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  • Articles  (3,458)
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  • Articles  (3,458)
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  • 1
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 209-237 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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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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  • 6
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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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  • 7
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    Palo Alto, Calif. : Annual Reviews
    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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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 85-116 
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  • 13
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 59-83 
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  • 14
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 117-140 
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  • 15
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 24 (1995), S. 141-165 
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  • 16
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    Palo Alto, Calif. : Annual Reviews
    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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  • 21
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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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  • 23
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 287-314 
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  • 24
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 315-342 
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  • 25
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 367-394 
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  • 26
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 25 (1996), S. 431-459 
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  • 27
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    Palo Alto, Calif. : Annual Reviews
    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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  • 33
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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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  • 36
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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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  • 37
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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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  • 38
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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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    Notes: Abstract Two types of flows dominate the large-scale structure of the solar wind: corotating flows and transient disturbances. Corotating flows are associated with spatial variability in the coronal expansion and solar rotation, whereas transient disturbances are associated with episodic ejections of material into interplanetary space from coronal regions not previously participating in the solar wind expansion. Ulysses' recent epic journey over the poles of the Sun has provided new insights on the three-dimensional nature of both corotating flows and transient disturbances in the solar wind and their evolution with heliocentric distance and latitude. This paper provides a simple physical description of the origins and dynamics of both of these types of solar wind flows, highlighting new understanding gained from the unique Ulysses high-latitude observations.
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    Notes: Abstract We summarize the properties of FU Orionis variables, and show how accretion disk models simply explain many peculiarities of these objects. FU Ori systems demonstrate that disk accretion in early stellar evolution is highly episodic, varying from ~ 10-7 yr-1 in the low (T Tauri) state to 10-4 yr-1 in the high (FU Ori) state. This variability in mass accretion is matched by a corresponding variability in mass ejection, with mass loss rates reaching ~ 10-1 of the mass accretion rates in outburst. It appears that the FU Ori phenomenon is restricted to early phases of stellar evolution, probably with infall still occuring to the disk, which may help drive repetitive outbursts. Thermal instabilities are a promising way to produce FU Ori disk outbursts, although many uncertainties remain in the theory; triggering by interactions with companion stars on eccentric orbits may also play a role.
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  • 93
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 34 (1996), S. 383-418 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract In most space environments, dust particles are exposed to plasmas and UV radiation and, consequently, carry electrostatic charges. Their motion is influenced by electric and magnetic fields in addition to gravity, drag, and radiation pressure. On the surface of the Moon, in planetary rings, or at comets, for example, electromagnetic forces can shape the spatial and size distribution of micron-sized charged dust particles. The dynamics of small charged dust particles can be surprisingly complex, leading to levitation, rapid transport, energization and ejection, capture, and the formation of new planetary rings. This review briefly discusses the most important processes that determine the charge state of dust particles immersed in plasmas and the resulting dynamics on exposed dusty surfaces and in planetary magnetospheres.
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  • 94
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 34 (1996), S. 279-329 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract The Goddard High-Resolution Spectrograph (GHRS) aboard the Hubble Space Telescope (HST) has yielded precision abundance results for a range of interstellar environments, including gas in the local medium, in the warm neutral medium, in cold diffuse clouds, and in distant halo clouds. Through GHRS studies, investigators have determined the abundances of elements such as C, N, O, Mg, Si, S, and Fe in individual interstellar clouds. These studies have provided new information about the composition of interstellar dust grains, the origin of the Galactic high-velocity cloud system, and the processes that transport gas between the disk and the halo. Precision measurements of the interstellar D to H ratio and of the abundances of r- and s-process elements have also provided fiducial reference values for cosmological and stellar evolutionary observations and theoretical models.
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  • 95
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 34 (1996), S. 645-701 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract The central half kiloparsec region of our Galaxy harbors a variety of phenomena unique to the central environment. This review discusses the observed structure and activity of the interstellar medium in this region in terms of its inevitable inflow toward the center of the Galactic gravitational potential well. A number of dissipative processes lead to a strong concentration of gas into a "Central Molecular Zone" of about 200-pc radius, in which the molecular medium is characterized by large densities, large velocity dispersions, high temperatures, and apparently strong magnetic fields. The physical state of the gas and the resultant star formation processes occurring in this environment are therefore quite unlike those occurring in the large-scale disk. Gas not consumed by star formation either enters a hot X ray-emitting halo and is lost as a thermally driven galactic wind or continues moving inward, probably discontinuously, through the domain of the few parsec-sized circumnuclear disks and eventually into the central parsec. There, the central radio source SgrA* currently accepts only a tiny fraction of the inflowing material, likely as a result of a limit cycle wherein the continual inflow of matter provokes star formation, which in turn can temporarily halt the inflow via mass-outflow winds.
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  • 96
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 34 (1996), S. 749-792 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract At luminosities above 1011 , infrared galaxies become the dominant population of extragalactic objects in the local Universe (z〈 0.3), being more numerous than optically selected starburst and Seyfert galaxies and quasi-stellar objects at comparable bolometric luminosity. The trigger for the intense infrared emission appears to be the strong interaction/merger of molecular gas-rich spirals, and the bulk of the infrared luminosity for all but the most luminous objects is due to dust heating from an intense starburst within giant molecular clouds. At the highest luminosities (Lir〉 1012 ), nearly all objects appear to be advanced mergers powered by a mixture of circumnuclear starburst and active galactic nucleus energy sources, both of which are fueled by an enormous concentration of molecular gas that has been funneled into the merger nucleus. These ultraluminous infrared galaxies may represent an important stage in the formation of quasi-stellar objects and powerful radio galaxies. They may also represent a primary stage in the formation of elliptical galaxy cores, the formation of globular clusters, and the metal enrichment of the intergalactic medium.
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  • 97
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 35 (1997), S. xiii 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
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  • 98
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 35 (1997), S. 33-67 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract To what extent are changes in the Earth's global environment linked with fluctuations in its primary energy source, the radiation from a variable star, the Sun? A firm scientific basis for policy making with regard to anthropogenic greenhouse warming of climate and chlorofluorocarbon depletion of ozone requires a reliable answer to this question. Reduction of the vulnerability of spacecraft operations and communications to space weather necessitates knowledge of solar induced variability in Earth's upper atmosphere. Toward these goals, solar radiation monitoring and studies of solar variability mechanisms facilitate an understanding of the sources and amplitudes of the Sun's changing radiation. Interdisciplinary studies that link these changes with a wide array of terrestrial phenomena over the longer time scales of global change and the shorter time scales of space weather address the relevance of solar radiation variability for Earth. However, although numerous associations are apparent between solar and terrestrial fluctuations, full comprehension of the physical mechanisms responsible for the many facets of radiative Sun-Earth coupling remains to be accomplished.
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  • 99
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 35 (1997), S. 267-307 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract The properties of galaxies that are lower in surface brightness than the dark night sky are reviewed. There are substantial selection effects against the discovery of galaxies that are unevolved or diffuse; these systems are missing from most wide field catalogs. Low surface brightness galaxies make up a significant amount of the luminosity density of the local universe. They contribute substantial but poorly determined amounts to the census of baryons and dark matter. Low surface brightness galaxies are also relevant to the interpretation of quasar absorption lines and to the understanding of rapidly evolving galaxy populations in the more distant universe. Theories of galaxy formation and evolution must accomodate the properties of these diffuse stellar systems.
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  • 100
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 35 (1997), S. 357-388 
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Notes: Abstract Compact groups of galaxies have posed a number of challenging questions. Intensive observational and theoretical studies are now providing answers to many of these and, at the same time, are revealing unexpected new clues about the nature and role of these systems. Most compact groups contain a high fraction of galaxies having morphological or kinematical peculiarities, nuclear radio and infrared emission, and starburst or active galactic nuclei (AGN) activity. They contain large quantities of diffuse gas and are dynamically dominated by dark matter. They most likely form as subsystems within looser associations and evolve by gravitational processes. Strong galaxy interactions result and merging is expected to lead to the ultimate demise of the group. Compact groups are surprisingly numerous and may play a significant role in galaxy evolution.
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