GLORIA

GEOMAR Library Ocean Research Information Access

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Electronic Resource
    Electronic Resource
    A nonlinear measure of subalignment similarity and its significance levels (1986)
    Springer
    Bulletin of mathematical biology 48 (1986), S. 617-632 
    Details
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract A new measure of subalignment similarity is introduced. Specifically, similaritys(l,c) is defined as the logarithm to the basep of the probability of findingc or fewer mismatches in a subalignment of lengthl, wherep is the probability of a match. Previous algorithms can not use this measure to find locally optimal subalignments because, unlike Needleman-Wunsch and Sellers similarities, this measure is nonlinear. A new pattern recognition algorithm is described for finding all locally optimal subalignments of two nucleotide sequences. The DD algorithm can uses(l, c) or any other reasonable similarity function to assess the relative interest of subalignments. The DD algorithm searches only the diagonal graph, which lacks insertions and deletions. This search strategy greatly decreases the computation time and does not require an arbitrary choice of gap cost. The paths of the resulting DD graph usually draw attention to likely locations for insertions and deletions. A heuristic formula is derived for estimating significance levels fors(l, c) in the context of the lengths of the two aligned sequences. The DD algorithm has been used to find interesting subalignments between the nucleotide sequences for human and murine interleukin 2.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02462327
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 2
    Electronic Resource
    Electronic Resource
    Locally optimal subalignments using nonlinear similarity functions (1986)
    Springer
    Bulletin of mathematical biology 48 (1986), S. 633-660 
    Details
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract Nonlinear similarity functions are often better than linear functions at distinguishing interesting subalignments from those due to chance. Nonlinear similarity functions useful for comparing biological sequences are developed. Several new algorithms are presented for finding locally optimal subalignments of two sequences. Unlike previous algorithms, they may use any reasonable similarity function as a selection criterion. Among these algorithms are VV-1, which finds all and only the locally optimal subalignments of two sequences, and CC-1, which finds all and only the weakly locally optimal subalignments of two sequences. The VV-1 algorithm is slow and interesting only for theoretical reasons. In contrast, the CC-1 algorithm has average time complexityO(MN) when used to find only very good subalignments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02462328
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 3
    Electronic Resource
    Electronic Resource
    Optimal sequence alignment using affine gap costs (1986)
    Springer
    Bulletin of mathematical biology 48 (1986), S. 603-616 
    Details
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract When comparing two biological sequences, it is often desirable for a gap to be assigned a cost not directly proportional to its length. If affine gap costs are employed, in other words if opening a gap costsv and each null in the gap costsu, the algorithm of Gotoh (1982,J. molec. Biol. 162, 705) finds the minimum cost of aligning two sequences in orderMN steps. Gotoh's algorithm attempts to find only one from among possibly many optimal (minimum-cost) alignments, but does not always succeed. This paper provides an example for which this part of Gotoh's algorithm fails and describes an algorithm that finds all and only the optimal alignments. This modification of Gotoh's algorithm still requires orderMN steps. A more precise form of path graph than previously used is needed to represent accurately all optimal alignments for affine gap costs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02462326
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 4
    Electronic Resource
    Electronic Resource
    Significance levels for biological sequence comparison using non-linear similarity functions (1988)
    Springer
    Bulletin of mathematical biology 50 (1988), S. 77-92 
    Details
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract A class of non-linear similarity functionss 1 has been proposed for comparing subalignments of biological sequences. The distribution of maximals 1-similarities is well approximated by the extreme value distribution. The significance levels ofs 1 are studied for a variety of nucleotide frequency distributions as well as for several matrices of amino acid substitution costs. Also, the significance levels ofs 1 are explored for comparing three biological sequences. Several previously described subalignments of bovine proenkephalin and porcine prodynorphin are shown to be highly significant.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02459979
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 5
    Electronic Resource
    Electronic Resource
    Larval release in brachyuran crustaceans Functional similarity of peptide pheromone receptor and catalytic site of trypsin (1990)
    Springer
    Journal of chemical ecology 16 (1990), S. 1359-1370 
    Details
    ISSN: 1573-1561
    Keywords: Rhithropanopeus harrisii ; crab ; Crustacea ; larval release pheromone ; peptide pheromone ; trypsin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Studies of crab egg hatching and larval release behavior in the crab,Rhithropanopeus harrisii, generated a model describing the process. In the model, carboxyl terminal arginine peptides serve as pheromones that synchronize larval release. In response to the peptides, the female performs Stereotypic larval release behavior and casts larvae into the water column. The peptides originate from trypsin-like enzymatic activity as part of the egghatching process. Hatching can be simulated experimentally by incubating ovigerous crabs in either bovine or porcine trypsin. The female performs the larval release behavior. Eggs detach from the female, and immobile larvae hatch prematurely. Preincubation of trypsin with trypsin inhibitors eliminates these effects. Approximately nanomolar concentrations of five different polypeptide trypsin inhibitors evoke the female's larval release behavior. Because both peptides and trypsin inhibitors evoke larval release behavior and because trypsin inhibitors bind to both the peptide receptor and the enzyme with high affinity, the receptor binding site and trypsin catalytic site must be very similar. A relationship between the binding site of a peptide receptor and the catalytic site of trypsin is postulated. The difference may be substitution by a basic amino acid for the catalytic site serine. Molecular graphics modeling indicates that all necessary conditions for receptor binding can be met by substitution with lysine for the active site serine in the trypsin catalytic site. This substitution eliminates catalytic activity, maintains the binding affinity for trypsin inhibitors, and increases binding strength for peptides.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01021032
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 6
    Electronic Resource
    Electronic Resource
    Engineering of betabellin 15D: Copper(II)-induced folding of a fibrillar β-sandwich protein (1999)
    Springer
    International journal of peptide research and therapeutics 6 (1999), S. 3-14 
    Details
    ISSN: 1573-3904
    Keywords: β-sandwich ; de novo design ; protein engineering ; protein fibrils
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The inverse protein-folding problem has been explored by designing de novo the betabellin target structure (a 64-residue β-sandwich protein), synthesizing a 32-residue peptide chain (HSLTAKIpkLTFSIAphTYTCAVpkYTAKVSH, where p = DPro, k = DLys, and h = DHis) that might fold into this structure, and studying how its disulfide-bridged form (betabellin 15D) folds in 10 mM ammonium acetate with and without Cu2+. Circular dichroic spectropolarimetry indicated that at pH 5.8, 6.4, or 6.7 betabellin 15D exhibited β-sheet structure in the presence of Cu2+ but not in its absence. Electrospray mass spectrometry demonstrated that at pH 6.3 each molecule of betabellin 15D bound one or two Cu(II) ions. Electron microscopy showed that at pH 6.7 betabellin 15D formed short broad fibrils in the presence of Cu2+ but not in its absence. The observed width of the fibrils (7 ± 2 nm) was consistent with the width (6.8 nm) of a structural model of a fibril that contained two adjacent rows of betabellin 15D β-sandwiches joined lengthwise by multiple intersheet hydrogen bonds and widthwise by multiple Cu(II)-imidazole bonds. Electron paramagnetic resonance spectrometry revealed that some pairs of Cu(II) ions in a Cu(II)/betabellin 15D complex were magnetically coupled, which is consistent with the structural model of the Cu(II)/betabellin 15D fibril.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008878308995
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 7
    Electronic Resource
    Electronic Resource
    Kinetics of isomerization for the proline helical forms of two oligoproline redox arrays by circular dichroic spectropolarimetry (1999)
    Springer
    International journal of peptide research and therapeutics 6 (1999), S. 61-69 
    Details
    ISSN: 1573-3904
    Keywords: biexponential kinetics ; proline helices ; substituted proline residues
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The kinetics of isomerization of the helical forms of three oligoprolines was determined by far-ultraviolet CD spectropolarimetry and kinetic analysis by singular value decomposition. ZRA (Pro3-X-Pro2-Y-Pro2-Z-Pro3) and ZRA2 (Pro7-X-Pro2-Y-Pro2-Z-Pro7) bear large redox-active substituents on proline residues X, Y, and Z, but P9 (Pro9) does not. All three peptides formed a stable proline-II helix in water. In acetonitrile, both ZRA2 and P9 were converted into a proline-I helical form but ZRA remained predominantly in the proline-II helical form. Evidently, in order to undergo substantial proline II→I isomerization, an oligoproline chain containing large substituents needs to have a segment of consecutive unsubstituted proline residues that is sufficiently long to form a stable proline helix. Biexponential kinetics (A→B, k1 = ∼3.3 × 10-4 s-1; B→C, k2 = ∼0.8 × 10-4 s-1) were observed for the proline II→I isomerization of ZRA2 and P9 in acetonitrile and for the proline I→II isomerization of ZRA2 in water, which provides evidence for the growth and decay of a major kinetic intermediate.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008819511721
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 8
    Electronic Resource
    Electronic Resource
    Engineering of deltoid and reduced deltoid: Two chimeric proteins containing the oligomerization site of the hepatitis delta antigen (1999)
    Springer
    International journal of peptide research and therapeutics 6 (1999), S. 23-32 
    Details
    ISSN: 1573-3904
    Keywords: antiparallel coiled coil ; deltoid ; hepatitis delta antigen ; molecular modeling ; oligomerization site ; protein engineering ; quadrin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Hepatitis delta antigen (HDAg) must form oligomers to be biologically active. Quandrin (HDAg-(12–60)-Tyr) is a 50-residue protein segment from the oligomerization domain of HDAg. The crystal structure of quadrin shows an octamer consisting of four identical copies of a dimer containing an antiparallel α-helical coiled coil. Each end of the dimer contains an oligomerization site that interacts isologously with the oligomerization site of another dimer to form a right-angled corner. The resulting quadrin octamer is a 400-residue square protein surrounding a large aqueous hole. We have designed, chemically synthesized, and characterized deltoid and reduced deltoid, two 51-residue chimeric proteins that structurally and functionally mimic one of the two oligomerization sites of the quadrin dimer. Dimerization of deltoid or reduced deltoid should emulate the dimerization of two quadrin dimers to form one right-angled corner of the square. Deltoid and reduced deltoid were designed by molecular modeling, mechanics, and dynamics and synthesized by the solid-phase method. The amino acid sequence of deltoid (GREDILEQWVSCRKKL+PKAPPEE+LRKLKKKCKKLEEDNPWLGNIKGIIGKY) is a chimera of three protein segments: HDAg-(12–28),Thermus thermophilus serine tRNA synthase-(59–65), and HDAg-(34–60)-Tyr. Cysteine (C) was introduced at two positions to explore the effects of the presence (deltoid) or absence (reduced deltoid) of an interhelical disulfide bond. Circular dichroic spectropolarimetry revealed that both synthetic proteins from an α-helical structure that is stable over a wide range of pH and KCl concentrations. Size-exclusion chromatography indicated that deltoid and reduced deltoid each form a dimer. Interconversion of these monomers and dimers should be useful model systems for studying the structural features of the right-angled corners of the quandrin octamer that contribute to HDAg oligomerization. If, like quadrin, deltoid or reduced deltoid interferes with HDAg oligomerization, it might serve as a lead compound for the design of potent HDV inhibitors.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02443615
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 9
    Electronic Resource
    Electronic Resource
    Engineering of betabellin 15D: Copper(II)-induced folding of a fibrillar β-sandwich protein (1999)
    Springer
    International journal of peptide research and therapeutics 6 (1999), S. 3-14 
    Details
    ISSN: 1573-3904
    Keywords: β-sandwich ; de novo design ; protein engineering ; protein fibrils
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The inverse protein-folding problem has been explored by designing de novo the betabellin target structure (a 64-residue β-sandwich protein), synthesizing a 32-residue peptide chain (HSLTAKIpkLTFSIAphTYTCAVpkYTAKVSH, wherep=DPro,k=DLys, andh=DHis) that might fold into this structure, and studying how its disulfide-bridged form (betabellin 15D) folds in 10 mM ammonium acetate with and without Cu2+. Circular dichroic spectropolarimetry indicated that at pH 5.8, 6.4, or 6.7 betabellin 15D exhibited β-sheet structure in the presence of Cu2+ but not in its absence. Electrospray mass spectrometry demonstrated that at pH 6.3 each molecule of betabellin 15D bound one or two Cu(II) ions. Electron microscopy showed that at pH 6.7 betabellin 15D formed short broad fibrils in the presence of Cu2+ but not in its absence. The observed width of the fibrils (7±2 nm) was consistent with the width (6.8nm) of a structural model of a fibril that contained two adjacent rows of betabellin 15D β-sandwiches joined lengthwise by multiple intersheet hydrogen bonds and widthwise by multiple Cu(II)-imidazole bonds. Electron paramagnetic resonance spectrometry revealed that some pairs of Cu(II) ions in a Cu(II)/betabellin 15D complex were magnetically coupled, which is consistent with the structural model of the Cu(II)/betabellin 15D fibril.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02443613
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 10
    Electronic Resource
    Electronic Resource
    Synthesis of an iron(II)-braced proline-II tripod protein (1999)
    Springer
    International journal of peptide research and therapeutics 6 (1999), S. 33-43 
    Details
    ISSN: 1573-3904
    Keywords: 4-amino-l-proline ; circular dichroic spectropolarimetry ; proline-II helix ; protein engineering
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary This paper describes the engineering of braced tripod proteins for use as molecular frameworks. Specifically, a 30-residue tripod-shaped protein with three proline-II helical legs braced by an iron(II)tris(bipyridine) complex was modularly designed, chemically synthesized, and biophysically characterized. Three copies of a 10-residue leg peptide were covalently linked through sulfide bonds to an N-terminal apex (1,3,5-tris(methylene)benzene) and by amide bonds to the brace (FeII (Mbc)3: Mbc is 4′-methyl-2,2′-bipyridine-4-carbonyl). The leg peptide (H-Cys-Pro5-Pra(Mbc)-Pro3-NH2: Pra iscis-4-amino-l-proline) was assembled by the solid-phase method using Boc-Pra(Mbc)-OH, which was synthesized in 75% overall yield by coupling Mbc-OH to the 4-amino group of Boc-Pra-OCH3 and saponifying the methyl ester group. The iron(II)-braced tripod was assembled by S-alkylation of three copies of the leg peptide with 1,3,5-tris(bromomethyl)benzene followed by ligation of Fe2+ to the resulting unbraced tripod. The CD spectrum of the iron(II)-braced tripod showed a positive MLCT band at 570 nm and a negative π-π* band at 312 nm, so its FeII(Mbc)3 brace was predominantly in the Δ configuration. In a mostly acetonitrile solution at 25°C, the leg peptide and the unbraced tripod isomerized from the proline-II helical form into the proline-I helical form but the iron(II)-braced tripod remained in the proline-II helical form.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02443616
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...