44 results on '"Huber R"'
Search Results
2. Tunable non-integer high-harmonic generation in a topological insulator
- Author
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Schmid, C. P., Weigl, L., Grössing, P., Junk, V., Gorini, C., Schlauderer, S., Ito, S., Meierhofer, M., Hofmann, N., Afanasiev, D., Kokh, K.A., Tereschenko, O.E., Gudde, J., Evers, F., Wilhelm, J., Richter, K., Hofer, U., and Huber, R.
- Subjects
Electric insulators -- Properties ,Bismuth -- Electric properties -- Optical properties ,Light -- Observations ,Tellurium -- Electric properties -- Optical properties ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
When intense lightwaves accelerate electrons through a solid, the emerging high-order harmonic (HH) radiation offers key insights into the material.sup.1-11. Sub-optical-cycle dynamics--such as dynamical Bloch oscillations.sup.2-5, quasiparticle collisions.sup.6,12, valley pseudospin switching.sup.13 and heating of Dirac gases.sup.10--leave fingerprints in the HH spectra of conventional solids. Topologically non-trivial matter.sup.14,15 with invariants that are robust against imperfections has been predicted to support unconventional HH generation.sup.16-20. Here we experimentally demonstrate HH generation in a three-dimensional topological insulator--bismuth telluride. The frequency of the terahertz driving field sharply discriminates between HH generation from the bulk and from the topological surface, where the unique combination of long scattering times owing to spin-momentum locking.sup.17 and the quasi-relativistic dispersion enables unusually efficient HH generation. Intriguingly, all observed orders can be continuously shifted to arbitrary non-integer multiples of the driving frequency by varying the carrier-envelope phase of the driving field--in line with quantum theory. The anomalous Berry curvature warranted by the non-trivial topology enforces meandering ballistic trajectories of the Dirac fermions, causing a hallmark polarization pattern of the HH emission. Our study provides a platform to explore topology and relativistic quantum physics in strong-field control, and could lead to non-dissipative topological electronics at infrared frequencies. High-harmonic generation from the Dirac-like surface state of a topological insulator is separated from bulk contributions and continuously tuned by the carrier-envelope phase of the driving lightwave., Author(s): C. P. Schmid [sup.1] , L. Weigl [sup.1] , P. Grössing [sup.2] , V. Junk [sup.2] , C. Gorini [sup.2] [sup.7] , S. Schlauderer [sup.1] , S. Ito [sup.3] [...]
- Published
- 2021
- Full Text
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3. Lightwave-driven quasiparticle collisions on a subcycle timescale
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Langer, F, Hohenleutner, M, Schmid, CP, Poellmann, C, Nagler, P, Korn, T, Schüller, C, Sherwin, MS, Huttner, U, Steiner, JT, Koch, SW, Kira, M, and Huber, R
- Subjects
Nuclear and Plasma Physics ,Physical Sciences ,General Science & Technology - Abstract
Ever since Ernest Rutherford scattered α-particles from gold foils, collision experiments have revealed insights into atoms, nuclei and elementary particles. In solids, many-body correlations lead to characteristic resonances--called quasiparticles--such as excitons, dropletons, polarons and Cooper pairs. The structure and dynamics of quasiparticles are important because they define macroscopic phenomena such as Mott insulating states, spontaneous spin- and charge-order, and high-temperature superconductivity. However, the extremely short lifetimes of these entities make practical implementations of a suitable collider challenging. Here we exploit lightwave-driven charge transport, the foundation of attosecond science, to explore ultrafast quasiparticle collisions directly in the time domain: a femtosecond optical pulse creates excitonic electron-hole pairs in the layered dichalcogenide tungsten diselenide while a strong terahertz field accelerates and collides the electrons with the holes. The underlying dynamics of the wave packets, including collision, pair annihilation, quantum interference and dephasing, are detected as light emission in high-order spectral sidebands of the optical excitation. A full quantum theory explains our observations microscopically. This approach enables collision experiments with various complex quasiparticles and suggests a promising new way of generating sub-femtosecond pulses.
- Published
- 2016
4. Build-up and dephasing of Floquet–Bloch bands on subcycle timescales
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Ito, S., primary, Schüler, M., additional, Meierhofer, M., additional, Schlauderer, S., additional, Freudenstein, J., additional, Reimann, J., additional, Afanasiev, D., additional, Kokh, K. A., additional, Tereshchenko, O. E., additional, Güdde, J., additional, Sentef, M. A., additional, Höfer, U., additional, and Huber, R., additional
- Published
- 2023
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5. Attosecond clocking of correlations between Bloch electrons
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Freudenstein, J., primary, Borsch, M., additional, Meierhofer, M., additional, Afanasiev, D., additional, Schmid, C. P., additional, Sandner, F., additional, Liebich, M., additional, Girnghuber, A., additional, Knorr, M., additional, Kira, M., additional, and Huber, R., additional
- Published
- 2022
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6. Real-time observation of interfering crystal electrons in high-harmonic generation
- Author
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Hohenleutner, M., Langer, F., Schubert, O., Knorr, M., Huttner, U., Koch, S.W., Kira, M., and Huber, R.
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Collisions (Nuclear physics) -- Properties -- Research ,Electrons -- Properties -- Research ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Acceleration and collision of particles has been a key strategy for exploring the texture of matter. Strong light waves can control and recollide electronic wavepackets, generating high-harmonic radiation that encodes the structure and dynamics of atoms and molecules and lays the foundations of attosecond science (1-3). The recent discovery of high-harmonic generation in bulk solids (4-6) combines the idea of ultrafast acceleration with complex condensed matter systems, and provides hope for compact solid-state attosecond sources (6-8) and electronics at optical frequencies (3, 5, 9, 10). Yet the underlying quantum motion has not so far been observable in real time. Here we study high-harmonic generation in a bulk solid directly in the time domain, and reveal a new kind of strong-field excitation in the crystal. Unlike established atomic sources (1-3, 9, 11), our solid emits high-harmonic radiation as a sequence of subcycle bursts that coincide temporally with the field crests of one polarity of the driving terahertz waveform. We show that these features are characteristic of a non-perturbative quantum interference process that involves electrons from multiple valence bands. These results identify key mechanisms for future solid-state attosecond sources and next-generation light-wave electronics. The new quantum interference process justifies the hope for all-optical band-structure reconstruction and lays the foundation for possible quantum logic operations at optical clock rates., Ultrafast time resolution in the few-femtosecond or attosecond regime has provided systematic insight into quantum control of individual atoms (12), molecules (13), and solids (14). A spectacular example has been [...]
- Published
- 2015
7. Sub-cycle switch-on of ultrastrong light-matter interaction
- Author
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Gunter, G., Anappara, A.A., Hees, J., Sell, A., Biasiol, G., Sorba, L., De Liberato, S., Ciuti, C., Tredicucci, A., Leitenstorfer, A., and Huber, R.
- Subjects
Photons -- Properties ,Environmental issues ,Science and technology ,Zoology and wildlife conservation ,Properties - Abstract
Controlling the way light interacts with material excitations is at the heart of cavity quantum electrodynamics (QED). In the strong-coupling regime, quantum emitters in a microresonator absorb and spontaneously re-emit a photon many times before dissipation becomes effective, giving rise to mixed light-matter eigenmodes (1-12). Recent experiments (13) in semiconductor microcavities reached a new limit of ultrastrong coupling (14), where photon exchange occurs on timescales comparable to the oscillation period of light. In this limit, ultrafast modulation of the coupling strength has been suggested to lead to unconventional QED phenomena (14,15). Although sophisticated light--matter coupling has been achieved in all three spatial dimensions, control in the fourth dimension, time, is little developed. Here we use a quantum-well waveguide structure to optically tune light--matter interaction from weak to ultrastrong and turn on maximum coupling within less than one cycle of light. In this regime, a class of extremely non-adiabatic phenomena becomes observable. In particular, we directly monitor how a coherent photon population converts to cavity polaritons during abrupt switching. This system forms a promising laboratory in which to study novel sub-cycle QED effects and represents an efficient room-temperature switching device operating at unprecedented speed., Microcavities enclosing a material resonance provide an elegant way to tailor the strength of light-matter interaction, quantified by the vacuum Rabi frequency, [Ω.sub.R]. Intuitively, [Ω.sub.R] represents the rate at which [...]
- Published
- 2009
8. How many-particle interactions develop after ultrafast excitation of an electron-hole plasma
- Author
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Huber, R., Tauser, F., Brodschelm, A., Bichler, M., Abstreiter, G., and Leitenstorfer, A.
- Subjects
Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): R. Huber [1]; F. Tauser [1]; A. Brodschelm [1]; M. Bichler [2]; G. Abstreiter [2]; A. Leitenstorfer (corresponding author) [1] Electrostatic coupling between particles is important in many microscopic [...]
- Published
- 2001
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9. Structure of astacin and implications for activation of astacins and zinc-ligation of collagenases
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Bode, W., Gomis-Ruth, F.X., Huber, R., Zwilling, R., and Stocker, W.
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Digestive enzymes -- Models ,Collagenases -- Research ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
The X-ray crystal arrangement of the enzyme astacin has been determined to the 10 to 1.8 angstrom level using multiple isomorphous heavy-atom replacement. Astacin, a digestive zinc-endopeptidase derived from the crayfish Astacus astacus, is a round molecule containing a deep active-site cleft, zinc at the bottom ligated by three histidines, a water molecule and a more distant tyrosine. The third histidine may be the long-sought third zinc ligand of this type of enzyme including the vertebrate collagenases.
- Published
- 1992
10. Hyperthermophilic archaebacteria within the crater and open-sea plume of erupting Macdonald Seamount
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Huber, R., Stoffers, P., Cheminee, J.L., Richnow, H.H., and Stetter, K.O.
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Archaeabacteria -- Genetic aspects ,Microbial ecology -- Research ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Published
- 1990
11. Temporal and spectral fingerprints of ultrafast all-coherent spin switching
- Author
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Schlauderer, S., primary, Lange, C., additional, Baierl, S., additional, Ebnet, T., additional, Schmid, C. P., additional, Valovcin, D. C., additional, Zvezdin, A. K., additional, Kimel, A. V., additional, Mikhaylovskiy, R. V., additional, and Huber, R., additional
- Published
- 2019
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12. Isolation of a hyperthermophilic archaeum predicted by in situ RNA analysis
- Author
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Huber, R., Burggraf, S., Mayer, T., Barns, S. M., Rossnagel, P., and Stetter, K. O.
- Published
- 1995
13. Subcycle observation of lightwave-driven Dirac currents in a topological surface band
- Author
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Reimann, J., primary, Schlauderer, S., additional, Schmid, C. P., additional, Langer, F., additional, Baierl, S., additional, Kokh, K. A., additional, Tereshchenko, O. E., additional, Kimura, A., additional, Lange, C., additional, Güdde, J., additional, Höfer, U., additional, and Huber, R., additional
- Published
- 2018
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14. Lightwave valleytronics in a monolayer of tungsten diselenide
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Langer, F., primary, Schmid, C. P., additional, Schlauderer, S., additional, Gmitra, M., additional, Fabian, J., additional, Nagler, P., additional, Schüller, C., additional, Korn, T., additional, Hawkins, P. G., additional, Steiner, J. T., additional, Huttner, U., additional, Koch, S. W., additional, Kira, M., additional, and Huber, R., additional
- Published
- 2018
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15. Hyperthermophilic archaea are thriving in deep North Sea and Alaskan oil reservoirs
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Stetter, K.O., Huber, R., Blochl, E., Kurr, M., Eden, R.D., Fielder, M., Cash, H., and Vance, I.
- Subjects
North Sea -- Research ,Alaska -- Natural history ,Hydrothermal deposits -- Alaska ,Geology, Stratigraphic -- Archaean ,Bacteria -- Research ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Samples from four reservoirs that have high temperatures and produce H2S indicated the presence of hyperthermophiles with coccoid, irregular cells. The phylogenetic relationship between the hyperthermophiles was established through DNA/DNA hybridization. These thermophiles are similar to microorganisms found in submarine hot vents. The hyperthermophiles, though inactive in surface soils, ground water flows and oil, can survive in subterranean organisms that enter the reservoirs through sea water addition.
- Published
- 1993
16. Detergent structure in crystals of a bacterial photosynthetic reaction centre
- Author
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Roth, M., Lewit-Bentley, A., Michel, H., Deisenhofer, J., Huber, R., and Oesterhelt, D.
- Subjects
Crystallization -- Research ,Bacteria, Photosynthetic -- Research ,Membrane proteins -- Research ,Surface active agents -- Research ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Published
- 1989
17. Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3Å resolution.
- Author
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Deisenhofer, J., Epp, O., Miki, K., Huber, R., and Michel, H.
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- 1985
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18. In vivo synthesis and properties of uracil-containing DNA
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Huber R. Warner and Bruce K. Duncan
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DNA Repair ,Uracil Nucleotides ,Base pair ,viruses ,Biology ,medicine.disease_cause ,Coliphages ,Structure-Activity Relationship ,chemistry.chemical_compound ,Bacteriolysis ,Escherichia coli ,medicine ,heterocyclic compounds ,Pyrophosphatases ,N-Glycosyl Hydrolases ,Multidisciplinary ,Wild type ,Uracil ,Molecular biology ,Thymine ,chemistry ,Biochemistry ,DNA, Viral ,Mutation ,Deoxyuracil Nucleotides ,Thymidine ,In vitro recombination ,DNA - Abstract
T4 bacteriophage DNA containing as much as 30% of its thymine replaced by uracil can be synthesised in Escherichia coli deficient in both dUTPase and uracil--DNA glycosidase. This uracil-containing DNA is competent for RNA transcription, and can be packaged into phage which are viable, if the host cells are deficient in uracil--DNA glycosidase activity. If the host cells are not deficient in this glycosidase activity the infecting phage DNA is rapidly attacked, resulting in more than 50% acid-solubilisation of the DNA. The infected cells are inefficiently killed, presumably because of very limited, if any, expression of the phage DNA. These results indicate that this replacement of thymine by uracil in DNA does not seriously impair the biological functionality of T4 DNA, provided the DNA is not subjected to the breakdown (repair) pathway initiated by uracil--DNA glycosidase.
- Published
- 1978
19. A novel group of abyssal methanogenic archaebacteria (Methanopyrus) growing at 110 C
- Author
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Huber, R., Kurr, M., Jannasch, H.W., and Stetter, K.O.
- Subjects
Bacteria, Aerobic -- Growth ,Heat -- Physiological aspects ,Methanobacteriaceae -- Research ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Published
- 1989
20. In vivo synthesis and properties of uracil-containing DNA.
- Author
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Warner, Huber R. and Duncan, Bruce K.
- Published
- 1978
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21. A novel group of abyssal methanogenic archaebacteria (Methanopyrus) growing at 110 °C
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Huber, R., primary, Kurr, M., additional, Jannasch, H. W., additional, and Stetter, K. O., additional
- Published
- 1989
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22. A novel group of abyssal methanogenic archaebacteria (Methanopyrus) growing at 110 degrees C.
- Author
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Huber, R. and Kurr, M.
- Subjects
- *
MICROBIOLOGY - Abstract
Isolates a novel group of methanogenic archaebacteria growing at least at 110 degrees C from sediment samples taken by the research submersible `Alvin' at the Guaymas Basin hot vents (Gulf of California). Methods; Results; Discussion.
- Published
- 1989
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23. Sub-cycle atomic-scale forces coherently control a single-molecule switch.
- Author
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Peller D, Kastner LZ, Buchner T, Roelcke C, Albrecht F, Moll N, Huber R, and Repp J
- Abstract
Scanning probe techniques can leverage atomically precise forces to sculpt matter at surfaces, atom by atom. These forces have been applied quasi-statically to create surface structures
1-7 and influence chemical processes8,9 , but exploiting local dynamics10-14 to realize coherent control on the atomic scale remains an intriguing prospect. Chemical reactions15-17 , conformational changes18,19 and desorption20 have been followed on ultrafast timescales, but directly exerting femtosecond forces on individual atoms to selectively induce molecular motion has yet to be realized. Here we show that the near field of a terahertz wave confined to an atomically sharp tip provides femtosecond atomic-scale forces that selectively induce coherent hindered rotation in the molecular frame of a bistable magnesium phthalocyanine molecule. Combining lightwave-driven scanning tunnelling microscopy21-24 with ultrafast action spectroscopy10,13 , we find that the induced rotation modulates the probability of the molecule switching between its two stable adsorption geometries by up to 39 per cent. Mapping the response of the molecule in space and time confirms that the force acts on the atomic scale and within less than an optical cycle (that is, faster than an oscillation period of the carrier wave of light). We anticipate that our strategy might ultimately enable the coherent manipulation of individual atoms within single molecules or solids so that chemical reactions and ultrafast phase transitions can be manipulated on their intrinsic spatio-temporal scales.- Published
- 2020
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24. Tracking the ultrafast motion of a single molecule by femtosecond orbital imaging.
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Cocker TL, Peller D, Yu P, Repp J, and Huber R
- Abstract
Watching a single molecule move on its intrinsic timescale has been one of the central goals of modern nanoscience, and calls for measurements that combine ultrafast temporal resolution with atomic spatial resolution. Steady-state experiments access the requisite spatial scales, as illustrated by direct imaging of individual molecular orbitals using scanning tunnelling microscopy or the acquisition of tip-enhanced Raman and luminescence spectra with sub-molecular resolution. But tracking the intrinsic dynamics of a single molecule directly in the time domain faces the challenge that interactions with the molecule must be confined to a femtosecond time window. For individual nanoparticles, such ultrafast temporal confinement has been demonstrated by combining scanning tunnelling microscopy with so-called lightwave electronics, which uses the oscillating carrier wave of tailored light pulses to directly manipulate electronic motion on timescales faster even than a single cycle of light. Here we build on ultrafast terahertz scanning tunnelling microscopy to access a state-selective tunnelling regime, where the peak of a terahertz electric-field waveform transiently opens an otherwise forbidden tunnelling channel through a single molecular state. It thereby removes a single electron from an individual pentacene molecule's highest occupied molecular orbital within a time window shorter than one oscillation cycle of the terahertz wave. We exploit this effect to record approximately 100-femtosecond snapshot images of the orbital structure with sub-ångström spatial resolution, and to reveal, through pump/probe measurements, coherent molecular vibrations at terahertz frequencies directly in the time domain. We anticipate that the combination of lightwave electronics and the atomic resolution of our approach will open the door to visualizing ultrafast photochemistry and the operation of molecular electronics on the single-orbital scale.
- Published
- 2016
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25. Photonics: Terahertz collisions.
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Huber R
- Published
- 2012
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26. Transdisciplinary EU science institute needs funds urgently.
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Vasbinder JW, Andersson B, Arthur WB, Boasson M, de Boer R, Changeux JP, Domingo E, Eigen M, Fersht A, Frenkel D, Rees M, Groen T, Huber R, Hunt T, Holland J, May R, Norrby E, Nijkamp P, Lehn JM, Rabbinge R, Scheffer M, Schuster P, Serageldin I, Stuip J, de Vries J, van Vierssen W, and Willems R
- Subjects
- Academies and Institutes trends, Conservation of Natural Resources economics, Conservation of Natural Resources trends, European Union, Humans, Internationality, Netherlands, Research trends, Academies and Institutes economics, Research economics, Research Design
- Published
- 2010
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27. A plant pathogen virulence factor inhibits the eukaryotic proteasome by a novel mechanism.
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Groll M, Schellenberg B, Bachmann AS, Archer CR, Huber R, Powell TK, Lindow S, Kaiser M, and Dudler R
- Subjects
- Antineoplastic Agents classification, Antineoplastic Agents pharmacology, Arabidopsis genetics, Arabidopsis metabolism, Burkholderia pseudomallei genetics, Catalysis drug effects, Crystallization, Humans, Papain metabolism, Peptides, Cyclic classification, Peptides, Cyclic genetics, Peptides, Cyclic metabolism, Phaseolus enzymology, Proteasome Endopeptidase Complex chemistry, Proteasome Endopeptidase Complex metabolism, Protein Subunits antagonists & inhibitors, Protein Subunits chemistry, Protein Subunits metabolism, Pseudomonas syringae chemistry, Pseudomonas syringae genetics, Saccharomyces cerevisiae enzymology, Substrate Specificity, Trypsin metabolism, Virulence genetics, Virulence Factors genetics, Virulence Factors metabolism, Eukaryotic Cells enzymology, Peptides, Cyclic pharmacology, Phaseolus microbiology, Proteasome Inhibitors, Pseudomonas syringae metabolism, Virulence Factors pharmacology
- Abstract
Pathogenic bacteria often use effector molecules to increase virulence. In most cases, the mode of action of effectors remains unknown. Strains of Pseudomonas syringae pv. syringae (Pss) secrete syringolin A (SylA), a product of a mixed non-ribosomal peptide/polyketide synthetase, in planta. Here we identify SylA as a virulence factor because a SylA-negative mutant in Pss strain B728a obtained by gene disruption was markedly less virulent on its host, Phaseolus vulgaris (bean). We show that SylA irreversibly inhibits all three catalytic activities of eukaryotic proteasomes, thus adding proteasome inhibition to the repertoire of modes of action of virulence factors. The crystal structure of the yeast proteasome in complex with SylA revealed a novel mechanism of covalent binding to the catalytic subunits. Thus, SylA defines a new class of proteasome inhibitors that includes glidobactin A (GlbA), a structurally related compound from an unknown species of the order Burkholderiales, for which we demonstrate a similar proteasome inhibition mechanism. As proteasome inhibitors are a promising class of anti-tumour agents, the discovery of a novel family of inhibitory natural products, which we refer to as syrbactins, may also have implications for the development of anti-cancer drugs. Homologues of SylA and GlbA synthetase genes are found in some other pathogenic bacteria, including the human pathogen Burkholderia pseudomallei, the causative agent of melioidosis. It is thus possible that these bacteria are capable of producing proteasome inhibitors of the syrbactin class.
- Published
- 2008
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28. Reduced sleep in Drosophila Shaker mutants.
- Author
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Cirelli C, Bushey D, Hill S, Huber R, Kreber R, Ganetzky B, and Tononi G
- Subjects
- Amino Acid Sequence, Animals, Behavior, Animal physiology, Circadian Rhythm genetics, Circadian Rhythm physiology, Conserved Sequence, Crosses, Genetic, Darkness, Drosophila Proteins, Drosophila melanogaster genetics, Female, Genes, Recessive genetics, Genetic Complementation Test, Homeostasis, Humans, Light, Longevity genetics, Longevity physiology, Male, Mammals physiology, Molecular Sequence Data, Motor Activity physiology, Phenotype, Potassium Channels chemistry, Potassium Channels genetics, Protein Structure, Tertiary, Shaker Superfamily of Potassium Channels, Sleep genetics, Sleep physiology, Time Factors, X Chromosome genetics, Drosophila melanogaster metabolism, Point Mutation genetics, Potassium Channels metabolism, Sleep Deprivation genetics, Sleep Deprivation physiopathology
- Abstract
Most of us sleep 7-8 h per night, and if we are deprived of sleep our performance suffers greatly; however, a few do well with just 3-4 h of sleep-a trait that seems to run in families. Determining which genes underlie this phenotype could shed light on the mechanisms and functions of sleep. To do so, we performed mutagenesis in Drosophila melanogaster, because flies also sleep for many hours and, when sleep deprived, show sleep rebound and performance impairments. By screening 9,000 mutant lines, we found minisleep (mns), a line that sleeps for one-third of the wild-type amount. We show that mns flies perform normally in a number of tasks, have preserved sleep homeostasis, but are not impaired by sleep deprivation. We then show that mns flies carry a point mutation in a conserved domain of the Shaker gene. Moreover, after crossing out genetic modifiers accumulated over many generations, other Shaker alleles also become short sleepers and fail to complement the mns phenotype. Finally, we show that short-sleeping Shaker flies have a reduced lifespan. Shaker, which encodes a voltage-dependent potassium channel controlling membrane repolarization and transmitter release, may thus regulate sleep need or efficiency.
- Published
- 2005
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29. Local sleep and learning.
- Author
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Huber R, Ghilardi MF, Massimini M, and Tononi G
- Subjects
- Brain cytology, Homeostasis physiology, Humans, Membrane Potentials physiology, Neuronal Plasticity physiology, Rotation, Synapses physiology, Wakefulness physiology, Brain physiology, Learning physiology, Sleep physiology
- Abstract
Human sleep is a global state whose functions remain unclear. During much of sleep, cortical neurons undergo slow oscillations in membrane potential, which appear in electroencephalograms as slow wave activity (SWA) of <4 Hz. The amount of SWA is homeostatically regulated, increasing after wakefulness and returning to baseline during sleep. It has been suggested that SWA homeostasis may reflect synaptic changes underlying a cellular need for sleep. If this were so, inducing local synaptic changes should induce local SWA changes, and these should benefit neural function. Here we show that sleep homeostasis indeed has a local component, which can be triggered by a learning task involving specific brain regions. Furthermore, we show that the local increase in SWA after learning correlates with improved performance of the task after sleep. Thus, sleep homeostasis can be induced on a local level and can benefit performance.
- Published
- 2004
- Full Text
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30. Staphylocoagulase is a prototype for the mechanism of cofactor-induced zymogen activation.
- Author
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Friedrich R, Panizzi P, Fuentes-Prior P, Richter K, Verhamme I, Anderson PJ, Kawabata S, Huber R, Bode W, and Bock PE
- Subjects
- Binding Sites, Coagulase chemistry, Coagulase genetics, Coenzymes metabolism, Crystallography, X-Ray, Enzyme Activation drug effects, Enzyme Precursors chemistry, Humans, Kinetics, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, Prothrombin chemistry, Structure-Activity Relationship, Thrombin chemistry, Coagulase metabolism, Coenzymes pharmacology, Enzyme Precursors metabolism, Prothrombin metabolism, Staphylococcus aureus enzymology, Thrombin metabolism
- Abstract
Many bacterial pathogens secrete proteins that activate host trypsinogen-like enzyme precursors, most notably the proenzymes of the blood coagulation and fibrinolysis systems. Staphylococcus aureus, an important human pathogen implicated in sepsis and endocarditis, secretes the cofactor staphylocoagulase, which activates prothrombin, without the usual proteolytic cleavages, to directly initiate blood clotting. Here we present the 2.2 A crystal structures of human alpha-thrombin and prethrombin-2 bound to a fully active staphylocoagulase variant. The cofactor consists of two domains, each with three-helix bundles; this is a novel fold that is distinct from known serine proteinase activators, particularly the streptococcal plasminogen activator streptokinase. The staphylocoagulase fold is conserved in other bacterial plasma-protein-binding factors and extracellular-matrix-binding factors. Kinetic studies confirm the importance of isoleucine 1 and valine 2 at the amino terminus of staphylocoagulase for zymogen activation. In addition to making contacts with the 148 loop and (pro)exosite I of prethrombin-2, staphylocoagulase inserts its N-terminal peptide into the activation pocket of bound prethrombin-2, allosterically inducing functional catalytic machinery. These investigations demonstrate unambiguously the validity of the zymogen-activation mechanism known as 'molecular sexuality'.
- Published
- 2003
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31. Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine.
- Author
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Krojer T, Garrido-Franco M, Huber R, Ehrmann M, and Clausen T
- Subjects
- Crystallography, X-Ray, Escherichia coli, Models, Molecular, Protein Conformation, Protein Structure, Tertiary, Recombinant Proteins chemistry, Heat-Shock Proteins, Molecular Chaperones chemistry, Periplasmic Proteins, Serine Endopeptidases chemistry
- Abstract
Molecular chaperones and proteases monitor the folded state of other proteins. In addition to recognizing non-native conformations, these quality control factors distinguish substrates that can be refolded from those that need to be degraded. To investigate the molecular basis of this process, we have solved the crystal structure of DegP (also known as HtrA), a widely conserved heat shock protein that combines refolding and proteolytic activities. The DegP hexamer is formed by staggered association of trimeric rings. The proteolytic sites are located in a central cavity that is only accessible laterally. The mobile side-walls are constructed by twelve PDZ domains, which mediate the opening and closing of the particle and probably the initial binding of substrate. The inner cavity is lined by several hydrophobic patches that may act as docking sites for unfolded polypeptides. In the chaperone conformation, the protease domain of DegP exists in an inactive state, in which substrate binding in addition to catalysis is abolished.
- Published
- 2002
- Full Text
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32. Crystal structure of the tricorn protease reveals a protein disassembly line.
- Author
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Brandstetter H, Kim JS, Groll M, and Huber R
- Subjects
- Archaeal Proteins genetics, Archaeal Proteins metabolism, Binding Sites, Catalysis, Cloning, Molecular, Crystallography, X-Ray, Endopeptidases genetics, Endopeptidases metabolism, Escherichia coli, Models, Molecular, Protein Conformation, Substrate Specificity, Thermoplasma genetics, Archaeal Proteins chemistry, Endopeptidases chemistry, Thermoplasma enzymology
- Abstract
The degradation of cytosolic proteins is carried out predominantly by the proteasome, which generates peptides of 7-9 amino acids long. These products need further processing. Recently, a proteolytic system was identified in the model organism Thermoplasma acidophilum that performs this processing. The hexameric core protein of this modular system, referred to as tricorn protease, is a 720K protease that is able to assemble further into a giant icosahedral capsid, as determined by electron microscopy. Here, we present the crystal structure of the tricorn protease at 2.0 A resolution. The structure reveals a complex mosaic protein whereby five domains combine to form one of six subunits, which further assemble to form the 3-2-symmetric core protein. The structure shows how the individual domains coordinate the specific steps of substrate processing, including channelling of the substrate to, and the product from, the catalytic site. Moreover, the structure shows how accessory protein components might contribute to an even more complex protein machinery that efficiently collects the tricorn-released products.
- Published
- 2001
- Full Text
- View/download PDF
33. The 3.2-A crystal structure of the human IgG1 Fc fragment-Fc gammaRIII complex.
- Author
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Sondermann P, Huber R, Oosthuizen V, and Jacob U
- Subjects
- Amino Acid Sequence, Crystallography, X-Ray, Humans, Immunoglobulin Fragments metabolism, Immunoglobulin G metabolism, Macromolecular Substances, Models, Molecular, Molecular Sequence Data, Protein Binding, Receptors, IgG metabolism, Recombinant Proteins chemistry, Recombinant Proteins metabolism, Immunoglobulin Fragments chemistry, Immunoglobulin G chemistry, Receptors, IgG chemistry
- Abstract
The immune response depends on the binding of opsonized antigens to cellular Fc receptors and the subsequent initiation of various cellular effector functions of the immune system. Here we describe the crystal structures of a soluble Fc gamma receptor (sFc gammaRIII, CD16), an Fc fragment from human IgG1 (hFc1) and their complex. In the 1:1 complex the receptor binds to the two halves of the Fc fragment in contact with residues of the C gamma2 domains and the hinge region. Upon complex formation the angle between the two sFc gammaRIII domains increases significantly and the Fc fragment opens asymmetrically. The high degree of amino acid conservation between sFc gammaRIII and other Fc receptors, and similarly between hFc1 and related immunoglobulins, suggest similar structures and modes of association. Thus the described structure is a model for immune complex recognition and helps to explain the vastly differing affinities of other Fc gammaR-IgG complexes and the Fc epsilonRI alpha-IgE complex.
- Published
- 2000
- Full Text
- View/download PDF
34. Structural basis for the anticoagulant activity of the thrombin-thrombomodulin complex.
- Author
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Fuentes-Prior P, Iwanaga Y, Huber R, Pagila R, Rumennik G, Seto M, Morser J, Light DR, and Bode W
- Subjects
- Amino Acid Sequence, Carboxypeptidase B2, Carboxypeptidases chemistry, Crystallography, X-Ray, Humans, Macromolecular Substances, Models, Molecular, Molecular Sequence Data, Peptide Fragments chemistry, Protein Binding, Protein C chemistry, Protein Conformation, Protein Structure, Tertiary, Static Electricity, Structure-Activity Relationship, Thrombin physiology, Thrombomodulin physiology, Anticoagulants chemistry, Thrombin chemistry, Thrombomodulin chemistry
- Abstract
The serine proteinase alpha-thrombin causes blood clotting through proteolytic cleavage of fibrinogen and protease-activated receptors and amplifies its own generation by activating the essential clotting factors V and VIII. Thrombomodulin, a transmembrane thrombin receptor with six contiguous epidermal growth factor-like domains (TME1-6), profoundly alters the substrate specificity of thrombin from pro- to anticoagulant by activating protein C. Activated protein C then deactivates the coagulation cascade by degrading activated factors V and VIII. The thrombin-thrombomodulin complex inhibits fibrinolysis by activating the procarboxypeptidase thrombin-activatable fibrinolysis inhibitor. Here we present the 2.3 A crystal structure of human alpha-thrombin bound to the smallest thrombomodulin fragment required for full protein-C co-factor activity, TME456. The Y-shaped thrombomodulin fragment binds to thrombin's anion-binding exosite-I, preventing binding of procoagulant substrates. Thrombomodulin binding does not seem to induce marked allosteric structural rearrangements at the thrombin active site. Rather, docking of a protein C model to thrombin-TME456 indicates that TME45 may bind substrates in such a manner that their zymogen-activation cleavage sites are presented optimally to the unaltered thrombin active site.
- Published
- 2000
- Full Text
- View/download PDF
35. The structures of HsIU and the ATP-dependent protease HsIU-HsIV.
- Author
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Bochtler M, Hartmann C, Song HK, Bourenkov GP, Bartunik HD, and Huber R
- Subjects
- ATP-Dependent Proteases, Adenosine Triphosphatases metabolism, Adenosine Triphosphate metabolism, Cloning, Molecular, Crystallography, X-Ray, Endopeptidases metabolism, Escherichia coli, Heat-Shock Proteins metabolism, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, Protein Structure, Tertiary, Recombinant Proteins chemistry, Recombinant Proteins metabolism, Adenosine Triphosphatases chemistry, Endopeptidases chemistry, Heat-Shock Proteins chemistry, Serine Endopeptidases
- Abstract
The degradation of cytoplasmic proteins is an ATP-dependent process. Substrates are targeted to a single soluble protease, the 26S proteasome, in eukaryotes and to a number of unrelated proteases in prokaryotes. A surprising link emerged with the discovery of the ATP-dependent protease HslVU (heat shock locus VU) in Escherichia coli. Its protease component HslV shares approximately 20% sequence similarity and a conserved fold with 20S proteasome beta-subunits. HslU is a member of the Hsp100 (Clp) family of ATPases. Here we report the crystal structures of free HslU and an 820,000 relative molecular mass complex of HslU and HslV-the first structure of a complete set of components of an ATP-dependent protease. HslV and HslU display sixfold symmetry, ruling out mechanisms of protease activation that require a symmetry mismatch between the two components. Instead, there is conformational flexibility and domain motion in HslU and a localized order-disorder transition in HslV. Individual subunits of HslU contain two globular domains in relative orientations that correlate with nucleotide bound and unbound states. They are surprisingly similar to their counterparts in N-ethylmaleimide-sensitive fusion protein, the prototype of an AAA-ATPase. A third, mostly alpha-helical domain in HslU mediates the contact with HslV and may be the structural equivalent of the amino-terminal domains in proteasomal AAA-ATPases.
- Published
- 2000
- Full Text
- View/download PDF
36. Crystal structures of the membrane-binding C2 domain of human coagulation factor V.
- Author
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Macedo-Ribeiro S, Bode W, Huber R, Quinn-Allen MA, Kim SW, Ortel TL, Bourenkov GP, Bartunik HD, Stubbs MT, Kane WH, and Fuentes-Prior P
- Subjects
- Amino Acid Sequence, Binding Sites, Crystallography, X-Ray, Factor VIIIa metabolism, Factor Va metabolism, Humans, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, Protein Structure, Tertiary, Sequence Alignment, Stereoisomerism, Factor Va chemistry
- Abstract
Rapid and controlled clot formation is achieved through sequential activation of circulating serine proteinase precursors on phosphatidylserine-rich procoagulant membranes of activated platelets and endothelial cells. The homologous complexes Xase and prothrombinase, each consisting of an active proteinase and a non-enzymatic cofactor, perform critical steps within this coagulation cascade. The activated cofactors VIIIa and Va, highly specific for their cognate proteinases, are each derived from precursors with the same A1-A2-B-A3-C1-C2 architecture. Membrane binding is mediated by the C2 domains of both cofactors. Here we report two crystal structures of the C2 domain of human factor Va. The conserved beta-barrel framework provides a scaffold for three protruding loops, one of which adopts markedly different conformations in the two crystal forms. We propose a mechanism of calcium-independent, stereospecific binding of factors Va and VIIIa to phospholipid membranes, on the basis of (1) immersion of hydrophobic residues at the apices of these loops in the apolar membrane core; (2) specific interactions with phosphatidylserine head groups in the groove enclosed by these loops; and (3) favourable electrostatic contacts of basic side chains with negatively charged membrane phosphate groups.
- Published
- 1999
- Full Text
- View/download PDF
37. Structure of cytochrome c nitrite reductase.
- Author
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Einsle O, Messerschmidt A, Stach P, Bourenkov GP, Bartunik HD, Huber R, and Kroneck PM
- Subjects
- Crystallography, X-Ray, Cytochrome c Group metabolism, Heme chemistry, Models, Molecular, Molecular Sequence Data, Nitrites metabolism, Oxidoreductases chemistry, Protein Conformation, Cytochrome c Group chemistry, Gram-Negative Anaerobic Bacteria enzymology, Sulfur-Reducing Bacteria enzymology
- Abstract
The enzyme cytochrome c nitrite reductase catalyses the six-electron reduction of nitrite to ammonia as one of the key steps in the biological nitrogen cycle, where it participates in the anaerobic energy metabolism of dissimilatory nitrate ammonification. Here we report on the crystal structure of this enzyme from the microorganism Sulfurospirillum deleyianum, which we solved by multiwavelength anomalous dispersion methods. We propose a reaction scheme for the transformation of nitrite based on structural and spectroscopic information. Cytochrome c nitrite reductase is a functional dimer, with 10 close-packed haem groups of type c and an unusual lysine-coordinated high-spin haem at the active site. By comparing the haem arrangement of this nitrite reductase with that of other multihaem cytochromes, we have been able to identify a family of proteins in which the orientation of haem groups is conserved whereas structure and function are not.
- Published
- 1999
- Full Text
- View/download PDF
38. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.
- Author
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Deckert G, Warren PV, Gaasterland T, Young WG, Lenox AL, Graham DE, Overbeek R, Snead MA, Keller M, Aujay M, Huber R, Feldman RA, Short JM, Olsen GJ, and Swanson RV
- Subjects
- Chromosome Mapping, Chromosomes, Bacterial, Citric Acid Cycle, DNA Repair, DNA, Bacterial biosynthesis, DNA, Bacterial genetics, Gram-Negative Aerobic Rods and Cocci metabolism, Molecular Sequence Data, Oxidative Stress, Phylogeny, Protein Biosynthesis, Temperature, Transcription, Genetic, Genome, Bacterial, Gram-Negative Aerobic Rods and Cocci genetics
- Abstract
Aquifex aeolicus was one of the earliest diverging, and is one of the most thermophilic, bacteria known. It can grow on hydrogen, oxygen, carbon dioxide, and mineral salts. The complex metabolic machinery needed for A. aeolicus to function as a chemolithoautotroph (an organism which uses an inorganic carbon source for biosynthesis and an inorganic chemical energy source) is encoded within a genome that is only one-third the size of the E. coli genome. Metabolic flexibility seems to be reduced as a result of the limited genome size. The use of oxygen (albeit at very low concentrations) as an electron acceptor is allowed by the presence of a complex respiratory apparatus. Although this organism grows at 95 degrees C, the extreme thermal limit of the Bacteria, only a few specific indications of thermophily are apparent from the genome. Here we describe the complete genome sequence of 1,551,335 base pairs of this evolutionarily and physiologically interesting organism.
- Published
- 1998
- Full Text
- View/download PDF
39. Human beta-tryptase is a ring-like tetramer with active sites facing a central pore.
- Author
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Pereira PJ, Bergner A, Macedo-Ribeiro S, Huber R, Matschiner G, Fritz H, Sommerhoff CP, and Bode W
- Subjects
- Amino Acid Sequence, Animals, Binding Sites, Cattle, Chymases, Crystallography, X-Ray, Electrochemistry, Humans, Lung cytology, Lung enzymology, Mast Cells enzymology, Models, Molecular, Molecular Sequence Data, Protein Conformation, Serine Endopeptidases metabolism, Serine Proteinase Inhibitors, Structure-Activity Relationship, Tryptases, Serine Endopeptidases chemistry
- Abstract
Human tryptase, a mast-cell-specific serine proteinase that may be involved in causing asthma and other allergic and inflammatory disorders, is unique in two respects: it is enzymatically active only as a heparin-stabilized tetramer, and it is resistant to all known endogenous proteinase inhibitors. The 3-A crystal structure of human beta-tryptase in a complex with 4-amidinophenyl pyruvic acid shows four quasi-equivalent monomers arranged in a square flat ring of pseudo 222 symmetry. Each monomer contacts its neighbours at two different interfaces through six loop segments. These loops are located around the active site of beta-tryptase and differ considerably in length and conformation from loops of other trypsin-like proteinases. The four active centres of the tetramer are directed towards an oval central pore, restricting access for macromolecular substrates and enzyme inhibitors. Heparin chains might stabilize the complex by binding to an elongated patch of positively charged residues spanning two adjacent monomers. The nature of this unique tetrameric architecture explains many of tryptase's biochemical properties and provides a basis for the rational design of monofunctional and bifunctional tryptase inhibitors.
- Published
- 1998
- Full Text
- View/download PDF
40. Mechanism of inhibition of the human matrix metalloproteinase stromelysin-1 by TIMP-1.
- Author
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Gomis-Rüth FX, Maskos K, Betz M, Bergner A, Huber R, Suzuki K, Yoshida N, Nagase H, Brew K, Bourenkov GP, Bartunik H, and Bode W
- Subjects
- Binding Sites, Crystallography, X-Ray, Drug Design, Glycoproteins pharmacology, Glycosylation, Humans, Matrix Metalloproteinase Inhibitors, Models, Molecular, Protease Inhibitors chemical synthesis, Protease Inhibitors pharmacology, Protein Conformation, Tissue Inhibitor of Metalloproteinases, Glycoproteins chemistry, Matrix Metalloproteinase 3 chemistry, Protease Inhibitors chemistry
- Abstract
Matrix metalloproteinases (MMPs) are zinc endopeptidases that are required for the degradation of extracellular matrix components during normal embryo development, morphogenesis and tissue remodelling. Their proteolytic activities are precisely regulated by endogenous tissue inhibitors of metalloproteinases (TIMPs). Disruption of this balance results in diseases such as arthritis, atherosclerosis, tumour growth and metastasis. Here we report the crystal structure of an MMP-TIMP complex formed between the catalytic domain of human stromelysin-1 (MMP-3) and human TIMP-1. TIMP-1, a 184-residue protein, has the shape of an elongated, contiguous wedge. With its long edge, consisting of five different chain regions, it occupies the entire length of the active-site cleft of MMP-3. The central disulphide-linked segments Cys 1-Thr 2-Cys 3-Val 4 and Ser 68-Val 69 bind to either side of the catalytic zinc. Cys 1 bidentally coordinates this zinc, and the Thr-2 side chain extends into the large specificity pocket of MMP-3. This unusual architecture of the interface between MMP-3 and TIMP-1 suggests new possibilities for designing TIMP variants and synthetic MMP inhibitors with potential therapeutic applications.
- Published
- 1997
- Full Text
- View/download PDF
41. Structure of 20S proteasome from yeast at 2.4 A resolution.
- Author
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Groll M, Ditzel L, Löwe J, Stock D, Bochtler M, Bartunik HD, and Huber R
- Subjects
- Acetylcysteine analogs & derivatives, Acetylcysteine pharmacology, Calpain antagonists & inhibitors, Crystallography, X-Ray, Cysteine Endopeptidases drug effects, Cysteine Endopeptidases metabolism, Endopeptidases chemistry, Endopeptidases metabolism, Enzyme Inhibitors pharmacology, Enzyme Precursors chemistry, Enzyme Precursors metabolism, Glycoproteins pharmacology, Histocompatibility Antigens Class I metabolism, Models, Molecular, Multienzyme Complexes drug effects, Multienzyme Complexes metabolism, Proteasome Endopeptidase Complex, Saccharomyces cerevisiae enzymology, Thermoplasma enzymology, Threonine chemistry, Cysteine Endopeptidases chemistry, Multienzyme Complexes chemistry, Protein Conformation
- Abstract
The crystal structure of the 20S proteasome from the yeast Saccharomyces cerevisiae shows that its 28 protein subunits are arranged as an (alpha1...alpha7, beta1...beta7)2 complex in four stacked rings and occupy unique locations. The interior of the particle, which harbours the active sites, is only accessible by some very narrow side entrances. The beta-type subunits are synthesized as proproteins before being proteolytically processed for assembly into the particle. The proforms of three of the seven different beta-type subunits, beta1/PRE3, beta2/PUP1 and beta5/PRE2, are cleaved between the threonine at position 1 and the last glycine of the pro-sequence, with release of the active-site residue Thr 1. These three beta-type subunits have inhibitor-binding sites, indicating that PRE2 has a chymotrypsin-like and a trypsin-like activity and that PRE3 has peptidylglutamyl peptide hydrolytic specificity. Other beta-type subunits are processed to an intermediate form, indicating that an additional nonspecific endopeptidase activity may exist which is important for peptide hydrolysis and for the generation of ligands for class I molecules of the major histocompatibility complex.
- Published
- 1997
- Full Text
- View/download PDF
42. Antibody-antigen flexibility.
- Author
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Huber R and Bennett WS
- Subjects
- Antibody Diversity, Immunoglobulin Constant Regions, Immunoglobulin Fab Fragments, Immunoglobulin Fc Fragments, Immunoglobulin G, Immunoglobulin Variable Region, Protein Conformation, Antibodies immunology, Antigens immunology
- Published
- 1987
- Full Text
- View/download PDF
43. Conformational flexibility in protein molecules.
- Author
-
Huber R
- Subjects
- Crystallography methods, Kinetics, Motion, Structure-Activity Relationship, Temperature, Protein Conformation
- Published
- 1979
- Full Text
- View/download PDF
44. Crystallographic structure studies of an IgG molecule and an Fc fragment.
- Author
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Huber R, Deisenhofer J, Colman PM, Matsushima M, and Palm W
- Subjects
- Antigen-Antibody Reactions, Carbohydrates, Humans, Hydrogen Bonding, Immunoglobulin Fab Fragments, Immunoglobulin Variable Region, Ligands, Models, Molecular, Protein Conformation, X-Ray Diffraction, Immunoglobulin Fc Fragments, Immunoglobulin G
- Abstract
The crystal structures of a human IgG antibody molecule Kol and a human Fc fragment have been determined at 4-A and 3.4-A resolution respectively, by isomorphous replacement. The electron-density maps were interpreted in terms of immunoglobulin domains based on the Rei and McPC 603 models (Kol) and by model-building (Fc). The Fab parts of Kol have a different quaternary structure from that observed in isolated crystalline Fab fragments, there being no longitudinal V-C contact in Kol. The Fc part C terminal to the hinge is disordered in the Kol crystals. It is suggested that the Kol molecule is flexible in solution, whereas fragments are rigid. In the Fc fragment both CH3 and CH2 show the immunoglobulin fold. The CH3 dimer aggregates as CH1-CL while CH2 are widely separated from each other. The carbohydrate bound to Fc is in fixed position. From these structures a hypothetical liganded antibody molecule has been constructed, which is assumed to be rigid.
- Published
- 1976
- Full Text
- View/download PDF
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