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  • 1
    Digitale Medien
    Digitale Medien
    How to determine protein secondary structure in solution by Raman spectroscopy: practical guide and test case DNase I (1989)
    s.l. : American Chemical Society
    Biochemistry 28 (1989), S. 4271-4277 
    Details
    ISSN: 1520-4995
    Quelle: ACS Legacy Archives
    Thema: Biologie , Chemie und Pharmazie
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1021/bi00436a023
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  • 2
    Digitale Medien
    Digitale Medien
    Novelties from the complete genome of Mycoplasma genitalium (1996)
    Oxford, UK : Blackwell Publishing Ltd
    Molecular microbiology 20 (1996), S. 0 
    Details
    ISSN: 1365-2958
    Quelle: Blackwell Publishing Journal Backfiles 1879-2005
    Thema: Biologie , Medizin
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1111/j.1365-2958.1996.tb02529.x
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  • 3
    Digitale Medien
    Digitale Medien
    Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology (1995)
    Oxford, UK : Blackwell Publishing Ltd
    Molecular microbiology 16 (1995), S. 0 
    Details
    ISSN: 1365-2958
    Quelle: Blackwell Publishing Journal Backfiles 1879-2005
    Thema: Biologie , Medizin
    Notizen: We report on the analysis of 214 kb of the parasitic eubacterium Mycoplasma capricolum sequenced by genomic walking techniques. The 287 putative proteins detected to date represent about half of the estimated total number of 500 predicted for this organism. A large fraction of these (75%) can be assigned a likely function as a result of similarity searches. Several important features of the functional organization of this small genome are already apparent. Among these are (i) the expected relatively large number of enzymes involved in metabolic transport and activation, for efficient use of host cell nutrients; (ii) the presence of anabolic enzymes; (iii) the unexpected diversity of enzymes involved in DNA replication and repair: and (iv) a sizeable number of orthologues (82 so far) in Escherichia coli. This survey is beginning to provide a detailed view of how M. capricolum manages to maintain essential cellular processes with a genome much smaller than that of its bacterial relatives.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1111/j.1365-2958.1995.tb02321.x
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  • 4
    Digitale Medien
    Digitale Medien
    A Drosophila hsp70 gene contains long, antiparallel, coupled open reading frames (LAC ORFs) conserved in homologous loci (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 414-420 
    Details
    ISSN: 1432-1432
    Schlagwort(e): Gene structure ; Heat shock ; hsp70 ; Antiparallel ORFs ; Drosophila
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Biologie
    Notizen: Abstract A clone isolated from a Drosophila auraria heat-shock cDNA library presents two long, antiparallel, coupled (LAC) open reading frames (ORFs). One strand ORF is 1,929 nucleotides long and exhibits great identity (87.5% at the nucleotide level and 94% at the amino acid level) with the hsp70 gene copies of D. melanogaster, while the second strand ORF, in antiparallel in-frame register arrangement, is 1,839 nucleotides long and exhibits 32% identity with a putative, recently identified, NAD+-dependent glutamate dehydrogenase (NAD+-GDH). The overlap of the two ORFs is 1,824 nucleotides long. Computational analysis shows that this LAC ORF arrangement is conserved in other hsp70 loci in a wide range of organisms, raising questions about possible evolutionary benefits of such a peculiar genomic organization.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1007/BF00160312
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  • 5
    Digitale Medien
    Digitale Medien
    Identical pentapeptides with different backbones (1985)
    [s.l.] : Nature Publishing Group
    Nature 317 (1985), S. 207-207 
    Details
    ISSN: 1476-4687
    Quelle: Nature Archives 1869 - 2009
    Thema: Biologie , Chemie und Pharmazie , Medizin , Allgemeine Naturwissenschaft , Physik
    Notizen: [Auszug] SIR-In a comment on a recent News and Views article by Harrison1, Fasman2 maintains that we drew a false conclusion from the finding of identical pentapeptides with different backbone configurations3. He also gives the impression that his algorithm is capable of correctly predicting the secondary ...
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1038/317207a0
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  • 6
    Digitale Medien
    Digitale Medien
    A method to predict functional residues in proteins (1995)
    [s.l.] : Nature Publishing Group
    Nature structural biology 2 (1995), S. 171-178 
    Details
    ISSN: 1072-8368
    Quelle: Nature Archives 1869 - 2009
    Thema: Biologie , Medizin
    Notizen: [Auszug] The biological activity of a protein typically depends on the presence of a small number of functional residues. Identifying these residues from the amino acid sequences alone would be useful. Classically, strictly conserved residues are predicted to be functional but often conservation patterns ...
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1038/nsb0295-171
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  • 7
    Digitale Medien
    Digitale Medien
    Errors in protein structures (1996)
    [s.l.] : Nature Publishing Group
    Nature 381 (1996), S. 272-272 
    Details
    ISSN: 1476-4687
    Quelle: Nature Archives 1869 - 2009
    Thema: Biologie , Chemie und Pharmazie , Medizin , Allgemeine Naturwissenschaft , Physik
    Notizen: [Auszug] SIR - In 1990 Branden and Jones1 wrote in a Commentary to Nature: "Protein crystallography is an exacting trade, and the result may contain errors that are difficult to identify. It is the crystallographers' responsibility to make sure that incorrect protein structures do not reach the literature." ...
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1038/381272a0
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  • 8
    Digitale Medien
    Digitale Medien
    Classification of protein families and detection of the determinant residues with an improved self-organizing map (1997)
    Springer
    Biological cybernetics 76 (1997), S. 441-450 
    Details
    ISSN: 1432-0770
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Biologie , Informatik , Physik
    Notizen: Abstract.  Using a SOM (self-organizing map) we can classify sequences within a protein family into subgroups that generally correspond to biological subcategories. These maps tend to show sequence similarity as proximity in the map. Combining maps generated at different levels of resolution, the structure of relations in protein families can be captured that could not otherwise be represented in a single map. The underlying representation of maps enables us to retrieve characteristic sequence patterns for individual subgroups of sequences. Such patterns tend to correspond to functionally important regions. We present a modified SOM algorithm that includes a convergence test that dynamically controls the learning parameters to adapt them to the learning set instead of being fixed and externally optimized by trial and error. Given the variability of protein family size and distribution, the addition of this feature is necessary. The method is successfully tested with a number of families. The rab family of small GTPases is used to illustrate the performance of the method.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1007/s004220050357
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  • 9
    Digitale Medien
    Digitale Medien
    The cytidylyltransferase superfamily: Identification of the nucleotide-binding site and fold prediction (1995)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 22 (1995), S. 259-266 
    Details
    ISSN: 0887-3585
    Schlagwort(e): homology search ; phosphodiesterases ; sequence analysis ; structure prediction ; threading ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The crystal structure of glycerol-3-phosphate cytidylyltransferase from B. subtilis (TagD) is about to be solved. Here, we report a testable structure prediction based on the identification by sequence analysis of a superfamily of functionally diverse but structurally similar nucleotide-binding enzymes. We predict that TagD is a member of this family. The most conserved region in this superfamily resembles the ATP-binding HiGH motif of class I aminoacyI-tRNA synthetases. The predicted secondary structure of cytidylyltransferase and its homologues is compatible with the α/β topography of the class I aminoacyl-tRNA synthetases. The hypothesis of similarity of fold is strengthened by sequence-structure alignment and 3D model building using the known structure of tyrosyl tRNA synthetase as template. The proposed 3D model of TagD is plausible both structurally, with a well packed hydrophobic core, and functionally, as the most conserved residues cluster around the putative nucleotide binding site. If correct, the model would imply a very ancient evolutionary link between class I tRNA synthetases and the novel cytidylyltransferase superfamily. © 1995 Wiley-Liss, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/prot.340220306
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  • 10
    Digitale Medien
    Digitale Medien
    Predicting protein structure using hidden Markov models (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 134-139 
    Details
    ISSN: 0887-3585
    Schlagwort(e): CASP2 ; fold-recognition ; HMM ; structure library ; remote homology ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over 1,000 structures from the Protein Data Bank (PDB). Each CASP2 target sequence was scored against this library of HMMs. In addition, an HMM was built for each of the target sequences and all of the sequences in PDB were scored against that target model, with a good score on both methods indicating a high probability that the target sequence is homologous to the structure. The method worked well in comparison to other methods used at CASP2 for targets of moderate difficulty, where the closest structure in PDB could be aligned to the target with at least 15% residue identity. Proteins, Suppl. 1:134-139, 1997. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
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