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  • Nature Publishing Group  (60,646)
  • American Geophysical Union (AGU)
  • Annual Reviews
  • 1995-1999  (16,975)
  • 1980-1984  (21,819)
  • 1945-1949  (14,746)
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  • 1
    Electronic Resource
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 209-237 
    ISSN: 1056-8700
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  • 2
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 239-267 
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  • 3
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 269-292 
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  • 4
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 293-318 
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  • 5
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 319-350 
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 351-377 
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    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 379-404 
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  • 8
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 405-434 
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  • 9
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 435-462 
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  • 10
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 463-493 
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  • 11
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    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 495-522 
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  • 12
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    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 85-116 
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  • 13
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    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 59-83 
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  • 14
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    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 117-140 
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  • 15
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    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 141-165 
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    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 523-549 
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  • 17
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 55-78 
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  • 18
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 113-136 
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    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 163-195 
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    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 231-258 
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    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 259-286 
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    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 197-229 
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    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 287-314 
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    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 315-342 
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  • 25
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    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 367-394 
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  • 26
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    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 431-459 
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  • 27
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    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 395-429 
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  • 28
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 1-25 
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  • 29
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 27-45 
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    Notes: Abstract The scope and utility of phage display is reviewed with emphasis on medical applications and structure-based ligand and drug design, from literature mostly after 1994. General principles by which phage-displayed peptides achieve affinity and selectivity for targets are described, along with selected structural or mechanistic studies of the binding of peptides or proteins discovered or engineered by phage display. Such engineered proteins whose wild-type or mutant crystal or 2D-NMR structures yield insight about the basis for enhanced affinity or altered specificity include antibodies, zinc fingers, human growth hormone, protein A, and atrial natriuretic peptide. Structures of complexes of de novo phage-discovered peptide ligands with targets such as the Src SH3 domain, streptavidin, and erythropoietin receptor reveal the structural basis for receptor-peptide recognition in these systems.
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  • 30
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 83-112 
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    Notes: Abstract Chromatin structure is now believed to be dynamic and intimately related with cellular processes such as transcription. Over the past few years, high-resolution structures for the histones have become available. These structures and their implications for nucleosome organization are reviewed here.
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  • 31
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 113-137 
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    Notes: Abstract The evidence showing that the self-assembly of complex RNAs occurs in discrete transitions, each relating to the folding of sub-systems of increasing size and complexity starting from a state with most of the secondary structure, is reviewed. The reciprocal influence of the concentration of magnesium ions and nucleotide mutations on tertiary structure is analyzed. Several observations demonstrate that detrimental mutations can be rescued by high magnesium concentrations, while stabilizing mutations lead to a lesser dependence on magnesium ion concentration. Recent data point to the central controlling and monitoring roles of RNA-binding proteins that can bind to the different folding stages, either before full establishment of the secondary structure or at the molten globule state before the cooperative transition to the final three-dimensional structure.
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  • 32
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 139-156 
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    Notes: Abstract One of the fundamental properties of the RNA helix is its intrinsic resistance to bend- or twist-deformations. Results of a variety of physical measurements point to a persistence length of 700-800 A for double-stranded RNA in the presence of magnesium cations, approximately 1.5-2.0-fold larger than the corresponding value for DNA. Although helix flexibility represents an important, quantifiable measure of the forces of interaction within the helix, it must also be considered in describing conformational variation of nonhelix elements (e.g. internal loops, branches), since the latter always reflect the properties of the flanking helices; that is, such elements are never completely rigid. For one important element of tertiary structure, namely, the core of yeast tRNAPhe, the above consideration has led to the conclusion that the core is not substantially more flexible than an equivalent length of pure helix.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 157-179 
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    Notes: Abstract Phospholamban is a 52-amino-acid protein that assembles into a pentamer in sarcoplasmic reticulum membranes. The protein has a role in the regulation of the resident calcium ATPase through an inhibitory association that can be reversed by phosphorylation. The phosphorylation of phospholamban is initiated by beta-adrenergic stimulation, identifying phospholamban as an important component in the stimulation of cardiac activity by beta-agonists. It is this role of phospholamban that has motivated studies in recent decades. There is evidence that phospholamban may also function as a Ca2+-selective ion channel. The structural properties of phospholamban have been studied by mutagenesis, modeling, and spectroscopy, resulting in a new view of the organization of this key molecule in membranes.
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  • 34
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 181-222 
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    Notes: Abstract Innovative algorithms have been developed during the past decade for simulating Newtonian physics for macromolecules. A major goal is alleviation of the severe requirement that the integration timestep be small enough to resolve the fastest components of the motion and thus guarantee numerical stability. This timestep problem is challenging if strictly faster methods with the same all-atom resolution at small timesteps are sought. Mathematical techniques that have worked well in other multiple-timescale contexts-where the fast motions are rapidly decaying or largely decoupled from others-have not been as successful for biomolecules, where vibrational coupling is strong. This review examines general issues that limit the timestep and describes available methods (constrained, reduced-variable, implicit, symplecttic, multiple-timestep, and normal-mode-based schemes). A section compares results of selected integrators for a model dipeptide, assessing physical and numerical performance. Included is our dual timestep method LN, which relies on an approximate linearization of the equations of motion every Deltat interval (5 fs or less), the solution of which is obtained by explicit integration at the inner timestep Deltatau (e.g., 0.5 fs). LN is computationally competitive, providing 4-5 speedup factors, and results are in good agreement, in comparison to 0.5 fs trajectories. These collective algorithmic efforts help fill the gap between the time range that can be simulated and the timespans of major biological interest (milliseconds and longer). Still, only a hierarchy of models and methods, along with experimentational improvements, will ultimately give theoretical modeling the status of partner with experiment.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 223-258 
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    Notes: Abstract Two sensory rhodopsins (SRI and SRII) mediate color-sensitive phototaxis responses in halobacteria. These seven-helix receptor proteins, structurally and functionally similar to animal visual pigments, couple retinal photoisomerization to receptor activation and are complexed with membrane-embedded transducer proteins (HtrI and HtrII) that modulate a cytoplasmic phosphorylation cascade controlling the flagellar motor. The Htr proteins resemble the chemotaxis transducers from Escherichia coli. The SR-Htr signaling complexes allow studies of the biophysical chemistry of signal generation and relay, from the photobiophysics of initial excitation of the receptors to the final output at the level of the flagellar motor switch, revealing fundamental principles of sensory transduction and more broadly the nature of dynamic interactions between membrane proteins. We review here recent advances that have led to new insights into the molecular mechanism of signaling by these membrane complexes.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 259-288 
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    Notes: Abstract A characteristic feature of cellular signal transduction pathways in eukaryotes is the separation of catalysis from target recognition. Several modular domains that recognize short peptide sequences and target signaling proteins to these sequences have been identified. The structural bases of the specificities of recognition by SH2, SH3, and PTB domains have been elucidated by X-ray crystallography and NMR, and these results are reviewed here. In addition, the mechanism of cooperative interactions between these domains is discussed.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 357-371 
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    Notes: Abstract Zinc-finger domains are small metal-binding modules that are found in a wide range of gene regulatory proteins. Peptides corresponding to these domains have provided valuable model systems for examining a number of biophysical parameters entirely unrelated to their nucleic acid binding properties. These include the chemical basis for metal-ion affinity and selectivity, thermodynamic properties related to hydrophobic packing and beta-sheet propensities, and constraints on the generation of ligand-binding and potential catalytic sites. These studies have laid the foundation for applications such as the generation of optically detected zinc probes and the design of metal-binding peptides and proteins with desired spectroscopic and chemical properties.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 327-355 
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    Notes: Abstract Over the past two decades, nanosecond absorption and vibrational spectroscopies have developed into powerful tools for monitoring the secondary, tertiary, and quaternary structural relaxations of biological macromolecules under near-physiological conditions of solvent and temperature. Observed through such methods, the dynamic response of a biomolecule to photoinitiated excursions from equilibrium can reveal valuable information about the structure-function relationship, information beyond that obtained from the static structures provided by X-ray crystallography, nuclear magnetic resonance spectroscopy, and other steady-state methods. Most recently, the development of ultra-sensitive polarization techniques for absorption spectroscopy has greatly enhanced the amount of time-resolved structural information that can be obtained from the broadened electronic spectra of biomolecules. This review examines nanosecond absorption, vibrational, and polarized absorption methods, and their applications to protein function and folding, emphasizing the complementary nature of information obtained from electronic and vibrational spectra measured on the nanosecond time scale.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 289-325 
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    Notes: Abstract Eukaryotes have three distinct RNA polymerases that catalyze transcription of nuclear genes. RNA polymerase II is responsible for transcribing nuclear genes encoding the messenger RNAs and several small nuclear RNAs. Like RNA polymerases I and III, polymerase II cannot recognize its target promoter directly and initiate transcription without accessory factors. Instead, this large multisubunit enzyme relies on general transcription factors and transcriptional activators and coactivators to regulate transcription from class II promoters. X-ray crystallography and nuclear magnetic resonance spectroscopy have been used to study complexes of general transcription factors and transcriptional activators with their specific DNA targets. This work has provided important structural insights into transcription initiation by polymerase II and the more general problem of DNA sequence recognition.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 47-82 
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    Notes: Abstract Researchers have made good progress in unraveling the molecular mechanisms of excitation-contraction (EC) coupling in striated muscle. Despite this progress, paradoxes abound. In skeletal muscle, the existence of a mechanical coupling between membrane charge movement and activation of sarcoplasmic reticulum (SR) release channels is essentially established, but the contribution of Ca2+-induced Ca2+ release (CICR) to the transient and steady-state components of Ca2+ release remains controversial. In cardiac muscle, the role of CICR as the primary mechanism of EC coupling is well established, but the stability and tight coupling between membrane Ca2+ current and release are paradoxical. Answers may lie in microdomain issues, and in the examination of discrete elementary release events, although quantitative treatments are needed. This review explores the theoretical and experimental methods used and the observations made in the study of microdomain Ca2+.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 373-399 
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    Notes: Abstract Measurements of trajectories of individual proteins or lipids in the plasma membrane of cells show a variety of types of motion. Brownian motion is observed, but many of the particles undergo non-Brownian motion, including directed motion, confined motion, and anomalous diffusion. The variety of motion leads to significant effects on the kinetics of reactions among membrane-bound species and requires a revision of existing views of membrane structure and dynamics.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 495-540 
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    Notes: Abstract This review focuses on the recent advances in EPR spectroscopy as they are applied both to photoinduced electron transfer in the photosynthetic apparatus and to biomimetic systems. The review deals with time-resolved direct-detection cw and pulsed EPR and ENDOR methods, both at conventional bands [X-(9.5 GHz), K-(24 GHz), and Q-(35 GHz)] and at high frequency bands (W-band, 95 GHz, and even highter frequency bands). EPR studies on photosynthetic and model systems in their doublet, triplet and radical pair states are surveyed, including their static and dynamic properties. Applications of time-resolved EPR in studying photoinduced electron and energy transfer in isotropic and anisotropic environments, and the concepts of electron spin polarization and magnetic field effects in photochemical reactions are also reviewed.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 541-566 
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    Notes: Abstract Surface plasmon resonance biosensors have become increasingly popular for the qualitative and quantitative characterization of the specific binding of a mobile reactant to a binding partner immobilized on the sensor surface. This article reviews the use of this new technique to measure the binding affinities and the kinetic constants of reversible interactions between biological macromolecules. Immobilization techniques, the most commonly employed experimental strategies, and various analytical approaches are summarized. In recent years, several sources of potential artifacts have been identified: immobilization of the binding partner, steric hindrance of binding to adjacent binding sites at the sensor surface, and finite rate of mass transport of the mobile reactant to the sensor surface. Described here is the influence of these artifacts on the measured binding kinetics and equilibria, together with suggested control experiments.
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    Annual Review of Biophysics and Biomolecular Structure 26 (1997), S. 597-627 
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    Notes: Abstract Analysis of the structures in the Protein Databank, released in June 1996, shows that the number of different protein folds, i.e. the number of different arrangements of major secondary structures and/or chain topologies, is 327. Of these folds, approximately 25% belong to the all-alpha class, 20% belong to the all-beta class, 30% belong to the alpha/beta class, and 25% belong to the alpha + beta class. We describe the types of folds now known for the all-beta and all-alpha classes, emphasizing those that have been discovered recently. Detailed theories for the physical determinants of the structures of most of these folds now exist, and these are reviewed.
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    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 59-75 
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    Notes: Abstract This review surveys the kinds of protein complex that participate in cell communication and identifies, where possible, general principles by which they form and act. It also advances the notion that biophysical constraints imposed by macromolecular crowding and diffusion have had a controlling influence on the evolution of cell signaling pathways. Complexes associated with the bacterial aspartate receptor, with eucaryotic tyrosine kinase receptors, with T-cell receptors, and with focal contacts are examined together with proteins that serve as adaptors, anchors, and scaffolds for signaling complexes. The importance of diffusion in controlling the numbers and locations of signaling complexes is discussed, as is the special role played by membranes in signaling pathways.
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    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 285-327 
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    Notes: Abstract The substrates for the essential biological processes of transcription, replication, recombination, DNA repair, and cell division are not naked DNA; rather, they are protein-DNA complexes known as chromatin, in one or another stage of a hierarchical series of compactions. These are exciting times for students of chromatin. New studies provide incontrovertible evidence linking chromatin structure to function. Exceptional progress has been made in studies of the structure of chromatin subunits. Surprising new dynamic properties have been discovered. And, much progress has been made in dissecting the functional roles of specific chromatin proteins and domains. This review focuses on in vitro studies of chromatin structure, dynamics, and function.
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    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 249-284 
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    Notes: Abstract Retroviral protease (PR) from the human immunodeficiency virus type 1 (HIV-1) was identified over a decade ago as a potential target for structure-based drug design. This effort was very successful. Four drugs are already approved, and others are undergoing clinical trials. The techniques utilized in this remarkable example of structure-assisted drug design included crystallography, NMR, computational studies, and advanced chemical synthesis. The development of these drugs is discussed in detail. Other approaches to designing HIV-1 PR inhibitors, based on the concepts of symmetry and on the replacement of a water molecule that had been found tetrahedrally coordinated between the enzyme and the inhibitors, are also discussed. The emergence of drug-induced mutations of HIV-1 PR leads to rapid loss of potency of the existing drugs and to the need to continue the development process. The structural basis of drug resistance and the ways of overcoming this phenomenon are mentioned.
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    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 199-224 
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    Notes: Abstract Biochemical and genetic approaches have identified the molecular mechanisms of many genetic reactions, particularly in bacteria. Now a comparably detailed understanding is needed of how groupings of genes and related protein reactions interact to orchestrate cellular functions over the cell cycle, to implement preprogrammed cellular development, or to dynamically change a cell's processes and structures in response to environmental signals. Simulations using realistic, molecular-level models of genetic mechanisms and of signal transduction networks are needed to analyze dynamic behavior of multigene systems, to predict behavior of mutant circuits, and to identify the design principles applicable to design of genetic regulatory circuits. When the underlying design rules for regulatory circuits are understood, it will be far easier to recognize common circuit motifs, to identify functions of individual proteins in regulation, and to redesign circuits for altered functions.
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    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 329-356 
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    Notes: Abstract Cytochrome c oxidase, the terminal enzyme of the respiratory chains of mitochondria and aerobic bacteria, catalyzes electron transfer from cytochrome c to molecular oxygen, reducing the latter to water. Electron transfer is coupled to proton translocation across the membrane, resulting in a proton and charge gradient that is then employed by the F0F1-ATPase to synthesize ATP. Over the last years, substantial progress has been made in our understanding of the structure and function of this enzyme. Spectroscopic techniques such as EPR, absorbance and resonance Raman spectroscopy, in combination with site-directed mutagenesis work, have been successfully applied to elucidate the nature of the cofactors and their ligands, to identify key residues involved in proton transfer, and to gain insight into the catalytic cycle and the structures of its intermediates. Recently, the crystal structures of a bacterial and a mitochondrial cytochrome c oxidase have been determined. In this review, we provide an overview of the crystal structures, summarize recent spectroscopic work, and combine structural and spectroscopic data in discussing mechanistic aspects of the enzyme. For the latter, we focus on the structure of the oxygen intermediates, proton-transfer pathways, and the much-debated issue of how electron transfer in the enzyme might be coupled to proton translocation.
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    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 357-406 
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    Notes: Abstract During the past thirty years, deuterium labeling has been used to improve the resolution and sensitivity of protein NMR spectra used in a wide variety of applications. Most recently, the combination of triple resonance experiments and 2H, 13C, 15N labeled samples has been critical to the solution structure determination of several proteins with molecular weights on the order of 30 kDa. Here we review the developments in isotopic labeling strategies, NMR pulse sequences, and structure-determination protocols that have facilitated this advance and hold promise for future NMR-based structural studies of even larger systems. As well, we detail recent progress in the use of solution 2H NMR methods to probe the dynamics of protein sidechains.
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    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 475-502 
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    Notes: Abstract The hammerhead ribozyme is a small catalytic RNA that cleaves a target phosphodiester bond in a reaction dependent on divalent metal ions. Crystal structures of the hammerhead reveal the tertiary fold of an enzymatic "ground state" of the molecule; however, they do not clarify the catalytic mechanism of the ribozyme, presumably because a significant conformational rearrangement is required to reach an enzymatic transition state. The structural domains seen in the hammerhead can be related to sequence or structural motifs in transfer and ribosomal RNAs, suggesting that they represent tertiary building blocks that will be found in large, complex RNAs.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 1-27 
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    Notes: Abstract The Raman spectrum of a protein or nucleic acid consists of numerous discrete bands representing molecular normal modes of vibration and serves as a sensitive and selective fingerprint of three-dimensional structure, intermolecular interactions, and dynamics. Recent improvements in instrumentation, coupled with innovative approaches in experimental design, dramatically increase the power and scope of the method, particularly for investigations of large supramolecular assemblies. Applications are considered that involve the use of (a) time-resolved Raman spectroscopy to elucidate assembly pathways in icosahedral viruses, (b) polarized Raman microspectroscopy to determine detailed structural parameters in filamentous viruses, (c) ultraviolet-resonance Raman spectroscopy to probe selective DNA and protein residues in nucleoprotein complexes, and (d) difference Raman methods to understand mechanisms of protein/DNA recognition in gene regulatory and chromosomal complexes.
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    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 503-528 
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    Notes: Abstract Pleckstrin homology (PH) motifs are approximately 100 amino-acid residues long and have been identified in nearly 100 different eukaryotic proteins, many of which participate in cell signaling and cytoskeletal regulation. Despite minimal sequence homology, the three-dimensional structures are remarkably conserved. This review gives an overview of the PH domain architecture and examines the best-studied examples in an attempt to understand their function.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 29-56 
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    Notes: Abstract Transcription in eukaryotes is frequently regulated by a mechanism termed combinatorial control, whereby several different proteins must bind DNA in concert to achieve appropriate regulation of the downstream gene. X-ray crystallographic studies of multiprotein complexes bound to DNA have been carried out to investigate the molecular determinants of complex assembly and DNA binding. This work has provided important insights into the specific protein-protein and protein-DNA interactions that govern the assembly of multiprotein regulatory complexes. The results of these studies are reviewed here, and the general insights into the mechanism of combinatorial gene regulation are discussed.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 75-100 
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    Notes: Abstract Analytical ultracentrifugation is a classical method of biochemistry and molecular biology. Because it is a primary technique, sedimentation can provide first-principle hydrodynamic and first-principle thermodynamic information for nearly any molecule, in a wide range of solvents and over a wide range of solute concentrations. For many questions, it is the technique of choice. This review stresses what information is available from analytical ultracentrifugation and how that information is being extracted and used in contemporary applications.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 129-153 
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    Notes: Abstract Measurement of the distance between two spin label probes in proteins permits the spatial orientation of elements of defined secondary structure. By using site-directed spin labeling, it is possible to determine multiple distance constraints and thereby build tertiary and quaternary structural models as well as measure the kinetics of structural changes. New analytical methods for determining interprobe distances and relative orientations for uniquely oriented spin labels have been developed using global analysis of multifrequency electron paramagnetic resonance data. New methods have also been developed for determining interprobe distances for randomly oriented spin labels. These methods are being applied to a wide range of structural problems, including peptides, soluble proteins, and membrane proteins, that are not readily characterized by other structural techniques.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 155-179 
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    Notes: Abstract Current computer simulations of biomolecules typically make use of classical molecular dynamics methods, as a very large number (tens to hundreds of thousands) of atoms are involved over timescales of many nanoseconds. The methodology for treating short-range bonded and van der Waals interactions has matured. However, long-range electrostatic interactions still represent a bottleneck in simulations. In this article, we introduce the basic issues for an accurate representation of the relevant electrostatic interactions. In spite of the huge computational time demanded by most biomolecular systems, it is no longer necessary to resort to uncontrolled approximations such as the use of cutoffs. In particular, we discuss the Ewald summation methods, the fast particle mesh methods, and the fast multipole methods. We also review recent efforts to understand the role of boundary conditions in systems with long-range interactions, and conclude with a short perspective on future trends.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 101-128 
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    Notes: Abstract Recent structural and biochemical studies have begun to illuminate how cells solve the problems of recognizing and removing damaged DNA bases. Bases damaged by environmental, chemical, or enzymatic mechanisms must be efficiently found within a large excess of undamaged DNA. Structural studies suggest that a rapid damage-scanning mechanism probes for both conformational deviations and local deformability of the DNA base stack. At susceptible lesions, enzyme-induced conformational changes lead to direct interactions with specific damaged bases. The diverse array of damaged DNA bases are processed through a two-stage pathway in which damage-specific enzymes recognize and remove the base lesion, creating a common abasic site intermediate that is processed by damage-general repair enzymes to restore the correct DNA sequence.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 181-204 
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    Notes: Abstract A significant number of exciting papain-like cysteine protease structures have been determined by crystallographic methods over the last several years. This trove of data allows for an analysis of the structural features that empower these molecules as they efficiently carry out their specialized tasks. Although the structure of the paradigm for the family, papain, has been known for twenty years, recent efforts have reaped several structures of specialized mammalian enzymes. This review first covers the commonalities of architecture and purpose of the papain-like cysteine proteases. From that broad platform, each of the lysosomal enzymes for which there is an X-ray structure (or structures) is then examined to gain an understanding of what structural features are used to customize specificity and activity. Structure-based design of inhibitors to control pathological cysteine protease activity will also be addressed.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 269-293 
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    Notes: Abstract For nuclear magnetic resonance determinations of the conformation of oligosaccharides in solution, simple molecular mechanics calculations and nuclear Overhauser enhancement measurements are adequate for small oligosaccharides that adopt single, relatively rigid conformations. Polysaccharides and larger or more flexible oligosaccharides generally require additional types of data, such as scalar and dipolar coupling constants, which are most conveniently measured in 13C-enriched samples. Nuclear magnetic resonance relaxation data provide information on the dynamics of oligosaccharides, which involves several different types of internal motion. Oligosaccharides complexed with lectins and antibodies have been successfully studied both by X-ray crystallography and by nuclear magnetic resonance spectroscopy. The complexes have been shown to be stabilized by a combination of polar hydrogen bonding interactions and van der Waals attractions. Although theoretical calculations of the conformation and stability of free oligosaccharides and of complexes with proteins can be carried out by molecular mechanics methods, the role of solvent water for these highly polar molecules continues to present computational problems.
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    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 295-317 
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    Notes: Abstract Proteasomes are large multisubunit proteases that are found in the cytosol, both free and attached to the endoplasmic reticulum, and in the nucleus of eukaryotic cells. Their ubiquitous presence and high abundance in these compartments reflects their central role in cellular protein turnover. Proteasomes recognize, unfold, and digest protein substrates that have been marked for degradation by the attachment of a ubiquitin moiety. Individual subcomplexes of the complete 26S proteasome are involved in these different tasks: The ATP-dependent 19S caps are believed to unfold substrates and feed them to the actual protease, the 20S proteasome. This core particle appears to be more ancient than the ubiquitin system. Both prokaryotic and archaebacterial ancestors have been identified. Crystal structures are now available for the E. coli proteasome homologue and the T. acidophilum and S. cerevisiae 20S proteasomes. All three enzymes are cylindrical particles that have their active sites on the inner walls of a large central cavity. They share the fold and a novel catalytic mechanism with an N-terminal nucleophilic threonine, which places them in the family of Ntn (N terminal nucleophile) hydrolases. Evolution has added complexity to the comparatively simple prokaryotic prototype. This minimal proteasome is a homododecamer made from two hexameric rings stacked head to head. Its heptameric version is the catalytic core of archaebacterial proteasomes, where it is sandwiched between two inactive antichambers that are made up from a different subunit. In eukaryotes, both subunits have diverged into seven different subunits each, which are present in the particle in unique locations such that a complex dimer is formed that has six active sites with three major specificities that can be attributed to individual subunits. Genetic, biochemical, and high-resolution electron microscopy data, but no crystal structures, are available for the 19S caps. A first step toward a mechanistic understanding of proteasome activation and regulation has been made with the elucidation of the X-ray structure of the alternative, mammalian proteasome activator PA28.
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    Annual Review of Cell and Developmental Biology 11 (1995), S. 35-71 
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    Annual Review of Cell and Developmental Biology 11 (1995), S. 241-265 
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    Annual Review of Cell and Developmental Biology 11 (1995), S. 497-518 
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    Annual Review of Cell and Developmental Biology 11 (1995), S. 633-675 
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    Annual Review of Cell and Developmental Biology 12 (1996), S. 1-26 
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    Notes: Abstract Most chloroplast proteins are nuclear encoded, synthesized as larger precursor proteins in the cytosol, posttranslationally imported into the organelle, and routed to one of six different compartments. Import across the outer and inner envelope membranes into the stroma is the major means for entry of proteins destined for the stroma, the thylakoid membrane, and the thylakoid lumen. Recent investigations have identified several unique protein components of the envelope translocation machinery. These include two GTP-binding proteins that appear to participate in the early events of import and probably regulate precursor recognition and advancement into the translocon. Localization of imported precursor proteins to the thylakoid membrane and thylakoid lumen is accomplished by four distinct mechanisms; two are homologous to bacterial and endoplasmic reticulum protein transport systems, one appears unique, and the last may be a spontaneous mechanism. Thus chloroplast protein targeting is a unique and surprisingly complex process. The presence of GTP-binding proteins in the envelope translocation machinery indicates a different precursor recognition process than is present in mitochondria. Mechanisms for thylakoid protein localization are in part derived from the prokaryotic endosymbiont, but are more unusual and diverse than expected.
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    Annual Review of Cell and Developmental Biology 12 (1996), S. 181-220 
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    Notes: Abstract Receptors for the Fc domain of immunoglobulins play an important role in immune defense. There are two well-defined functional classes of mammalian receptors. One class of receptors transports immunoglobulins across epithelial tissues to their main sites of action. This class includes the neonatal Fc receptor (FcRn), which transports immunoglobulin G (IgG), and the polymeric immunoglobulin receptor (pIgR), which transports immunoglobulin A (IgA) and immunoglobulin M (IgM). Another class of receptors present on the surfaces of effector cells triggers various biological responses upon binding antibody-antigen complexes. Of these, the IgG receptors (FcgammaR) and immunoglobulin E (IgE) receptors (FcepsilonR) are the best characterized. The biological responses elicited include antibody-dependent, cell-mediated cytotoxicity, phagocytosis, release of inflammatory mediators, and regulation of lymphocyte proliferation and differentiation. We summarize the current knowledge of the structures and functions of FcRn, pIgR, and the FcgammaR and FcepsilonRI proteins, concentrating on the interactions of the extracellular portions of these receptors with immunoglobulins.
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    Annual Review of Cell and Developmental Biology 12 (1996), S. 335-363 
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    Notes: Abstract Peroxisome proliferator-activated receptors (PPARs) are lipid-activated transcription factors that belong to the steroid/thyroid/retinoic acid receptor superfamily. All their characterized target genes encode proteins that participate in lipid homeostasis. The recent finding that antidiabetic thiazolidinediones and adipogenic prostanoids are ligands of one of the PPARs reveals a novel signaling pathway that directly links these compounds to processes involved in glucose homeostasis and lipid metabolism including adipocyte differentiation. A detailed understanding of this pathway could designate PPARs as targets for the development of novel efficient treatments for several metabolic disorders.
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    Annual Review of Cell and Developmental Biology 12 (1996), S. 441-461 
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    Notes: Abstract Proteins that function in transport vesicle docking are being identified at a rapid rate. So-called v- and t-SNAREs form the core of a vesicle docking complex. Additional accessory proteins are required to protect SNAREs from promiscuous binding and to deprotect SNAREs under conditions in which transport vesicle docking should occur. Because access to SNAREs must be regulated, other proteins must also contain specificity determinants to accomplish delivery of transport vesicles to their distinct and specific membrane targets.
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    Annual Review of Cell and Developmental Biology 12 (1996), S. 417-439 
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    Notes: Abstract Myosin is a highly conserved, ubiquitous protein found in all eukaryotic cells, where it provides the motor function for diverse movements such as cytokinesis, phagocytosis, and muscle contraction. All myosins contain an amino-terminal motor/head domain and a carboxy-terminal tail domain. Due to the extensive number of different molecules identified to date, myosins have been divided into seven distinct classes based on the properties of the head domain. One such class, class II myosins, consists of the conventional two-headed myosins that form filaments and are composed of two myosin heavy chain (MYH) subunits and four myosin light chain subunits. The MYH subunit contains the ATPase activity providing energy that is the driving force for contractile processes mentioned above, and numerous MYH isoforms exist in vertebrates to carry out this function. The MYHs involved in striated muscle contraction in mammals are the focus of the current review. The genetics, molecular biology, and biochemical properties of mammalian MYHs are discussed below. MYH gene expression patterns in developing and adult striated muscles are described in detail, as are studies of regulation of MYH genes in the heart. The discovery that mutant MYH isoforms have a causal role in the human disease familial hypertrophic cardiomyopathy (FHC) has implemented structure/function investigations of MYHs. The regulation of MYH genes expressed in skeletal muscle and the potential functional implications that distinct MYH isoforms may have on muscle physiology are addressed.
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    Annual Review of Cell and Developmental Biology 12 (1996), S. 697-715 
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    Notes: Abstract Proteins that contain the Arg-Gly-Asp (RGD) attachment site, together with the integrins that serve as receptors for them, constitute a major recognition system for cell adhesion. The RGD sequence is the cell attachment site of a large number of adhesive extracellular matrix, blood, and cell surface proteins, and nearly half of the over 20 known integrins recognize this sequence in their adhesion protein ligands. Some other integrins bind to related sequences in their ligands. The integrin-binding activity of adhesion proteins can be reproduced by short synthetic peptides containing the RGD sequence. Such peptides promote cell adhesion when insolubilized onto a surface, and inhibit it when presented to cells in solution. Reagents that bind selectively to only one or a few of the RGD-directed integrins can be designed by cyclizing peptides with selected sequences around the RGD and by synthesizing RGD mimics. As the integrin-mediated cell attachment influences and regulates cell migration, growth, differentiation, and apoptosis, the RGD peptides and mimics can be used to probe integrin functions in various biological systems. Drug design based on the RGD structure may provide new treatments for diseases such as thrombosis, osteoporosis, and cancer.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 1-23 
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    Notes: Abstract Transcriptional regulation is important in all eukaryotic organisms for cell growth, development, and responses to environmental change. Saccharomyces cerevisiae, or bakers' yeast, has provided a powerful system for genetic analysis of transcriptional regulation, and findings from the study of this model system have proven broadly applicable to higher organisms. Transcriptional regulation requires the interactions of regulatory proteins with various components of the transcription machinery. Recently, genetic analysis of a diverse set of transcriptional regulatory responses has converged with studies of the function of the RNA polymerase II carboxy-terminal domain (CTD) to reveal regulatory roles for proteins associated with the CTD. These proteins, designated Srb/mediator proteins, are broadly involved in both positive and negative regulatory responses in vivo. This review focuses on the connections between genetic analysis of transcriptional regulation and the functions of the Srb/mediator proteins associated with the RNA polymerase II CTD.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 53-82 
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    Notes: Abstract Most animal species exhibit left-right asymmetry in their body plans and show a strong bias for one handedness over the other. The mechanism of handedness choice, recognized as an intriguing problem over a century ago, is still a mystery. However, from recent advances in understanding when and how asymmetry arises in both invertebrates and vertebrates, developmental pathways for establishment and maintenance of left-right differences are beginning to take shape, and speculations can be made on the initial choice mechanism.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 83-117 
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    Notes: Abstract The polymerization dynamics of microtubules are central to their biological functions. Polymerization dynamics allow microtubules to adopt spatial arrangements that can change rapidly in response to cellular needs and, in some cases, to perform mechanical work. Microtubules utilize the energy of GTP hydrolysis to fuel a unique polymerization mechanism termed dynamic instability. In this review, we first describe progress toward understanding the mechanism of dynamic instability of pure tubulin and then discuss the function and regulation of microtubule dynamic instability in living cells.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 25-51 
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    Notes: Abstract Mitochondria import most of their proteins from the cytosol. Dynamic protein complexes in the mitochondrial outer and inner membranes are responsible for the specific recognition and membrane translocation of preproteins. The preprotein translocase of the outer mitochondrial membrane contains several import receptors and a general import pore. The preprotein translocase of the inner membrane consists of a channel interacting with preproteins in transit and an import motor that includes the matrix heat shock protein Hsp70. Acidic patches of import components are thought to guide the import of positively charged signal sequences (acid chain hypothesis). Energy input is derived from the inner membrane potential and ATP. Proteins in the mitochondrial matrix are required for proteolytic processing and folding of imported proteins. The dynamic nature of the membrane translocase permits sorting of preproteins at distinct stages of the import pathway.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 119-146 
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    Notes: Abstract Adherens junctions are specialized forms of cadherin-based adhesive contacts important for tissue organization in developing and adult organisms. Cadherins form protein complexes with cytoplasmic proteins (catenins) that convert the specific, homophilic-binding capacity of the extracellular domain into stable cell adhesion. The extracellular domains of cadherins form parallel dimers that possess intrinsic homophilic-binding activity. Cytoplasmic interactions can influence the function of the ectodomain by a number of potential mechanisms, including redistribution of binding sites into clusters, providing cytoskeletal anchorage, and mediating physiological regulation of cadherin function. Adherens junctions are likely to serve specific, specialized functions beyond the basic adhesive process. These functions include coupling cytoskeletal force generation to strongly adherent sites on the cell surface and the regulation of intracellular signaling events.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 147-170 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract The Drosophila ovary provides a favorable model system in which to study cellular morphogenesis. The development of a mature egg involves a syncytium of 16 germline cells and over 1000 somatically derived follicle cells. Intercellular transport, stable intercellular bridges, cell migrations, cell shape changes, and specific subcellular localization of many embryonic patterning determinants contribute to egg development and require a dynamic cytoskeleton. We discuss many of the recent genetic and cell biological studies that have led to insights into how the actin cytoskeleton is assembled and regulated during the morphogenesis of the Drosophila egg.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 333-361 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Notch, LIN-12, and GLP-1 are receptors that mediate a broad range of cell interactions during Drosophila and nematode development. Signaling by these receptors relies on a conserved pathway with three core components: DSL ligand, LNG receptor, and a CSL effector that links the receptor to its transcriptional response. Although key functional regions have been identified in each class of proteins, the mechanism for signal transduction is not yet understood. Diverse regulatory mechanisms influence signaling by the LIN-12/Notch pathway. Inductive signaling relies on the synthesis of ligand and receptor in distinct but neighboring cells. By contrast, lateral signaling leads to the transformation of equivalent cells that express both ligand and receptor into nonequivalent cells that express either ligand or receptor. This transformation appears to rely on regulatory feedback loops within the LIN-12/Notch pathway. In addition, the pathway can be regulated by intrinsic factors that are asymmetrically segregated during cell division or by extrinsic cues via other signaling pathways. Specificity in the pathway does not appear to reside in the particular ligand or receptor used for a given cell-cell interaction. The existence of multiple ligands and receptors may have evolved from the stringent demands placed upon the regulation of genes encoding them.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 363-393 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Molecules involved in cell adhesion processes are often both structurally and functionally modular, with subdomains that are members of large protein families. Recently, high-resolution structures have been determined for representative members of many of these families including fragments of integrins, cadherins, fibronectin-like domains, and immunoglobulin-like domains. These structures have enhanced our understanding of cell adhesion processes at several levels. In almost all cases, ligand-binding sites have been visualized and provide insight into how these molecules mediate biologically important interactions. Metal-binding sites have been identified and characterized, allowing assessment of the role of bound ions in cell adhesion processes. Many of these structures serve as templates for modeling homologous domains in other proteins or, when the structure of a fragment consisting of more than one domain is determined, the structure of multidomain arrays of homologous domains. Knowledge of atomic structure also allows rational design of drugs that either mimic or target specific binding sites. In many cases, high-resolution structures have revealed unexpected relationships that pose questions about the evolutionary origin of specific domains. This review briefly describes several recently determined structures of cell adhesion molecules, summarizes some of the main results of each structure, and highlights common features of different systems.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 395-424 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Bacteria usually divide by building a central septum across the middle of the cell. This review focuses on recent results indicating that the tubulin-like FtsZ protein plays a central role in cytokinesis as a major component of a contractile cytoskeleton. Assembly of this cytoskeletal element abutting the membrane is a key point for regulation. The characterization of FtsZ homologues in Mycoplasmas, Archaea, and chloroplasts implies that the constriction mechanism is conserved and that FtsZ can constrict in the absence of peptidoglycan synthesis. In most Eubacteria, the internal cytoskeleton must also regulate synthesis of septal peptidoglycan. The Escherichia coli septum-specific penicillin-binding protein 3 (PBP3) forms a complex with other enzymes involved in murein metabolism, suggesting a centrally located transmembrane complex capable of splicing multiple new strands of peptidoglycan into the cell wall. Important questions remain about the spatial and temporal control of bacterial division.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 425-456 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract NCAM, L1, and DCC-immunoglobulin cell adhesion molecules (Ig CAMs)-are widely expressed during development. Many workers have dismissed a role for such molecules in the control of axonal growth and guidance because they do not show highly restricted expression patterns. Yet evidence from a number of model systems suggests all three CAMs play a role in the development of specific projections in the nervous system. For example, there is a reduction in mossy fiber tracts in the hippocampus of mice that lack NCAM, a requirement for DCC in the response of commissural neurons to a floor plate-derived chemoattractant, and a loss of corticospinal tracts in humans who carry mutations in the L1 gene. The above paradox might be explained by the observation that differential post-translational processing can modulate CAMs function and that alternative splicing can generate functionally distinct isoforms of a CAM. Activation of the FGF tyrosine kinase receptor is required for the responses stimulated by NCAM and L1, and the importance of regulated tyrosine phosphorylation for growth and guidance is underscored by the involvement of receptor tyrosine phosphatases in this process.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 513-609 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Src family protein tyrosine kinases are activated following engagement of many different classes of cellular receptors and participate in signaling pathways that control a diverse spectrum of receptor-induced biological activities. While several of these kinases have evolved to play distinct roles in specific receptor pathways, there is considerable redundancy in the functions of these kinases, both with respect to the receptor pathways that activate these kinases and the downstream effectors that mediate their biological activities. This chapter reviews the evidence implicating Src family kinases in specific receptor pathways and describes the mechanisms leading to their activation, the targets that interact with these kinases, and the biological events that they regulate.
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  • 83
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    Notes: Abstract The chemosensory pathway of bacterial chemotaxis has become a paradigm for the two-component superfamily of receptor-regulated phosphorylation pathways. This simple pathway illustrates many of the fundamental principles and unanswered questions in the field of signaling biology. A molecular description of pathway function has progressed rapidly because it is accessible to diverse structural, biochemical, and genetic approaches. As a result, structures are emerging for most of the pathway elements, biochemical studies are elucidating the mechanisms of key signaling events, and genetic methods are revealing the intermolecular interactions that transmit information between components. Recent advances include (a) the first molecular picture of a conformational transmembrane signal in a cell surface receptor, (b) four new structures of kinase domains and adaptation enzymes, and (c) significant new insights into the mechanisms of receptor-mediated kinase regulation, receptor adaptation, and the phospho-activation of signaling proteins. Overall, the chemosensory pathway and the propulsion system it regulates provide an ideal system in which to probe molecular principles underlying complex cellular signaling and behavior.
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    Annual Review of Cell and Developmental Biology 13 (1997), S. 611-667 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract The organizer is formed in an equatorial sector of the blastula stage amphibian embryo by cells that have responded to two maternal agents: a general meso-endoderm inducer (involving the TFG-beta signaling pathway) and a dorsal modifier (probably involving the Wnt signaling pathway). The meso-endoderm inducer is secreted by most vegetal cells, those containing maternal materials that had been localized in the vegetal hemisphere of the oocyte during oogenesis. As a consequence of the inducer's distribution and action, the competence domains of prospective ectoderm, mesoderm, and endoderm are established in an animal-to-vegetal order in the blastula. The dorsal modifier signal is secreted by a sector of cells of the animal and vegetal hemispheres on one side of the blastula. These cells contain maternal materials transported there in the first cell cycle from the vegetal pole of the egg along microtubules aligned by cortical rotation. The Nieuwkoop center is the region of blastula cells secreting both maternal signals, and hence specifying the organizer in an equatorial sector. Final steps of organizer formation at the late blastula or early gastrula stage may involve locally secreted zygotic signals as well. At the gastrula stage, the organizer secretes a variety of zygotic proteins that act as antagonists to various members of the BMP and Wnt families of ligands, which are secreted by cells of the competence domains surrounding the organizer. BMPs and Wnts favor ventral development, and cells near the organizer are protected from these agents by the organizer's inducers. The nearby cells are derepressed in their inherent capacity for dorsal development, which is apparent in the neural induction of the ectoderm, dorsalization of the mesoderm, and anteriorization of the endoderm. The organizer also engages in extensive specialized morphogenesis, which brings it within range of responsive cell groups. It also self-differentiates to a variety of axial tissues of the body.
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    Annual Review of Cell and Developmental Biology 14 (1998), S. 305-338 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract The actin cytoskeleton is a highly dynamic network composed of actin polymers and a large variety of associated proteins. The main functions of the actin cytoskeleton are to mediate cell motility and cell shape changes during the cell cycle and in response to extracellular stimuli, to organize the cytoplasm, and to generate mechanical forces within the cell. The reshaping and functions of the actin cytoskeleton are regulated by signaling pathways. Here we broadly review the actin cytoskeleton and the signaling pathways that regulate it. We place heavy emphasis on the yeast actin cytoskeleton.
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    Annual Review of Cell and Developmental Biology 14 (1998), S. 265-303 
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    Notes: Abstract Proteins that control mitochondrial dynamics in yeast are being identified at a rapid pace. These proteins include cytoskeletal elements that regulate organelle distribution and inheritance and several outer membrane proteins that are required to maintain the branched, mitochondrial reticulum. Interestingly, three of the high molecular weight GTPases encoded by the yeast genome are required for mitochondrial integrity and are potential regulators of mitochondrial branching, distribution, and membrane fusion. The recent finding that mtDNA mixing is restricted in the mitochondrial matrix has stimulated the hunt for the molecular machinery that anchors mitochondrial nucleoids in the organelle. Considering that many aspects of mitochondrial structure and behavior are strikingly similar in different cell types, the functional analyses of these yeast proteins should provide general insights into the mechanisms governing mitochondrial dynamics in all eukaryotes.
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    Annual Review of Cell and Developmental Biology 14 (1998), S. 459-485 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Cells respond to an accumulation of unfolded proteins in the endoplasmic reticulum (ER) by increasing transcription of genes encoding ER resident proteins. The information is transmitted from the ER lumen to the nucleus by an intracellular signaling pathway called the unfolded protein response (UPR). Recent work has shown that this signaling pathway utilizes several novel mechanisms, including translational attenuation and a regulated mRNA splicing step. In this review we aim to integrate these recent advances with current knowledge about maintenance of ER composition and abundance.
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    Annual Review of Cell and Developmental Biology 15 (1999), S. 185-230 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Ubiquitous among eukaryotes, the ADF/cofilins are essential proteins responsible for the high turnover rates of actin filaments in vivo. In vertebrates, ADF and cofilin are products of different genes. Both bind to F-actin cooperatively and induce a twist in the actin filament that results in the loss of the phalloidin-binding site. This conformational change may be responsible for the enhancement of the off rate of subunits at the minus end of ADF/cofilin-decorated filaments and for the weak filament-severing activity. Binding of ADF/cofilin is competitive with tropomyosin. Other regulatory mechanisms in animal cells include binding of phosphoinositides, phosphorylation by LIM kinases on a single serine, and changes in pH. Although vertebrate ADF/cofilins contain a nuclear localization sequence, they are usually concentrated in regions containing dynamic actin pools, such as the leading edge of migrating cells and neuronal growth cones. ADF/cofilins are essential for cytokinesis, phagocytosis, fluid phase endocytosis, and other cellular processes dependent upon actin dynamics.
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    Annual Review of Cell and Developmental Biology 15 (1999), S. 393-410 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Endoderm, one of the three principal germ layers, contributes to all organs of the alimentary tract. For simplicity, this review divides formation of endodermal organs into four fundamental steps: (a) formation of endoderm during gastrulation, (b) morphogenesis of a gut tube from a sheet of cells, (c) budding of organ domains from the tube, and (d) differentiation of organ-specific cell types within the growing buds. We discuss possible mechanisms that regulate how undifferentiated endoderm becomes specified into a myriad of cell types that populate the respiratory and gastrointestinal tracts.
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    Annual Review of Cell and Developmental Biology 15 (1999), S. 291-339 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Information can be transferred between the nucleus and the cytoplasm by translocating macromolecules across the nuclear envelope. Communication of extracellular or intracellular changes to the nucleus frequently leads to a transcriptional response that allows cells to survive in a continuously changing environment. Eukaryotic cells have evolved ways to regulate this movement of macromolecules between the cytoplasm and the nucleus such that the transfer of information occurs only under conditions in which a transcriptional response is required. This review focuses on the ways in which cells regulate movement of proteins across the nuclear envelope and the significance of this regulation for controlling diverse biological processes.
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    Annual Review of Cell and Developmental Biology 15 (1999), S. 469-517 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract In Dictyostelium amoebae, cell-type differentiation, spatial patterning, and morphogenesis are controlled by a combination of cell-autonomous mechanisms and intercellular signaling. A chemotactic aggregation of ~105 cells leads to the formation of a multicellular organism. Cell-type differentiation and cell sorting result in a small number of defined cell types organized along an anteroposterior axis. Finally, a mature fruiting body is created by the terminal differentiation of stalk and spore cells. Analysis of the regulatory program demonstrates a role for several molecules, including GSK-3, signal transducers and activators of transcription (STAT) factors, and cAMP-dependent protein kinase (PKA), that control spatial patterning in metazoans. Unexpectedly, two component systems containing histidine kinases and response regulators also play essential roles in controlling Dictyostelium development. This review focuses on the role of cAMP, which functions intracellularly to mediate the activity of PKA, an essential component in aggregation, cell-type specification, and terminal differentiation. Cytoplasmic cAMP levels are controlled through both the regulated activation of adenylyl cyclases and the degradation by a phosphodiesterase containing a two-component system response regulator. Extracellular cAMP regulates G-protein-dependent and -independent pathways to control aggregation as well as the activity of GSK-3 and the transcription factors GBF and STATa during multicellular development. The integration of these pathways with others regulated by the morphogen DIF-1 to control cell fate decisions are discussed.
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    Annual Review of Cell and Developmental Biology 15 (1999), S. 799-842 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Cotranslational protein translocation across and integration into the membrane of the endoplasmic reticulum (ER) occur at sites termed translocons. Translocons are composed of several ER membrane proteins that associate to form an aqueous pore through which secretory proteins and lumenal domains of membrane proteins pass from the cytoplasm to the ER lumen. These sites are not passive holes in the bilayer, but instead are quite dynamic both structurally and functionally. Translocons cycle between ribosome-bound and ribosome-free states, and convert between translocation and integration modes of operation. These changes in functional state are accompanied by structural rearrangements that alter translocon conformation, composition, and interactions with ligands such as the ribosome and BiP. Recent studies have revealed that the translocon is a complex and sophisticated molecular machine that regulates the movement of polypeptides through the bilayer, apparently in both directions as well as laterally into the bilayer, all while maintaining the membrane permeability barrier.
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    Annual Review of Cell and Developmental Biology 15 (1999), S. 733-798 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract Synaptic vesicles, which have been a paradigm for the fusion of a vesicle with its target membrane, also serve as a model for understanding the formation of a vesicle from its donor membrane. Synaptic vesicles, which are formed and recycled at the periphery of the neuron, contain a highly restricted set of neuronal proteins. Insight into the trafficking of synaptic vesicle proteins has come from studying not only neurons but also neuroendocrine cells, which form synaptic-like microvesicles (SLMVs). Formation and recycling of synaptic vesicles/SLMVs takes place from the early endosome and the plasma membrane. The cytoplasmic machinery of synaptic vesicle/SLMV formation and recycling has been studied by a variety of experimental approaches, in particular using cell-free systems. This has revealed distinct machineries for membrane budding and fission. Budding is mediated by clathrin and clathrin adaptors, whereas fission is mediated by dynamin and its interacting protein SH3p4, a lysophosphatidic acid acyl transferase.
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    Annual Review of Astronomy and Astrophysics 18 (1980), S. 43-75 
    ISSN: 0066-4146
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    Annual Review of Astronomy and Astrophysics 18 (1980), S. 77-113 
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    Annual Review of Astronomy and Astrophysics 18 (1980), S. 115-164 
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    Annual Review of Astronomy and Astrophysics 18 (1980), S. 439-488 
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    Annual Review of Astronomy and Astrophysics 18 (1980), S. 165-218 
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    Annual Review of Astronomy and Astrophysics 18 (1980), S. 537-560 
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    Annual Review of Astronomy and Astrophysics 19 (1981), S. 77-113 
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