J. Am. Chem. Soc.
PUBLISHED: 11-06-2009
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Soluble oligomers are potent toxins in many neurodegenerative diseases, but little is known about the structure of soluble oligomers and their structure-toxicity relationship. Here we prepared on-pathway oligomers of the 140-residue protein alpha-synuclein, a key player in Parkinsons disease, at concentrations an order of magnitude higher than previously possible. The oligomers form ion channels with well-defined conductance states in a variety of membranes, and their beta-structure differs from that of amyloid fibrils of alpha-synuclein.
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1H, 13C and 15N resonance assignments of the Calmodulin-Munc13-1 peptide complex.
Biomol NMR Assign
PUBLISHED: 10-05-2009
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Ca(2+)-Calmodulin binding to the variable N-terminal region of the diacylglycerol/phorbol ester-binding UNC13/Munc13 family of proteins modulates the short-term synaptic plasticity characteristics in neurons. Here, we report the sequential backbone and side chain resonance assignment of the Ca(2+)-Calmodulin/Munc13-1(458-492) peptide complex at pH 6.8 and 35 degrees C (BMRB No. 15470).
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Modular architecture of Munc13/calmodulin complexes: dual regulation by Ca2+ and possible function in short-term synaptic plasticity.
EMBO J.
PUBLISHED: 08-04-2009
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Ca(2+) signalling in neurons through calmodulin (CaM) has a prominent function in regulating synaptic vesicle trafficking, transport, and fusion. Importantly, Ca(2+)-CaM binds a conserved region in the priming proteins Munc13-1 and ubMunc13-2 and thus regulates synaptic neurotransmitter release in neurons in response to residual Ca(2+) signals. We solved the structure of Ca(2+)(4)-CaM in complex with the CaM-binding domain of Munc13-1, which features a novel 1-5-8-26 CaM-binding motif with two separated mobile structural modules, each involving a CaM domain. Photoaffinity labelling data reveal the same modular architecture in the complex with the ubMunc13-2 isoform. The N-module can be dissociated with EGTA to form the half-loaded Munc13/Ca(2+)(2)-CaM complex. The Ca(2+) regulation of these Munc13 isoforms can therefore be explained by the modular nature of the Munc13/Ca(2+)-CaM interactions, where the C-module provides a high-affinity interaction activated at nanomolar [Ca(2+)](i), whereas the N-module acts as a sensor at micromolar [Ca(2+)](i). This Ca(2+)/CaM-binding mode of Munc13 likely constitutes a key molecular correlate of the characteristic Ca(2+)-dependent modulation of short-term synaptic plasticity.
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Structural characterization of alpha-synuclein in an aggregation prone state.
Protein Sci.
PUBLISHED: 06-26-2009
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The relation of alpha-synuclein (alphaS) aggregation to Parkinsons disease has long been recognized, but the pathogenic species and its molecular properties have yet to be identified. To obtain insight into the properties of alphaS in an aggregation-prone state, we studied the structural properties of alphaS at acidic pH using NMR spectroscopy and computation. NMR demonstrated that alphaS remains natively unfolded at lower pH, but secondary structure propensities were changed in proximity to acidic residues. The ensemble of conformations of alphaS at acidic pH is characterized by a rigidification and compaction of the Asp and Glu-rich C-terminal region, an increased probability for proximity between the NAC-region and the C-terminal region and a lower probability for interactions between the N- and C-terminal regions.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.