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  • 1
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Physiologia plantarum 97 (1996), S. 0 
    ISSN: 1399-3054
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The physiology of individual somatic embryo developmental stages otDaucus carota L. was examined by in vivo nuclear magnetic resonance (NMR) spectroscopy, amino acid analysis and 14C-labeling. 15N NMR spectroscopy was used to examine the uptake and incorporation of 15N isotopically labeled inorganic nitrogen sources. NMR spectra of proembryogenic masses (PEMs) contained resonances for histidine, amino sugars, glutamine, arginine, urea, alanine. α-amino nitrogen, serine, aliphatic amines and several unknowns. Similar resonances were found in various embryo developmental stages. However, resonances for arginine and aliphatic amines peaked during globular and torpedo stages and substantially decreased in germinating stage embryos. The dominant resonances observed in non-embryogenic cells and germinating embryos were glutamine and α-amino nitrogen. Amino acid analysis of the various embryo stages showed that glutamate, glutamine and arginine were the major contributors to the soluble amino acid profiles. During development, glutamate and glutamine continued to increase in concentration whereas arginine and its related metabolites (i.e. ornithine and y-aminobutyric acid [GABA]) were biphasic; increasing in globular and torpedo stage embryos and decreasing in germinating embryos. Carbon-14 labeling indicated that labeled glutamine pools in non-embryogenic and germinating embryos were greatest compared to other embryo stages, whereas labeled GABA pools were greatest in globular and torpedo stage embryos. Taken together, these data indicate that the physiology of each embryo developmental stage is distinct. They also suggest that during somatic embryo development, a switch takes place in metabolism whereby the glutamine synthetase/glutamate synthase (GS/GOGAT) pathway is predominant in non-embryogenic cells and germinating stage embryos. Furthermore, during early to mid-embryo development (PEMs, globular and torpedo stage embryos), metabolism utilizing the omithine cycle is enhanced and predominant.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    BioMetals 11 (1998), S. 213-222 
    ISSN: 1572-8773
    Keywords: calmodulin ; fluorescence spectroscopy ; metal ions ; NMR
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Calmodulin is an important second messenger protein which is involved in a large variety of cellular path-ways.Calmodulin is sensitive to fluctuations in the intracellular Ca levels and is activated by the bindingof four Ca ions. In spite of the important role it plays in signal transduction pathways, it shows a surpris-inglybroad specificity for binding metal ions. Using 15N-Gly biosynthetically-labelled calmodulin, we havestudied the binding of different metal ions to calmodulin, including K+, Na+, Ca, Mg, Zn, Cd, Pb, Hg, Sr, La and Lu, by 1H, 15N HMQC NMR experiments. The effects of these ions on the substrate-bindingability of calmodulin have also been studied by fluorescence spectroscopy of the single tryptophan residue in a 22-residue synthetic peptide encompassing the skeletal muscle myosin light chain kinase calmod-ulin-binding domain. Most of these metal ions can activate a calmodulin target enzyme to some extent,though they bind to calmodulin in a different manner. Mg, which is of direct physiological interest, has adistinct site-preference for calmodulin, as it shows the highest affinity for site I in the N-terminal domain,while the C-terminal sites III and IV are the high affinity binding sites for Ca (as well as for Cd ). At ahigh concentration of Mg and a low concentration of Ca, calmodulin can bind Mg in its N-terminallobe while the C-terminal domain is occupied by Ca; this species could exist in resting cells in which the Mg level significantly exceeds that of Ca. Moreover, our data suggest that the toxicity of Pb-which,like Sr, binds with an equal and high affinity to all four sites-may be related to its capacity to tightlybind and improperly activate calmodulin.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1432-1017
    Keywords: Calmodulin ; Calmodulin fragments ; FTIR spectroscopy ; Ca2+-binding effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Fourier transform infrared spectra were obtained for mammalian calmodulin and two of its fragments produced by limited proteolysis with trypsin TR1C (1–77) and TR2C (78–148). Experiments were done in H2O, D2O and D2O/trifluoroethanol (TFE) mixtures. Information about secondary structure was obtained from analysis of the amide I and II bands; while characteristic absorbances for tyrosine, phenylalanine and carboxylate groups were analyzed for changes in tertiary structure. Our data indicate that the secondary and tertiary structure is preserved in the two half molecules of CaM, both in the apo- and Ca2+-saturated state. Addition of the structure-inducing solvent TFE causes marked changes only in the apo-TR1C domain. The maximum wavenumber for the amide I band of the two domains of CaM in D20 was markedly different (1642 cm−1 for TR1C versus 1646/1648 cm−1 for Ca 2+ and apo-TR2C). This renders the amide I band for the intact protein very broad in comparison to that in other proteins and is indicative of a distribution of α-helices with slightly different hydrogen bonding patterns.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Molecular and cellular biochemistry 149-150 (1995), S. 3-15 
    ISSN: 1573-4919
    Keywords: calmodulin ; calcium NMR studies ; methionine protein-protein interaction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Abstract The calcium regulatory protein calmodulin (CaM) plays a role as an on-off switch in the activation of many enzymes and proteins. CaM has a dumbbell shaped structure with two folded domains, which are connected by a flexible linker in solution. The calmodulin-binding domains of the target proteins are contained in 20 residue long amino acid sequences, that share no obvious amino acid sequence homology. In this contribution, we discuss the features of CaM, which allow it to be rather promiscous, and bind effectively to all these distinct domains. In particular, we describe the role of the methionine-rich hydrophobic surfaces of the protein in providing a malleable and sticky surface for binding many hydrophobic peptides. The enzyme activation properties of various Met→Leu mutants of CaM are discussed. In addition, the role of the flexible linker region that connects the two domains is also analyzed. Finally, we describe various NMR and spectroscopic experiments that aid in determining the CaM-bound structures of synthetic peptides containing various CaM-binding domains. All structures analyzed to date are α-helical when bound to CaM, and they interact with CaM only through amino acid sidechains. This form of protein-protein interaction is rather unique, and may contribute to CaM's capacity to bind effectively to such a wide range of distinct partners.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Journal of computer aided molecular design 12 (1998), S. 289-299 
    ISSN: 1573-4951
    Keywords: boundary element method ; continuum electrostatics ; solvent-accessible surface ; triangulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract A relatively simple protein solvent-accessible surface triangulation method for continuum electrostatics applications employing the boundary element method is presented. First, the protein is placed onto a three-dimensional lattice with a specified lattice spacing. To each lattice point, a box is assigned. Boxes located in the solvent region and in the interior of the protein are removed from the set. Improper connections between boxes and the possible existence of cavities in the interior of the protein which would destroy the proper connectivity of the triangulated surface are taken care of. The remaining set of boxes define the outer contour of the protein. Each free face exposed to the solvent of the remaining set of boxes is triangulated after the surface defined by the free faces has been smoothed to follow the shape of the macromolecule more accurately. The final step consists of a mapping of triangle vertices onto a set of surface points which define the solvent-accessible surface. Normal vectors at triangle vertices are obtained also from the free faces which define the orientation of the surface. The algorithm was tested for six molecules including four proteins; a dipeptide, a helical peptide consisting of 25 residues, calbindin, lysozyme, calmodulin and cutinase. For each molecule, total areas have been calculated and compared with the result computed from a dotted solvent-accessible surface. Since the boundary element method requires a low number of vertices and triangles to reduce the number of unknowns for reasons of efficiency, the number of triangles should not be too high. Nevertheless, credible results are obtained for the total area with relative errors not exceeding 12% for a large lattice spacing (0.30 nm) while close to zero for a smaller lattice spacing (down to 0.16 nm). The output of the triangulation computer program (written in C++) is rather simple so that it can be easily converted to any format acceptable for any molecular graphics programs.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical chemistry accounts 101 (1999), S. 159-162 
    ISSN: 1432-2234
    Keywords: Keywords:β-Elicitin ; pKa Calculations ; Continuum electrostatics ; boundary element method
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. Elicitins are small proteins that are secreted by plant pathogenic fungi. In this work we have used a computer program that utilizes the boundary element method for heterogeneous dielectrics with ionic strength to calculate the pK a of all titrating groups in the 98-residue protein β-cryptogein. Our results are in reasonable agreement with the experimentally determined pK a values for the Tyr residues in the protein. We find that the functionally important Lys13 residue has a normal pK a of 10.3. Our work also shows that there is no direct correlation between the exposure of an amino acid sidechain and its pK a.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 495-501 
    ISSN: 0887-3585
    Keywords: ab initio calculations ; density functional theory ; semiempirical calculations ; solvent reaction field ; phosphoserine ; phosphothreonine ; phosphotyrosine ; hydrogen bonding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Protein phosphorylation is one of the major signal transduction mechanisms for controlling and regulating intracellular processes. Phosphorylation of specific hydroxylated amino acid side chains (Ser, Thr, Tyr) by protein kinases can activate numerous enzymes; this effect can be reversed by the action of protein phosphatases. Here we report ab initio (HF/6-31G* and Becke3LYP/6-31G*) and semiempirical (PM3) molecular orbital calculations pertinent to the ion pair formation of the phosphorylated amino acids with the basic side chains of Lys and Arg. Methyl-, ethyl-, and phenylphosphate, as well as methylamine and methylguanidinium were used as model compounds for the phosphorylated and basic amino acids, respectively. Phosphorylated amino acids were calculated as mono- and divalent anions. Our results indicate that the PSer/PThr ion pair interaction energies are stronger than those with PTyr. Moreover, the interaction energies with the amino group of Lys are generally more favorable than with the guanidinium group of Arg. The Lys amino groups form stable bifurcated hydrogen bonded structures; while the Arg guanidinium group can form a bidentate hydrogen bonded structure. Reasonable values for the interaction free energies in aqueous solution were obtained for some complexes by the inclusion of a solvent reaction field in the computation (PM3-SM3).
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 450-466 
    ISSN: 0887-3585
    Keywords: lactate dehydrogenase ; Rossmann fold ; cotranslational folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics (MD) simulations of N-terminal peptides from lactate dehydrogenase (LDH) with increasing length and individual secondary structure elements were used to study their stability in relation to folding. Ten simulations of 1-2 ns of different peptides in water starting from the coordinates of the crystal structure were performed. The stability of the peptides was compared qualitatively by analyzing the root mean square deviation (RMSD) from the crystal structure, radius of gyration, secondary and tertiary structure, and solvent accessible surface area. In agreement with earlier MD studies, relatively short (〈 15 amino acids) peptides containing individual secondary structure elements were generally found to be unstable; the hydrophobic α1-helix of the nucleotide binding fold displayed a significantly higher stability, however. Our simulations further showed that the first βαβ supersecondary unit of the characteristic dinucleotide binding fold (Rossmann fold) of LDH is somewhat more stable than other units of similar length and that the α2-helix, which unfolds by itself, is stabilized by binding to this unit. This finding suggests that the first βαβ unit could function as an N-terminal folding nucleus, upon which the remainder of the polypeptide chain can be assembled. Indeed, simulations with longer units (βαβα and βαβαββ) showed that all structural elements of these units are rather stable. The outcome of our studies is in line with suggestions that folding of the N-terminal portion of LDH in vivo can be a cotranslational process that takes place during the ribosomal peptide synthesis.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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