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  • Articles  (37,128)
  • Nature Publishing Group  (35,031)
  • Annual Reviews
  • 2005-2009  (9,416)
  • 2000-2004  (9,338)
  • 1980-1984  (18,374)
  • Chemistry and Pharmacology  (37,128)
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  • Articles  (37,128)
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  • 101
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    Annual Review of Biochemistry 52 (1983), S. 17-34 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 102
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 52 (1983), S. 67-91 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 103
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 52 (1983), S. 125-157 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 104
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 52 (1983), S. 159-186 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 105
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 70 (2001), S. 247-279 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract Protein tyrosine phosphatases (PTPs) are a diverse group of enzymes that contain a highly conserved active site motif, Cys-x5-Arg (Cx5R). The PTP super-family enzymes, which include tyrosine-specific, dual specificity, low-molecular-weight, and Cdc25 phosphatases, are key mediators of a wide variety of cellular processes, including growth, metabolism, differentiation, motility, and programmed cell death. The PTEN/MMAC1/TEP1 gene was originally identified as a candidate tumor suppressor gene located on human chromosome 10q23; it encodes a protein with sequence similarity to PTPs and tensin. Recent studies have demonstrated that PTEN plays an essential role in regulating signaling pathways involved in cell growth and apoptosis, and mutations in the PTEN gene are now known to cause tumorigenesis in a number of human tissues. In addition, germ line mutations in the PTEN gene also play a major role in the development of Cowden and Bannayan-Zonana syndromes, in which patients often suffer from increased risk of breast and thyroid cancers. Biochemical studies of the PTEN phosphatase have revealed a molecular mechanism by which tumorigenesis may be caused in individuals with PTEN mutations. Unlike most members of the PTP superfamily, PTEN utilizes the phosphoinositide second messenger, phosphatidylinositol 3,4,5-trisphosphate (PIP3), as its physiologic substrate. This inositol lipid is an important regulator of cell growth and survival signaling through the Ser/Thr protein kinases PDK1 and Akt. By specifically dephosphorylating the D3 position of PIP3, the PTEN tumor suppressor functions as a negative regulator of signaling processes downstream of this lipid second messenger. Mutations that impair PTEN function result in a marked increase in cellular levels of PIP3 and constitutive activation of Akt survival signaling pathways, leading to inhibition of apoptosis, hyperplasia, and tumor formation. Certain structural features of PTEN contribute to its specificity for PIP3, as well as its role(s) in regulating cellular proliferation and apoptosis. Recently, myotubularin, a second PTP superfamily enzyme associated with human disease, has also been shown to utilize a phosphoinositide as its physiologic substrate.
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  • 106
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    Annual Review of Biochemistry 70 (2001), S. 313-340 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract Cys2His2 zinc finger proteins offer a stable and versatile framework for the design of proteins that recognize desired target sites on double-stranded DNA. Individual fingers from these proteins have a simple betabetaalpha structure that folds around a central zinc ion, and tandem sets of fingers can contact neighboring subsites of 3-4 base pairs along the major groove of the DNA. Although there is no simple, general code for zinc finger-DNA recognition, selection strategies have been developed that allow these proteins to be targeted to almost any desired site on double-stranded DNA. The affinity and specificity of these new proteins can also be improved by linking more fingers together or by designing proteins that bind as dimers and thus recognize an extended site. These new proteins can then be modified by adding other domains-for activation or repression of transcription, for DNA cleavage, or for other activities. Such designer transcription factors and other new proteins will have important applications in biomedical research and in gene therapy.
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  • 107
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 52 (1983), S. 537-579 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 108
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    Annual Review of Biochemistry 71 (2002), S. 71-100 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract The primary function of bacterial recombination systems is the nonmutagenic repair of stalled or collapsed replication forks. The RecA protein plays a central role in these repair pathways, and its biochemistry must be considered in this context. RecA protein promotes DNA strand exchange, a reaction that contributes to fork regression and DNA end invasion steps. RecA protein activities, especially formation and disassembly of its filaments, affect many additional steps. So far, Escherichia coli RecA appears to be unique among its nearly ubiquitous family of homologous proteins in that it possesses a motorlike activity that can couple the branch movement in DNA strand exchange to ATP hydrolysis. RecA is also a multifunctional protein, serving in different biochemical roles for recombinational processes, SOS induction, and mutagenic lesion bypass. New biochemical and structural information highlights both the similarities and distinctions between RecA and its homologs. Increasingly, those differences can be rationalized in terms of biological function.
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  • 109
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    Annual Review of Biochemistry 71 (2002), S. 191-219 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract Various physicochemical factors influence DNA replication fidelity. Since it is now known that Watson-Crick hydrogen bonds are not necessary for efficient and selective replication of a base pair by DNA polymerase enzymes, a number of alternative physical factors have been examined to explain the efficiency of these enzymes. Among these factors are minor groove hydrogen bonding, base stacking, solvation, and steric effects. We discuss the concept of active site tightness in DNA polymerases, and consider how it might influence steric (size and shape) effects of nucleotide selection in synthesis of a base pair. A high level of active site tightness is expected to lead to higher fidelity relative to proteins with looser active sites. We review the current data on what parts and dimensions of active sites are most affected by size and shape, based on data with modified nucleotides that have been examined as polymerase substrates. We also discuss recent data on nucleotide analogs displaying higher fidelity than the natural ones. The published data are discussed with a view toward testing this sterically based hypothesis and unifying existing observations into a narrowly defined range of effects.
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  • 110
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    Annual Review of Biochemistry 71 (2002), S. 1-16 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: My undergraduate education at Cornell University was followed by graduate studies on methane fermentations under the guidance of H.A. Barker at the University of California, Berkeley. My Ph.D. degree was granted in June 1949. Two anaerobic microorganisms isolated from the mud flats of San Francisco Bay served as sources of biochemical research material for later studies at the National Institutes of Health in Bethesda. These organisms, Methanococcus vannielii and Clostridium sticklandii, proved to be especially rich sources of selenium-dependent enzymes and seleno-tRNAs. New B12 coenzyme-dependent enzymes that catalyzed intermediate steps in the anaerobic conversion of lysine to fatty acids and ammonia were isolated from C. sticklandii and characterized. My research efforts since 1970 have dealt primarily with various aspects of selenium biochemistry. We have shown that selenium is an essential constituent of several enzymes in prokaryotes. Se is present in these either as a selenocysteine residue in the protein or alternatively, in a few molybdoenzymes, as a component of a bound cofactor. Recent studies with a human adenocarcinoma cell line led to the unexpected discovery that selenocysteine occurs in mammalian thioredoxin reductase. The selenium located in a redox center of this enzyme is essential for catalytic activity.
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  • 111
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    Annual Review of Biochemistry 71 (2002), S. 435-471 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract Virtually every cell type in metazoan organisms produces heparan sulfate. These complex polysaccharides provide docking sites for numerous protein ligands and receptors involved in diverse biological processes, including growth control, signal transduction, cell adhesion, hemostasis, and lipid metabolism. The binding sites consist of relatively small tracts of variably sulfated glucosamine and uronic acid residues in specific arrangements. Their formation occurs in a tissue-specific fashion, generated by the action of a large family of enzymes involved in nucleotide sugar metabolism, polymer formation (glycosyltransferases), and chain processing (sulfotransferases and an epimerase). New insights into the specificity and organization of the biosynthetic apparatus have emerged from genetic studies of cultured cells, nematodes, fruit flies, zebrafish, rodents, and humans. This review covers recent developments in the field and provides a resource for investigators interested in the incredible diversity and specificity of this process.
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  • 112
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    Annual Review of Biochemistry 53 (1984), S. 493-535 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 113
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    Annual Review of Biochemistry 71 (2002), S. 511-535 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract The Na,K-ATPase or sodium pump carries out the coupled extrusion and uptake of Na and K ions across the plasma membranes of cells of most higher eukaryotes. It is a member of the P-type ATPase superfamily. This heterodimeric integral membrane protein is composed of a 100-kDa alpha-subunit with ten transmembrane segments and a heavily glycosylated beta subunit of about 55 kDa, which is a type II membrane protein. Current ideas on how the protein achieves active transport are based on a fusion of results of transport physiology, protein chemistry, and heterologous expression of mutant proteins. Recently acquired high resolution structural information provides an important new avenue for a more complete understanding of this protein. In this review, the current status of knowledge of Na,K-ATPase is discussed, and areas where there is still considerable uncertainty are highlighted.
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  • 114
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    Annual Review of Biochemistry 71 (2002), S. 635-700 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract Bacterial lipopolysaccharides (LPS) typically consist of a hydrophobic domain known as lipid A (or endotoxin), a nonrepeating "core" oligosaccharide, and a distal polysaccharide (or O-antigen). Recent genomic data have facilitated study of LPS assembly in diverse Gram-negative bacteria, many of which are human or plant pathogens, and have established the importance of lateral gene transfer in generating structural diversity of O-antigens. Many enzymes of lipid A biosynthesis like LpxC have been validated as targets for development of new antibiotics. Key genes for lipid A biosynthesis have unexpectedly also been found in higher plants, indicating that eukaryotic lipid A-like molecules may exist. Most significant has been the identification of the plasma membrane protein TLR4 as the lipid A signaling receptor of animal cells. TLR4 belongs to a family of innate immunity receptors that possess a large extracellular domain of leucine-rich repeats, a single trans-membrane segment, and a smaller cytoplasmic signaling region that engages the adaptor protein MyD88. The expanding knowledge of TLR4 specificity and its downstream signaling pathways should provide new opportunities for blocking inflammation associated with infection.
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  • 115
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    Annual Review of Biochemistry 72 (2003), S. 1-18 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract A childhood fascination with animals, plants, and insects was aided and abetted by many giants, beginning with my parents. The Bronx High School of Science and the City College of New York (CCNY) made a solid and priceless grounding in chemistry and biology available free of charge. Abe Mazur at CCNY revealed the wonders of biochemistry and illustrated that it was possible to pursue these wonders while being paid to do so. He also directed me to Duke University Medical School for PhD work under the tutelage of Phil Handler. With the exception of a sabbatical year at Harvard with Frank Westheimer, my entire career has been spent at Duke serving under three fine and supportive chairmen: Handler, Hill, and Raetz. The premier discoveries to emanate from my laboratory have been the sulfite oxidase, the several superoxide dismutases, the manganese catalase, and the catalase/peroxidase. Many other topics piqued my interest and resulted in ~ 400 publications. Herein I have recounted some of the circumstances surrounding that work and named a few of the people involved. The first 20 years I worked happily at the bench and the next 35 years just as happily facilitating the work of younger people. It has been so rewarding that I wish for nothing more than to be allowed to keep at it.
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  • 116
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    Annual Review of Biochemistry 72 (2003), S. 137-174 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract The synthesis and excretion of bile acids comprise the major pathway of cholesterol catabolism in mammals. Synthesis provides a direct means of converting cholesterol, which is both hydrophobic and insoluble, into a water-soluble and readily excreted molecule, the bile acid. The biosynthetic steps that accomplish this transformation also confer detergent properties to the bile acid, which are exploited by the body to facilitate the secretion of cholesterol from the liver. This role in the elimination of cholesterol is counterbalanced by the ability of bile acids to solubilize dietary cholesterol and essential nutrients and to promote their delivery to the liver. The synthesis of a full complement of bile acids requires 17 enzymes. The expression of selected enzymes in the pathway is tightly regulated by nuclear hormone receptors and other transcription factors, which ensure a constant supply of bile acids in an ever changing metabolic environment. Inherited mutations that impair bile acid synthesis cause a spectrum of human disease; this ranges from liver failure in early childhood to progressive neuropathy in adults.
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  • 117
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    Annual Review of Biochemistry 72 (2003), S. 249-289 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract Expressed protein ligation (EPL) is a protein engineering approach that allows recombinant and synthetic polypeptides to be chemoselectively and regioselectively joined together. The approach makes the primary structure of most proteins accessible to the tools of synthetic organic chemistry, enabling the covalent structure of proteins to be modified in an unprecedented fashion. The ability to incorporate noncoded amino acids, biophysical probes, and stable isotopes into specific locations within proteins provides research tools to peer into the inner workings of these molecules. In this review I discuss the development of this technology, its broad application to biological systems, and its possible role in the area of proteomics.
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  • 118
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    Annual Review of Biochemistry 72 (2003), S. 395-447 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract Sorting of transmembrane proteins to endosomes and lysosomes is mediated by signals present within the cytosolic domains of the proteins. Most signals consist of short, linear sequences of amino acid residues. Some signals are referred to as tyrosine-based sorting signals and conform to the NPXY or YXXO consensus motifs. Other signals known as dileucine-based signals fit [DE]XXXL[LI] or DXXLL consensus motifs. All of these signals are recognized by components of protein coats peripherally associated with the cytosolic face of membranes. YXXO and [DE]XXXL[LI] signals are recognized with characteristic fine specificity by the adaptor protein (AP) complexes AP-1, AP-2, AP-3, and AP-4, whereas DXXLL signals are recognized by another family of adaptors known as GGAs. Several proteins, including clathrin, AP-2, and Dab2, have been proposed to function as recognition proteins for NPXY signals. YXXO and DXXLL signals bind in an extended conformation to the mu2 subunit of AP-2 and the VHS domain of the GGAs, respectively. Phosphorylation events regulate signal recognition. In addition to peptide motifs, ubiquitination of cytosolic lysine residues also serves as a signal for sorting at various stages of the endosomal-lysosomal system. Conjugated ubiquitin is recognized by UIM, UBA, or UBC domains present within many components of the internalization and lysosomal targeting machinery. This complex array of signals and recognition proteins ensures the dynamic but accurate distribution of transmembrane proteins to different compartments of the endosomal-lysosomal system.
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  • 119
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    Annual Review of Biochemistry 72 (2003), S. 517-571 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract Since the discovery of enzymes as biological catalysts, study of their enormous catalytic power and exquisite specificity has been central to biochemistry. Nevertheless, there is no universally accepted comprehensive description. Rather, numerous proposals have been presented over the past half century. The difficulty in developing a comprehensive description for the catalytic power of enzymes derives from the highly cooperative nature of their energetics, which renders impossible a simple division of mechanistic features and an absolute partitioning of catalytic contributions into independent and energetically additive components. Site-directed mutagenesis has emerged as an enormously powerful approach to probe enzymatic catalysis, illuminating many basic features of enzyme function and behavior. The emphasis of site-directed mutagenesis on the role of individual residues has also, inadvertently, limited experimental and conceptual attention to the fundamentally cooperative nature of enzyme function and energetics. The first part of this review highlights the structural and functional interconnectivity central to enzymatic catalysis. In the second part we ask: What are the features of enzymes that distinguish them from simple chemical catalysts? The answers are presented in conceptual models that, while simplified, help illustrate the vast amount known about how enzymes achieve catalysis. In the last section, we highlight the molecular and energetic questions that remain for future investigation and describe experimental approaches that will be necessary to answer these questions. The promise of advancing and integrating cutting edge conceptual, experimental, and computational tools brings mechanistic enzymology to a new era, one poised for novel fundamental insights into biological catalysis.
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  • 120
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    Annual Review of Biochemistry 72 (2003), S. 717-742 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract Recognition of foreign antigens by T lymphocytes is a very important component of vertebrate immunity-vital to the clearance of pathogenic organisms and particular viruses and necessary, indirectly, for the production of high affinity antibodies. T cell recognition is mediated by the systematic scanning of cell surfaces by T cells, which collectively express many antigen receptors. When the appropriate antigenic peptide bound to a molecule of the major histocompatibility complex is found-even in minute quantities-a series of elaborate cell-surface molecule and internal rearrangements take place. The sequence of events and the development of techniques required to observe these events have significantly enhanced our understanding of T cell recognition and may find application in other systems of transient cell:cell interactions as well.
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    Annual Review of Biochemistry 73 (2004), S. 861-890 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Eukaryotic mRNAs are primarily degraded by removal of the 3' poly(A) tail, followed either by cleavage of the 5' cap structure (decapping) and 5'-〉3' exonucleolytic digestion, or by 3' to 5' degradation. mRNA decapping represents a critical step in turnover because this permits the degradation of the mRNA and is a site of numerous control inputs. Recent analyses suggest decapping of an mRNA consists of four central and related events. These include removal, or inactivation, of the poly(A) tail as an inhibitor of decapping, exit from active translation, assembly of a decapping complex on the mRNA, and sequestration of the mRNA into discrete cytoplasmic foci where decapping can occur. Each of these steps is a demonstrated, or potential, site for the regulation of mRNA decay. We discuss the decapping process in the light of these central properties, which also suggest fundamental aspects of cytoplasmic mRNA physiology that connect decapping, translation, and storage of mRNA.
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  • 122
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    Annual Review of Biochemistry 73 (2004), S. 617-656 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: The prion hypothesis proposes that proteins can act as infectious agents. Originally formulated to explain transmissible spongiform encephalopathies (TSEs), the prion hypothesis has been extended with the finding that several non-Mendelian traits in fungi are due to heritable changes in protein conformation, which may in some cases be beneficial. Although much remains to be learned about the specific role of cellular cofactors, mechanistic parallels between the mammalian and yeast prion phenomena point to universal features of conformation-based infection and inheritance involving propagation of ordered beta-sheet-rich protein aggregates commonly referred to as amyloid. Here we focus on two such features and discuss recent efforts to explain them in terms of the physical properties of amyloid-like aggregates. The first is prion strains, wherein chemically identical infectious particles cause distinct phenotypes. The second is barriers that often prohibit prion transmission between different species. There is increasing evidence suggesting that both of these can be manifestations of the same phenomenon: the ability of a protein to misfold into multiple self-propagating conformations. Even single mutations can change the spectrum of favored misfolded conformations. In turn, changes in amyloid conformation can shift the specificity of propagation and alter strain phenotypes. This model helps explain many common and otherwise puzzling features of prion inheritance as well as aspects of noninfectious diseases involving toxic misfolded proteins.
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    Annual Review of Biochemistry 72 (2003), S. 783-812 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract Fueled by ever-growing DNA sequence information, proteomics-the large scale analysis of proteins-has become one of the most important disciplines for characterizing gene function, for building functional linkages between protein molecules, and for providing insight into the mechanisms of biological processes in a high-throughput mode. It is now possible to examine the expression of more than 1000 proteins using mass spectrometry technology coupled with various separation methods. High-throughput yeast two-hybrid approaches and analysis of protein complexes using affinity tag purification have yielded valuable protein-protein interaction maps. Large-scale protein tagging and subcellular localization projects have provided considerable information about protein function. Finally, recent developments in protein microarray technology provide a versatile tool to study protein-protein, protein-nucleic acid, protein-lipid, enzyme-substrate, and protein-drug interactions. Other types of microarrays, though not fully developed, also show great potential in diagnostics, protein profiling, and drug identification and validation. This review discusses high-throughput technologies for proteome analysis and their applications. Also discussed are the approaches used for the integrated analysis of the voluminous sets of data generated by proteome analysis conducted on a global scale.
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    Annual Review of Biochemistry 73 (2004), S. 383-415 
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    Topics: Chemistry and Pharmacology , Biology
    Notes: Pyridoxal phosphate (PLP)-dependent enzymes are unrivaled in the diversity of reactions that they catalyze. New structural data have paved the way for targeted mutagenesis and mechanistic studies and have provided a framework for interpretation of those results. Together, these complementary approaches yield new insight into function, particularly in understanding the origins of substrate and reaction type specificity. The combination of new sequences and structures enables better reconstruction of their evolutionary heritage and illuminates unrecognized similarities within this diverse group of enzymes. The important metabolic roles of many PLP-dependent enzymes drive efforts to design specific inhibitors, which are now guided by the availability of comprehensive structural and functional databases. Better understanding of the function of this important group of enzymes is crucial not only for inhibitor design, but also for the design of improved protein-based catalysts.
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    Annual Review of Biochemistry 73 (2004), S. 749-789 
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    Topics: Chemistry and Pharmacology , Biology
    Notes: The superfamily of intermediate filament (IF) proteins contains at least 65 distinct proteins in man, which all assemble into ~10 nm wide filaments and are principal structural elements both in the nucleus and the cytoplasm with essential scaffolding functions in metazoan cells. At present, we have only circumstantial evidence of how the highly divergent primary sequences of IF proteins lead to the formation of seemingly similar polymers and how this correlates with their function in individual cells and tissues. Point mutations in IF proteins, particularly in lamins, have been demonstrated to lead to severe, inheritable multi-systemic diseases, thus underlining their importance at several functional levels. Recent structural work has now begun to shed some light onto the complex fine tuning of structure and function in these fibrous, coiled coil forming multidomain proteins and their contribution to cellular physiology and gene regulation.
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    Annual Review of Biochemistry 73 (2004), S. 559-587 
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    Topics: Chemistry and Pharmacology , Biology
    Notes: Protein S-palmitoylation is the thioester linkage of long-chain fatty acids to cysteine residues in proteins. Addition of palmitate to proteins facilitates their membrane interactions and trafficking, and it modulates protein-protein interactions and enzyme activity. The reversibility of palmitoylation makes it an attractive mechanism for regulating protein activity, and this feature has generated intensive investigation of this modification. The regulation of palmitoylation occurs through the actions of protein acyltransferases and protein acylthioesterases. Identification of the protein acyltransferases Erf2/Erf4 and Akr1 in yeast has provided new insight into the palmitoylation reaction. These molecules work in concert with thioesterases, such as acyl-protein thioesterase 1, to regulate the palmitoylation status of numerous signaling molecules, ultimately influencing their function. This review discusses the function and regulation of protein palmitoylation, focusing on intracellular proteins that participate in cell signaling or protein trafficking.
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    Annual Review of Biochemistry 73 (2004), S. 657-704 
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    Topics: Chemistry and Pharmacology , Biology
    Notes: Great advances have been made in the past three decades in understanding the molecular mechanics underlying protein synthesis in bacteria, but our understanding of the corresponding events in eukaryotic organisms is only beginning to catch up. In this review we describe the current state of our knowledge and ignorance of the molecular mechanics underlying eukaryotic translation. We discuss the mechanisms conserved across the three kingdoms of life as well as the important divergences that have taken place in the pathway.
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    Annual Review of Biochemistry 73 (2004), S. 539-557 
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    Notes: The signal recognition particle (SRP) directs integral membrane and secretory proteins to the cellular protein translocation machinery during translation. The SRP is an evolutionarily conserved RNA-protein complex whose activities are regulated by GTP hydrolysis. Recent structural investigations of SRP functional domains and interactions provide new insights into the mechanisms of SRP activity in all cells, leading toward a comprehensive understanding of protein trafficking by this elegant pathway.
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    Annual Review of Biochemistry 73 (2004), S. 1019-1049 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: From a process involved in cell wall synthesis in archaea and some bacteria, N-linked glycosylation has evolved into the most common covalent protein modification in eukaryotic cells. The sugars are added to nascent proteins as a core oligosaccharide unit, which is then extensively modified by removal and addition of sugar residues in the endoplasmic reticulum (ER) and the Golgi complex. It has become evident that the modifications that take place in the ER reflect a spectrum of functions related to glycoprotein folding, quality control, sorting, degradation, and secretion. The glycans not only promote folding directly by stabilizing polypeptide structures but also indirectly by serving as recognition "tags" that allow glycoproteins to interact with a variety of lectins, glycosidases, and glycosyltranferases. Some of these (such as glucosidases I and II, calnexin, and calreticulin) have a central role in folding and retention, while others (such as alpha-mannosidases and EDEM) target unsalvageable glycoproteins for ER-associated degradation. Each residue in the core oligosaccharide and each step in the modification program have significance for the fate of newly synthesized glycoproteins.
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    Annual Review of Biochemistry 73 (2004), S. 657-704 
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    Notes: Great advances have been made in the past three decades in understanding the molecular mechanics underlying protein synthesis in bacteria, but our understanding of the corresponding events in eukaryotic organisms is only beginning to catch up. In this review we describe the current state of our knowledge and ignorance of the molecular mechanics underlying eukaryotic translation. We discuss the mechanisms conserved across the three kingdoms of life as well as the important divergences that have taken place in the pathway.
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    Annual Review of Biochemistry 73 (2004), S. 791-836 
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    Notes: Just as Darwinian evolution in nature has led to the development of many sophisticated enzymes, Darwinian evolution in vitro has proven to be a powerful approach for obtaining similar results in the laboratory. This review focuses on the development of nucleic acid enzymes starting from a population of random-sequence RNA or DNA molecules. In order to illustrate the principles and practice of in vitro evolution, two especially well-studied categories of catalytic nucleic acid are considered: RNA enzymes that catalyze the template-directed ligation of RNA and DNA enzymes that catalyze the cleavage of RNA. The former reaction, which involves attack of a 2'- or 3'-hydroxyl on the alpha-phosphate of a 5'-triphosphate, is more difficult. It requires a comparatively larger catalytic motif, containing more nucleotides than can be sampled exhaustively within a starting population of random-sequence RNAs. The latter reaction involves deprotonation of the 2'-hydroxyl adjacent to the cleavage site, resulting in cleaved products that bear a 2',3'-cyclic phosphate and 5'-hydroxyl. The difficulty of this reaction, and therefore the complexity of the corresponding DNA enzyme, depends on whether a catalytic cofactor, such as a divalent metal cation or small molecule, is present in the reaction mixture.
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    Annual Review of Biochemistry 73 (2004), S. 891-923 
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    Notes: Secreted signaling proteins function in a diverse array of essential patterning events during metazoan development, ranging from embryonic segmentation in insects to neural tube differentiation in vertebrates. These proteins generally are expressed in a localized manner, and they may elicit distinct concentration-dependent responses in the cells of surrounding tissues and structures, thus functioning as morphogens that specify the pattern of cellular responses by their tissue distribution. Given the importance of signal distribution, it is notable that the Hedgehog (Hh) and Wnt proteins, two of the most important families of such signals, are known to be covalently modified by lipid moieties, the membrane-anchoring properties of which are not consistent with passive models of protein mobilization within tissues. This review focuses on the mechanisms underlying biogenesis of the mature Hh proteins, which are dually modified by cholesteryl and palmitoyl adducts, as well as on the relationship between Hh proteins and the self-splicing proteins (i.e., proteins containing inteins) and the Hh-like proteins of nematodes. We further discuss the cellular mechanisms that have evolved to handle lipidated Hh proteins in the spatial deployment of the signal in developing tissues and the more recent findings that implicate palmitate modification as an important feature of Wnt signaling proteins.
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    Annual Review of Biochemistry 74 (2005), S. 129-177 
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    Notes: The underlying basis for the accuracy of protein synthesis has been the subject of over four decades of investigation. Recent biochemical and structural data make it possible to understand at least in outline the structural basis for tRNA selection, in which codon recognition by cognate tRNA results in the hydrolysis of GTP by EF-Tu over 75??A?? away. The ribosome recognizes the geometry of codon-anticodon base pairing at the first two positions but monitors the third, or wobble position, less stringently. Part of the additional binding energy of cognate tRNA is used to induce conformational changes in the ribosome that stabilize a transition state for GTP hydrolysis by EF-Tu and subsequently result in accelerated accommodation of tRNA into the peptidyl transferase center. The transition state for GTP hydrolysis is characterized, amongf other things, by a distorted tRNA. This picture explains a large body of data on the effect of antibiotics and mutations on translational fidelity. However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting.
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    Annual Review of Biochemistry 73 (2004), S. 491-537 
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    Notes: Researchers have long predicted that complex carbohydrates on cell surfaces would play important roles in developmental processes because of the observation that specific carbohydrate structures appear in specific spatial and temporal patterns throughout development. The astounding number and complexity of carbohydrate structures on cell surfaces added support to the concept that glycoconjugates would function in cellular communication during development. Although the structural complexity inherent in glycoconjugates has slowed advances in our understanding of their functions, the complete sequencing of the genomes of organisms classically used in developmental studies (e.g., mice, Drosophila melanogaster, and Caenorhabditis elegans) has led to demonstration of essential functions for a number of glycoconjugates in developmental processes. Here we present a review of recent studies analyzing function of a variety of glycoconjugates (O-fucose, O-mannose, N-glycans, mucin-type O-glycans, proteoglycans, glycosphingolipids), focusing on lessons learned from human disease and genetic studies in mice, D. melanogaster, and C. elegans.
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    Annual Review of Biochemistry 73 (2004), S. 617-656 
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    Notes: The prion hypothesis proposes that proteins can act as infectious agents. Originally formulated to explain transmissible spongiform encephalopathies (TSEs), the prion hypothesis has been extended with the finding that several non-Mendelian traits in fungi are due to heritable changes in protein conformation, which may in some cases be beneficial. Although much remains to be learned about the specific role of cellular cofactors, mechanistic parallels between the mammalian and yeast prion phenomena point to universal features of conformation-based infection and inheritance involving propagation of ordered beta-sheet-rich protein aggregates commonly referred to as amyloid. Here we focus on two such features and discuss recent efforts to explain them in terms of the physical properties of amyloid-like aggregates. The first is prion strains, wherein chemically identical infectious particles cause distinct phenotypes. The second is barriers that often prohibit prion transmission between different species. There is increasing evidence suggesting that both of these can be manifestations of the same phenomenon: the ability of a protein to misfold into multiple self-propagating conformations. Even single mutations can change the spectrum of favored misfolded conformations. In turn, changes in amyloid conformation can shift the specificity of propagation and alter strain phenotypes. This model helps explain many common and otherwise puzzling features of prion inheritance as well as aspects of noninfectious diseases involving toxic misfolded proteins.
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    Annual Review of Biochemistry 73 (2004), S. 861-890 
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    Notes: Eukaryotic mRNAs are primarily degraded by removal of the 3' poly(A) tail, followed either by cleavage of the 5' cap structure (decapping) and 5'-〉3' exonucleolytic digestion, or by 3' to 5' degradation. mRNA decapping represents a critical step in turnover because this permits the degradation of the mRNA and is a site of numerous control inputs. Recent analyses suggest decapping of an mRNA consists of four central and related events. These include removal, or inactivation, of the poly(A) tail as an inhibitor of decapping, exit from active translation, assembly of a decapping complex on the mRNA, and sequestration of the mRNA into discrete cytoplasmic foci where decapping can occur. Each of these steps is a demonstrated, or potential, site for the regulation of mRNA decay. We discuss the decapping process in the light of these central properties, which also suggest fundamental aspects of cytoplasmic mRNA physiology that connect decapping, translation, and storage of mRNA.
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    Annual Review of Biochemistry 73 (2004), S. 991-1018 
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    Notes: Cytochrome P450 enzymes are heme-containing monooxygenases that are named after an absorption band at 450 nm when complexed with carbon monoxide. They catalyze a wide variety of reactions and are unique in their ability to hydroxylate nonactivated hydrocarbons. P450 enzymes are involved in numerous biological processes, which include the biosynthesis of lipids, steroids, antibiotics, and the degradation of xenobiotics. In line with the variety of reactions catalyzed, the size of their substrates varies significantly. Some P450s have open active sites (e.g., BM3), and some have shielded active sites that open only transiently (e.g., P450cam), whereas others bind the substrate only when attached to carrier proteins (e.g., Oxy proteins). Structural aspects of both organic and gaseous ligand binding and electron transfer are described.
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    Annual Review of Biochemistry 74 (2005), S. 515-534 
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    Notes: Because energy balance is important for survival, a system is required to monitor energy status and to make appropriate adjustments in energy intake and energy expenditure. In higher animals, a centrally located system has evolved to accomplish this task. When caloric intake exceeds expenditure, the surplus is channeled into energy storage pathways, primarily the synthesis of fatty acids, which are converted into fat and stored in adipose tissue. Thus, metabolic flux through the pathway of fatty acid synthesis, located in the lipogenic tissues, reflects the "energy status" of the animal. The enzymatic machinery of this pathway is also expressed in the brain, notably the hypothalamus. In the hypothalamus, intermediates in this pathway appear to serve as energy sensors that signal higher brain centers to produce appropriate responses, e.g., altered food intake and energy expenditure.
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    Annual Review of Biochemistry 74 (2005), S. 481-514 
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    Notes: Large-genome eukaryotes use heritable cytosine methylation to silence promoters, especially those associated with transposons and imprinted genes. Cytosine methylation does not reinforce or replace ancestral gene regulation pathways but instead endows methylated genomes with the ability to repress specific promoters in a manner that is buffered against changes in the internal and external environment. Recent studies have shown that the targeting of de novo methylation depends on multiple inputs; these include the interaction of repeated sequences, local states of histone lysine methylation, small RNAs and components of the RNAi pathway, and divergent and catalytically inert cytosine methyltransferase homologues that have acquired regulatory roles. There are multiple families of DNA (cytosine-5) methyltransferases in eukaryotes, and each family appears to be controlled by different regulatory inputs. Sequence-specific DNA-binding proteins, which regulate most aspects of gene expression, do not appear to be involved in the establishment or maintenance of genomic methylation patterns.
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    Annual Review of Physical Chemistry 35 (1984), S. 75-108 
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    Annual Review of Physical Chemistry 35 (1984), S. 265-289 
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    Annual Review of Physical Chemistry 35 (1984), S. 591-612 
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    Annual Review of Physical Chemistry 51 (2000), S. 41-63 
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    Notes: Abstract The surface-sensitive optical technique of surface plasmon resonance (SPR) imaging is used to characterize ultrathin organic and biopolymer films at metal interfaces in a spatially resolved manner. Because of its high surface sensitivity and its ability to measure in real time the interaction of unlabeled biological molecules with arrays of surface-bound species, SPR imaging has the potential to become a powerful tool in biomolecular investigations. Recently, SPR imaging has been successfully implemented in the characterization of supported lipid bilayer films, the monitoring of antibody-antigen interactions at surfaces, and the study of DNA hybridization adsorption. The following is included in this review: (a) an introduction to the principles of surface plasmon resonance, (b) the details of SPR imaging instrumental design, (c) a short discussion concerning resolution, sensitivity, and quantitation in SPR imaging, (d) the details of DNA array fabrication on chemically modified gold surfaces, and (e) two examples that demonstrate the application of the SPR imaging technique to the study of protein-DNA interactions.
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    Annual Review of Physical Chemistry 51 (2000), S. 179-207 
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    Notes: Abstract This article provides a review of recent studies of the properties of unsolvated (and partially solvated) peptides and proteins. The methods used to produce vapor-phase peptide and protein ions are described along with some of the techniques used to study them, such as H/D exchange, blackbody infrared radiative dissociation, and ion mobility measurements. Studies of unsolvated peptides and proteins provide information about their intrinsic intramolecular interactions. The topics covered include the role of zwitterions and salt bridges in the vapor phase, Coulomb interactions in multiply charged ions, the unfolding and refolding of vapor-phase proteins, and the stability of unsolvated helices and sheets. Finally, dehydration and rehydration studies of proteins in the vapor phase are described. These can provide exquisitely detailed information about hydration interactions, such as the enthalpy and entropy changes associated with adsorbing individual water molecules.
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    Annual Review of Physical Chemistry 51 (2000), S. 275-296 
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    Notes: Abstract Dynamic processes in crystalline solids are reflected in the atomic displacement amplitudes determined, together with the atomic coordinates, by crystal structure analysis. The interpretation of such amplitudes poses two severe problems: (a) The relative phases of the atomic displacements are lost; and (b) the amplitudes may reflect disorder in the structure and systematic error in the diffraction experiment in addition to motion, but the three contributions cannot be separated on the basis of measurements at a single temperature. Several approximate ways to solve these problems, e.g. rigid-body and segmented-rigid-body analysis, are reviewed together with their limitations. A more recent approach that represents a significant advance with respect to both difficulties is also described: Crystal structures are determined over a range of temperatures; the mean square amplitude quantities are interpreted by taking explicit account of their temperature dependence, i.e. by exploiting the difference in behavior of a microscopic oscillator in the low-temperature, quantum regime and in the high-temperature, classical regime. A distinction between low-frequency and high-frequency motion, disorder, and systematic error becomes possible with this model; this is illustrated with the help of case studies.
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    Annual Review of Physical Chemistry 51 (2000), S. 473-499 
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    Notes: Abstract Ice particles found within polar stratospheric clouds (PSCs) and upper tropospheric cirrus clouds can dramatically impact the chemistry and climate of the Earth's atmosphere. The formation of PSCs and the subsequent chemical reactions that occur on their surfaces are key components of the massive ozone hole observed each spring over Antarctica. Cirrus clouds also provide surfaces for heterogeneous reactions and significantly modify the Earth's climate by changing the visible and infrared radiation fluxes. Although the role of ice particles in climate and chemistry is well recognized, the exact mechanisms of cloud formation are still unknown, and thus it is difficult to predict how anthropogenic activities will change cloud abundances in the future. This article focuses on the nucleation, chemistry, and microphysical properties of ice particles composing PSCs and cirrus clouds. A general overview of the current state of research is presented along with some unresolved issues facing scientists in the future.
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    Annual Review of Physical Chemistry 52 (2001), S. 1-13 
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    Notes: This chapter describes my research career, spanning the period from 1955 to 2000. My initial PhD work at the University of Southampton was concerned with the electronic structure and spectra of transition metal complexes and included studies of the electronic spin resonance (ESR) spectra of magnetically dilute single crystals. After a year at the University of Minnesota, I went to Cambridge University and for the next six years studied the ESR spectra of liquid phase organic free radicals. I commenced work on the microwave magnetic resonance (MMR) spectra of gaseous free radicals in 1965, and this work continued until 1975. I moved from Cambridge to Southampton in 1967. In 1975 I turned to the study of gas phase molecular ions, using ion beam methods. In the earlier years of this period I concentrated on simple fundamental species like H+2, HD+, and H+3. In the later years until my retirement in 1999, I concentrated on the observation and analysis of microwave spectra involving energy levels lying very close to a dissociation asymptote. DEDICATION This chapter is dedicated to the memory of Harry E. Radford, who died while it was being written. Harry was a quiet and shy man, who often worked alone and never indulged in self-promotion. So far as I know, he was never awarded any medals or prizes, nor elected to any academies or learned societies. Nevertheless he was an experimentalist of the highest originality and quality, a theorist of true intellectual depth, and a remarkable pioneer in many of the techniques of studying free radicals that are now commonplace.
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    Annual Review of Physical Chemistry 52 (2001), S. 193-231 
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    Notes: Abstract Photoexcitation of a semiconductor with photons above the semiconductor band gap creates electrons and holes that are out of equilibrium. The rates at which the photogenerated charge carriers return to equilibrium via thermalization through carrier scattering, cooling by phonon emission, and radiative and nonradiative recombination are important issues. The relaxation processes can be greatly affected by quantization effects that arise when the carriers are confined to regions of space that are small compared with their deBroglie wavelength or the Bohr radius of bulk excitons. The effects of size quantization in semiconductor quantum wells (carrier confinement in one dimension) and quantum dots (carrier confinement in three dimensions) on the respective carrier relaxation processes are reviewed, with emphasis on electron cooling dynamics. The implications of these effects for applications involving radiant energy conversion are also discussed.
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    Annual Review of Physical Chemistry 52 (2001), S. 357-389 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract Significant advances toward understanding the structure of aqueous surfaces on a molecular level have been made in recent years. This review focuses on the recent contributions of surface vibrational sum frequency spectroscopy (VSFS) to this field of study. An overview of recent VSFS studies of the molecular structure and orientation of molecules at the vapor-water interface and the interface between water and an immiscible organic liquid is presented, with particular emphasis on studies that compare the molecular properties and adsorbate behavior at these two different but related interfaces. This discussion is preceded by a general introduction to VSFS studies at aqueous surfaces and a description of the fundamental principles underlying the technique.
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    Annual Review of Physical Chemistry 52 (2001), S. 463-498 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract Novel applications of solid state nuclear magnetic resonance (NMR) to the study of small molecules, synthetic polymers, biological systems, and inorganic materials continue at an accelerated rate. Instrumental to this uninterrupted expansion has been an improved understanding of the chemical physics underlying NMR. Such deeper understanding has led to novel forms of controlling the various components that make up the spin interactions, which have in turn redefined the analytical capabilities of solid state NMR measurements. This review presents a perspective on the basic phenomena and manipulations that have made this progress possible and describes the new opportunities and challenges that are being opened in the realms of spin-1/2 and quadrupole nuclei spectroscopies.
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    Annual Review of Physical Chemistry 52 (2001), S. 575-606 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract Solid state nuclear magnetic resonance (NMR) methods can provide atomic-level structural constraints on peptides and proteins in forms that are not amenable to characterization by other high-resolution structural techniques, owing to insolubility, high molecular weight, noncrystallinity, or other characteristics. Important examples include peptide and protein fibrils and membrane-bound peptides and proteins. Recent advances in solid state NMR methodology aimed at structural problems in biological systems are reviewed. The power of these methods is illustrated by experimental results on amyloid fibrils and other protein fibrils.
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    Annual Review of Physical Chemistry 52 (2001), S. 233-253 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract We outline recent developments in biological single-molecule fluorescence detection with particular emphasis on observations by ratiometric fluorescence resonance energy transfer (FRET) of biomolecules freely diffusing in solution. Single-molecule-diffusion methodologies were developed to minimize perturbations introduced by interactions between molecules and surfaces. Confocal microscopy is used in combination with sensitive detectors to observe bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract ratiometric observables such as FRET efficiency and polarization anisotropy. We describe the development of single-molecule FRET methodology and its application to the observation of the Forster distance dependence and the study of protein folding and polymer physics problems. Finally, we discuss future advances in data acquisition and analysis techniques that can provide a more complete picture of the accessible molecular information.
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    Annual Review of Physical Chemistry 52 (2001), S. 391-422 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract Electrochemical processes leading to light emission are reviewed, with emphasis on aspects of this subject relevant to the understanding and optimization of electrogenerated luminescence (EL) in organic thin-film materials. The basic energetic requirements of light emission from electrochemically initiated solution redox reactions [electrogenerated chemiluminescence (ECL)] are reviewed first. This review is followed by a discussion of light-emitting electrochemical processes that have been observed in hybrids of ionically conducting polymers and electronically conducting polymers. Finally, the features of EL in insulating polymers and molecular thin films are reviewed, along with recent electrochemical and ECL studies of the small-molecule components of certain organic light-emitting diodes. These studies provide a conceptual framework for understanding and optimizing these materials and the EL process.
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    Annual Review of Physical Chemistry 52 (2001), S. 537-573 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract Driven by prospective applications, there is much interest in developing materials that can perform specific functions in response to external conditions. One way to design such materials is to create systems which, in response to external inputs, can self-assemble to form structures that are functionally useful. This review focuses on the principles that can be employed to design macromolecules that when presented with an appropriate two-dimensional surface, will self-assemble to form nanostructures that may be functionally useful. We discuss three specific examples: (a) biomimetic recognition between polymers and patterned surfaces. (b) control and manipulation of nanomechanical motion generated by biopolymer adsorption and binding, and (c) creation of patterned nanostructuctures by exposing molten diblock copolymers to patterned surfaces. The discussion serves to illustrate how polymer sequence can be manipulated to affect self-assembly characteristics near adsorbing surfaces. The focus of this review is on theoretical and computational work aimed toward elucidating the principles underlying the phenomena pertinent to the three topics noted above. However, synergistic experiments are also described in the appropriate context.
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    Annual Review of Physical Chemistry 52 (2001), S. 499-535 
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    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract Beginning with simplified lattice and continuum "minimalist" models and progressing to detailed atomic models, simulation studies have augmented and directed development of the modern landscape perspective of protein folding. In this review we discuss aspects of detailed atomic simulation methods applied to studies of protein folding free energy surfaces, using biased-sampling free energy methods and temperature-induced protein unfolding. We review studies from each on systems of particular experimental interest and assess the strengths and weaknesses of each approach in the context of "exact" results for both free energies and kinetics of a minimalist model for a beta-barrel protein. We illustrate in detail how each approach is implemented and discuss analysis methods that have been developed as components of these studies. We describe key insights into the relationship between protein topology and the folding mechanism emerging from folding free energy surface calculations. We further describe the determination of detailed "pathways" and models of folding transition states that have resulted from unfolding studies. Our assessment of the two methods suggests that both can provide, often complementary, details of folding mechanism and thermodynamics, but this success relies on (a) adequate sampling of diverse conformational regions for the biased-sampling free energy approach and (b) many trajectories at multiple temperatures for unfolding studies. Furthermore, we find that temperature-induced unfolding provides representatives of folding trajectories only when the topology and sequence (energy) provide a relatively funneled landscape and "off-pathway" intermediates do not exist.
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    Annual Review of Physical Chemistry 53 (2002), S. 291-318 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract This article reviews the concepts and methods of transition path sampling. These methods allow computational studies of rare events without requiring prior knowledge of mechanisms, reaction coordinates, and transition states. Based upon a statistical mechanics of trajectory space, they provide a perspective with which time dependent phenomena, even for systems driven far from equilibrium, can be examined with the same types of importance sampling tools that in the past have been applied so successfully to static equilibrium properties.
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    Annual Review of Physical Chemistry 53 (2002), S. 533-562 
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    Topics: Chemistry and Pharmacology , Physics
    Notes: Abstract This article reviews a new and general theory of nonuniform fluids that naturally incorporates molecular scale information into the classical van der Waals theory of slowly varying interfaces. The method optimally combines two standard approximations, molecular (mean) field theory to describe interface formation and linear response (or Gaussian fluctuation) theory to describe local structure. Accurate results have been found in many different applications in nonuniform simple fluids and these ideas may have important implications for the theory of hydrophobic interactions in water.
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    Annual Review of Physical Chemistry 55 (2004), S. 391-426 
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    Topics: Chemistry and Pharmacology , Physics
    Notes: Recent applications of neutron reflectometry to the study of wet interfaces are described. An outline is given of the basic principles that allow the techniques to determine composition and structure in a variety of situations. These are the adsorption of surfactant molecules at air/liquid and solid/liquid interfaces, the shape of the segment-density profiles of different types of polymer, including block copolymers and polyelectrolytes, adsorption in mixed surfactant and polymer/surfactant systems, and interfacial systems of biophysical interest.
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    Annual Review of Physical Chemistry 55 (2004), S. 257-298 
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    Topics: Chemistry and Pharmacology , Physics
    Notes: Charge transport at conjugated polymer interfaces with metals and inorganic semiconductors is reviewed. Experiments on the equilibrium properties and DC current-voltage behavior of four specific classes of interfaces-metal-doped conjugated polymer, inorganic semiconductor-doped conjugated polymer, metal-intrinsic conjugated polymer, and metal-intrinsic conjugated polymer/electrolyte-are discussed. To facilitate this discussion, classic models of equilibration at ideal interfaces between electronic conductors and free-electron transport are introduced and their limitations discussed. Particular emphasis is placed on the charge distributions and interfacial potential profiles expected at various types of electroactive interfaces.
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    Annual Review of Physical Chemistry 55 (2004), S. 299-332 
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    Topics: Chemistry and Pharmacology , Physics
    Notes: Recent progress in the development of semiclassical methods to describe quantum effects in molecular dynamics is reviewed. Focusing on rigorous semiclassical methods that are based on the initial-value representation of the semiclassical propagator, we discuss several promising schemes that have been developed in the past few years to extend the applicability of semiclassical approaches to complex molecular systems. In particular, integral-filtering techniques and forward-backward methods are surveyed. Furthermore, recently proposed approaches that allow the semiclassical description of nonadiabatic molecular dynamics are discussed. The potential and efficiency of these methods is illustrated by selected applications.
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    Annual Review of Physical Chemistry 55 (2004), S. 427-455 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Time-dependent density functional theory (TDDFT) can be viewed as an exact reformulation of time-dependent quantum mechanics, where the fundamental variable is no longer the many-body wave function but the density. This time-dependent density is determined by solving an auxiliary set of noninteracting Schrodinger equations, the Kohn-Sham equations. The nontrivial part of the many-body interaction is contained in the so-called exchange-correlation potential, for which reasonably good approximations exist. Within TDDFT two regimes can be distinguished: (a) If the external time-dependent potential is "small," the complete numerical solution of the time-dependent Kohn-Sham equations can be avoided by the use of linear response theory. This is the case, e.g., for the calculation of photoabsorption spectra. (b) For a "strong" external potential, a full solution of the time-dependent Kohn-Sham equations is in order. This situation is encountered, for instance, when matter interacts with intense laser fields. In this review we give an overview of TDDFT from its theoretical foundations to several applications both in the linear and in the nonlinear regime.
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    Annual Review of Physical Chemistry 55 (2004), S. 509-557 
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    Topics: Chemistry and Pharmacology , Physics
    Notes: The review describes the studies of the magneto-optical properties of II-VI and III-V semiconductor nanocrystals (NCs) capped with organic or inorganic epitaxial shells. The investigations focused on the chemical identification of localization sites (core, shell, or interface) of photogenerated carriers in spherical NCs and elucidated the influence of the surface/interface quality on the optical properties of the materials. Optically detected magnetic resonance (ODMR) spectroscopy was used for the study of the proposed physical properties. The ODMR method provides the means to identify the surface/interface sites and correlate them with specific optical transition. In addition, this method reveals information about the spin multiplicity of band edge and trapped states and the electron-hole exchange interaction, determines the spectroscopic g-factors, distinguishes between the radiative and nonradiative characteristic of a trapping site, and evaluates the spin-lattice relaxation times.
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    Annual Review of Physical Chemistry 56 (2005), S. 337-367 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Time-resolved infrared (IR) and Raman spectroscopy elucidates molecular structure evolution during ultrafast chemical reactions. Following vibrational marker modes in real time provides direct insight into the structural dynamics, as is evidenced in studies on intramolecular hydrogen transfer, bimolecular proton transfer, electron transfer, hydrogen bonding during solvation dynamics, bond fission in organometallic compounds and heme proteins, cis-trans isomerization in retinal proteins, and transformations in photochromic switch pairs. Femtosecond IR spectroscopy monitors the site-specific interactions in hydrogen bonds. Conversion between excited electronic states can be followed for intramolecular electron transfer by inspection of the fingerprint IR- or Raman-active vibrations in conjunction with quantum chemical calculations. Excess internal vibrational energy, generated either by optical excitation or by internal conversion from the electronic excited state to the ground state, is observable through transient frequency shifts of IR-active vibrations and through nonequilibrium populations as deduced by Raman resonances.
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    Annual Review of Physical Chemistry 56 (2005), S. 25-56 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: We review prototype studies in the area of quantum control with femtosecond lasers. We restrict this discussion to atoms and diatomics under gas-phase collision-free conditions to allow for a comparison between theory and experiment. Both the perturbative regime and the nonperturbative regime of the light-matter interaction are addressed. To that end, atomic/molecular beam techniques are combined together with femtosecond laser techniques and energy-resolved photoelectron spectroscopy and ion detection. Highly detailed information on the laser-induced quantum dynamics is extracted with the help of kinetic energy-resolved photoelectron spectroscopy.
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    Annual Review of Physical Chemistry 56 (2005), S. 475-490 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Transport spectroscopy, a technique based on current-voltage measurements of individual nanostructures in a three-terminal transistor geometry, has emerged as a powerful new tool to investigate the electronic properties of chemically derived nanostructures. In this review, we discuss the utility of this approach using the recent studies of single-nanotube transistors as an example. Specifically, we discuss how transport measurements can be used to gain detailed insight into the electronic motion in metallic single-walled carbon nanotubes in several distinct regimes, depending on the coupling strength of the contacts to the nanotubes. Measurements of nanotube devices in these different conductance regimes have enabled a detailed analysis of the transport properties, including the experimental determination of all Hartree-Fock parameters that govern the electronic structure of metallic nanotubes and the demonstration of Fabry-Perot resonators based on the interference of electron waves.
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    Annual Review of Physical Chemistry 56 (2005), S. 91-117 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Physics
    Notes: Significant advances in laser technology have led to an increasing interest in the time evolution of Rydberg wavepackets as a means to understanding, and ultimately controlling, quantum phenomena. Rydberg wavepackets in molecules are particularly interesting as they possess many of the dynamical complications of large molecules, such as nonadiabatic coupling between the various degrees of freedom, yet they remain tractable experimentally and theoretically. This review explains in detail how the method of interfering wavepackets can be applied to observe and control Rydberg wavepackets in molecules; it discusses the achievements to date and the possibilities for the future.
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    Annual Review of Physical Chemistry 56 (2005), S. 221-254 
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    Topics: Chemistry and Pharmacology , Physics
    Notes: Molecular structures during chemical processes are crucial for predicting molecular reactivity and reaction mechanisms. Using a laser pulse as an internal clock for starting fundamental chemical processes, molecular structural dynamics can be characterized by coherent vibrational motions and by incoherent transitions between different intermediate states. Recent developments in pulsed X-ray facilities allow structural determination of discrete excited states and reaction intermediates using laser-initiated time-resolved X-ray absorption spectroscopy (LITR-XAS). Moreover, femtosecond X-ray sources have begun making significant contributions in monitoring coherent molecular motions. This review summarizes recent developments in the field, including technical and scientific challenges as well as several examples involving excited state molecular structure and electronic configuration determinations. Future applications of this technique with high time resolution will enable visualization of fundamental chemical events in many systems and further our understanding in photochemistry.
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    Annual Review of Pharmacology 20 (1980), S. 173-199 
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    Topics: Medicine , Chemistry and Pharmacology
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    Annual Review of Pharmacology 21 (1981), S. 133-163 
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    Annual Review of Pharmacology 21 (1981), S. 165-204 
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    Annual Review of Pharmacology 22 (1982), S. 19-29 
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    Annual Review of Pharmacology 22 (1982), S. 31-55 
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    Annual Review of Pharmacology 22 (1982), S. 57-87 
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    Annual Review of Pharmacology 23 (1983), S. 649-656 
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    Annual Review of Pharmacology 20 (1980), S. 151-172 
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    Annual Review of Pharmacology 20 (1980), S. 45-54 
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    Annual Review of Pharmacology 20 (1980), S. 201-234 
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    Annual Review of Pharmacology 21 (1981), S. 323-356 
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    Annual Review of Pharmacology 21 (1981), S. 417-429 
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