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  • Articles  (29,153)
  • American Association for the Advancement of Science (AAAS)  (22,446)
  • Oxford University Press  (4,229)
  • Annual Reviews  (1,790)
  • Institute of Physics
  • 2000-2004  (13,882)
  • 1980-1984  (14,324)
  • 1935-1939  (690)
  • 1925-1929
  • Chemistry and Pharmacology  (29,153)
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  • Articles  (29,153)
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Year
  • 101
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 5 (1936), S. 181-204 
    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 5 (1936), S. 295-314 
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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 5 (1936), S. 247-270 
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    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 5 (1936), S. 485-512 
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    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 49 (1980), S. 765-811 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 106
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 49 (1980), S. 813-841 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 107
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 49 (1980), S. 845-876 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 108
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 49 (1980), S. 877-919 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 109
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 49 (1980), S. 921-956 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 110
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 4 (1935), S. 169-182 
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  • 111
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 4 (1935), S. 183-198 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 112
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 4 (1935), S. 199-224 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 113
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 4 (1935), S. 225-242 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 114
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 4 (1935), S. 243-261 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 115
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 4 (1935), S. 263-278 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 116
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 4 (1935), S. 279-310 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 117
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 4 (1935), S. 331-382 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 118
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 4 (1935), S. 311-330 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 119
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 4 (1935), S. 383-412 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 120
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 4 (1935), S. 449-468 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 121
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 4 (1935), S. 435-448 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 122
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 4 (1935), S. 413-434 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 123
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 50 (1981), S. 193-206 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 124
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 50 (1981), S. 159-192 
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  • 125
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 50 (1981), S. 233-260 
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  • 126
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 50 (1981), S. 207-231 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 127
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 50 (1981), S. 261-284 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 128
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 50 (1981), S. 285-315 
    ISSN: 0066-4154
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  • 129
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 69 (2000), S. 31-67 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract Circadian rhythms are oscillations in the biochemical, physiological, and behavioral functions of organisms that occur with a periodicity of approximately 24 h. They are generated by a molecular clock that is synchronized with the solar day by environmental photic input. The cryptochromes are the mammalian circadian photoreceptors. They absorb light and transmit the electromagnetic signal to the molecular clock using a pterin and flavin adenine dinucleotide (FAD) as chromophore/cofactors, and are evolutionarily conserved and structurally related to the DNA repair enzyme photolyase. Humans and mice have two cryptochrome genes, CRY1 and CRY2, that are differentially expressed in the retina relative to the opsin-based visual photoreceptors. CRY1 is highly expressed with circadian periodicity in the mammalian circadian pacemaker, the suprachiasmatic nucleus (SCN). Mutant mice lacking either Cry1 or Cry2 have impaired light induction of the clock gene mPer1 and have abnormally short or long intrinsic periods, respectively. The double mutant has normal vision but is defective in mPer1 induction by light and lacks molecular and behavioral rhythmicity in constant darkness. Thus, cryptochromes are photoreceptors and central components of the molecular clock. Genetic evidence also shows that cryptochromes are circadian photoreceptors in Drosophila and Arabidopsis, raising the possibility that they may be universal circadian photoreceptors. Research on cryptochromes may provide new understanding of human diseases such as seasonal affective disorder and delayed sleep phase syndrome.
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  • 130
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 51 (1982), S. 123-154 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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  • 131
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 51 (1982), S. 185-217 
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  • 132
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 51 (1982), S. 155-183 
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  • 133
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 51 (1982), S. 219-250 
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  • 134
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 51 (1982), S. 251-282 
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  • 135
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 51 (1982), S. 283-308 
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  • 136
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 51 (1982), S. 309-333 
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  • 137
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 51 (1982), S. 335-364 
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  • 138
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 51 (1982), S. 365-394 
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  • 139
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 51 (1982), S. 395-427 
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  • 140
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 51 (1982), S. 491-530 
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  • 141
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    Annual Review of Biochemistry 69 (2000), S. 399-418 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract This review summarizes the progress made in our understanding of peroxisome biogenesis in the last few years, during which the functional roles of many of the 23 peroxins (proteins involved in peroxisomal protein import and peroxisome biogenesis) have become clearer. Previous reviews in the field have focussed on the metabolic functions of peroxisomes (1, 2), aspects of import/biogenesis (3, 4, 5, 6, 7), the role of peroxins in human disease (2, 8), and involvement of the endoplasmic reticulum in peroxisome membrane biogenesis (9, 10, 11) as well as the degradation of this organelle (5, 12). This review refers to some of the earlier work for the sake of introduction and continuity but deals primarily with the more recent progress. The principal areas of progress are the identification of new peroxins, definition of protein-protein interactions among peroxins leading to the recognition of complexes involved in peroxisomal protein import, insight into the biogenesis of peroxisomal membrane proteins, and, of most importance, the elucidation of the role of many conserved peroxins in human disease. Given the rapid progress in the field, this review also highlights some of the unanswered questions that remain to be tackled.
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  • 142
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 51 (1982), S. 587-616 
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  • 143
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 6 (1937), S. 1-18 
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  • 144
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 6 (1937), S. 19-42 
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  • 145
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    Annual Review of Biochemistry 69 (2000), S. 651-697 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Abstract Helicases are motor proteins that couple the hydrolysis of nucleoside triphosphate (NTPase) to nucleic acid unwinding. The hexameric helicases have a characteristic ring-shaped structure, and all, except the eukaryotic minichromosomal maintenance (MCM) helicase, are homohexamers. Most of the 12 known hexameric helicases play a role in DNA replication, recombination, and transcription. A human genetic disorder, Bloom's syndrome, is associated with a defect in one member of the class of hexameric helicases. Significant progress has been made in understanding the biochemical properties, structures, and interactions of these helicases with DNA and nucleotides. Cooperativity in nucleotide binding was observed in many, and sequential NTPase catalysis has been observed in two proteins, gp4 of bacteriophage T7 and rho of Escherichia coli. The crystal structures of the oligomeric T7 gp4 helicase and the hexamer of RepA helicase show structural features that substantiate the observed cooperativity, and both are consistent with nucleotide binding at the subunit interface. Models are presented that show how sequential NTP hydrolysis can lead to unidirectional and processive translocation. Possible unwinding mechanisms based on the DNA exclusion model are proposed here, termed the wedge, torsional, and helix-destabilizing models.
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  • 146
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    Annual Review of Biochemistry 69 (2000), S. 829-880 
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    Notes: Abstract The initiation of DNA replication in eukaryotic cells is tightly controlled to ensure that the genome is faithfully duplicated once each cell cycle. Genetic and biochemical studies in several model systems indicate that initiation is mediated by a common set of proteins, present in all eukaryotic species, and that the activities of these proteins are regulated during the cell cycle by specific protein kinases. Here we review the properties of the initiation proteins, their interactions with each other, and with origins of DNA replication. We also describe recent advances in understanding how the regulatory protein kinases control the progress of the initiation reaction. Finally, we describe the checkpoint mechanisms that function to preserve the integrity of the genome when the normal course of genome duplication is perturbed by factors that damage the DNA or inhibit DNA synthesis.
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    Annual Review of Biochemistry 69 (2000), S. 1005-1075 
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    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract The cytochrome bc complexes represent a phylogenetically diverse group of complexes of electron-transferring membrane proteins, most familiarly represented by the mitochondrial and bacterial bc1 complexes and the chloroplast and cyanobacterial b6f complex. All these complexes couple electron transfer to proton translocation across a closed lipid bilayer membrane, conserving the free energy released by the oxidation-reduction process in the form of an electrochemical proton gradient across the membrane. Recent exciting developments include the application of site-directed mutagenesis to define the role of conserved residues, and the emergence over the past five years of X-ray structures for several mitochondrial complexes, and for two important domains of the b6f complex.
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  • 148
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    Annual Review of Biochemistry 6 (1937), S. 115-138 
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  • 149
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    Annual Review of Biochemistry 51 (1982), S. 869-900 
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    Annual Review of Biochemistry 52 (1983), S. 1-16 
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    Annual Review of Biochemistry 51 (1982), S. 935-971 
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    Annual Review of Biochemistry 52 (1983), S. 35-65 
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    Annual Review of Biochemistry 52 (1983), S. 17-34 
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    Annual Review of Biochemistry 52 (1983), S. 67-91 
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 52 (1983), S. 125-157 
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    Annual Review of Biochemistry 52 (1983), S. 159-186 
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    Annual Review of Biochemistry 70 (2001), S. 247-279 
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    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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    Annual Review of Biochemistry 70 (2001), S. 313-340 
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    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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    Annual Review of Biochemistry 52 (1983), S. 537-579 
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    Annual Review of Biochemistry 71 (2002), S. 71-100 
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    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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    Annual Review of Biochemistry 71 (2002), S. 191-219 
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    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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    Annual Review of Biochemistry 71 (2002), S. 1-16 
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    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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    Annual Review of Biochemistry 71 (2002), S. 435-471 
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    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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    Annual Review of Biochemistry 53 (1984), S. 493-535 
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    Annual Review of Biochemistry 71 (2002), S. 511-535 
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    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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    Annual Review of Biochemistry 71 (2002), S. 635-700 
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    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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    Annual Review of Biochemistry 72 (2003), S. 1-18 
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    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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    Annual Review of Biochemistry 72 (2003), S. 137-174 
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    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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    Annual Review of Biochemistry 72 (2003), S. 249-289 
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    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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    Annual Review of Biochemistry 72 (2003), S. 395-447 
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    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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    Annual Review of Biochemistry 72 (2003), S. 517-571 
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    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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    Annual Review of Biochemistry 72 (2003), S. 717-742 
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    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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    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. 617-656 
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    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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    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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    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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    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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    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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    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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    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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    Topics: Chemistry and Pharmacology , Biology
    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 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    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 73 (2004), S. 491-537 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    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 
    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 73 (2004), S. 861-890 
    ISSN: 0066-4154
    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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    Annual Review of Biochemistry 73 (2004), S. 991-1018 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    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 Physical Chemistry 31 (1980), S. 401-433 
    ISSN: 0066-426X
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    Topics: Chemistry and Pharmacology , Physics
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    Annual Review of Physical Chemistry 32 (1981), S. 1-24 
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    Annual Review of Physical Chemistry 32 (1981), S. 103-138 
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    Annual Review of Physical Chemistry 32 (1981), S. 179-204 
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    Annual Review of Physical Chemistry 32 (1981), S. 267-309 
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    Annual Review of Physical Chemistry 32 (1981), S. 311-329 
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    Annual Review of Physical Chemistry 33 (1982), S. 1-46 
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    Annual Review of Physical Chemistry 33 (1982), S. 173-189 
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    Annual Review of Physical Chemistry 33 (1982), S. 223-255 
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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. 159-189 
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    Annual Review of Physical Chemistry 35 (1984), S. 241-263 
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