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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 258-270 
    ISSN: 0887-3585
    Keywords: IIAglc ; NMR ; protein phosphorylation ; PTS ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The high-resolution solution structure of the phosphocarrier protein IIAglc from Bacillus subtilis is determined using 3D and 4D heteronuclear NMR methods. B. subtilis IIAglc contains 162 amino acid residues and is one of the larger proteins for which high-resolution solution structure has been determined by NMR methods. The structures have been calculated from a total of 2,232 conformational constraints. Comparison with the X-ray crystal structure indicates that the overall fold is the same in solution and in crystalline environments, although some local structural differences are observed. These occur largely in turns and loops, and mostly correspond to regions with high-temperature factors in the crystal structure. The N-terminus of IIAglc is disordered in solution. The active site is located in a concave region of the protein surface. The histidine, which accepts the phosphoryl group (His 83), interacts with a neighboring histidine (His 68) and is surrounded by hydrophobic residues. Proteins 31:258-270, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 56 (1995), S. 95-102 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present nonlocal density-functional calculations for a model of the [Fe4S4]3+ cluster found in high potential iron proteins, which consists formally of a ferric pair Fe 3+Fe3+ and a mixed-valence pair Fe 2.5+—Fe2.5+. Three Spin Hamiltonian parameters, J (the interlayer Heisenberg interaction), B (a resonance delocalization term) and ΔJ12 (associated with the ferric pair) have been estimated using density-functional energies of a high-spin state as well as two different broken symmetry states. We obtain J=673 cm-1, B=878 cm-1, and Δ J12=160 cm-1. These results are discussed in the light of experimental work on a model compound in the same oxidation state, in which the temperature dependence of the magnetic susceptibility was analyzed with this sort of spin Hamiltonian. Good overall agreement between theory and experiment (J=652 cm-1, B=592 cm-1), and ΔJ12=145 cm-1 is found. In particular, the antiferromagnetic spin coupling constant for the ferric pair exceeds in magnitude all other Heisenberg-type interactions (ΔJ12 〉 0) as expected from previous theoretical and experimental work; this is the first time that the broken symmetry method has been used to analyze a spin Hamiltonian with multiple coupling constants in an Fe4S4 cluster. © 1995 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 33 (1993), S. 1567-1580 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have carried out a nanosecond molecular dynamics simulation of an analogue of the ribonuclease C-peptide in water. The overall conformation has an extended region for the first three amino acids connected to an α-helix for residues 4-13, and this basic structure is preserved throughout the simulation, with helical hydrogen bonds present 87% of the time, on average. The final helical hydrogen bond is spontaneously broken and re-formed several times, providing a detailed picture of such winding/unwinding events. The simulation was used to estimate the effects of internal motion on proton nuclear Overhauser effect spectroscopy (NOESY) intensities for several classes of important cross peaks. Within the helical regions, the effects of internal motion vary only a little from one residue to another for backbone-backbone cross peaks, and the relevant correlation functions reach plateau values within about 50 ps. The spectral simulations show, however, that it may be difficult to establish a close quantitative connection between NOESY cross-peak volumes and measures of helical content. © 1993 John Wiley & Sons, Inc.
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 28 (1989), S. 851-871 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Vibrational normal mode calculations are presented for a DNA hexanucleoside pentaphosphate, d(CpGpCpGpCpG)2, and for its complex with the cationic interclator ethidium. Two intercalation sites are modeled that differ in DNA backbone torsion angles. Normal mode frequencies for the DNA fragment itself are significantly lower than those reported earlier using different force fields, but an analysis of “effective” frequencies suggests that somewhat higher frequencies are more appropriate. Intercalation leads to significant lowering of mobility for the base pairs adjacent to the drug; in this sequence, the ethidium binding affects the guanosine atoms more strongly than the cytosine atoms. Motions of the bases and the intercalator are analyzed in terms of “twist” about the local helix axis and a “tilt” angle relative to this axis, and the results are compared to fluorescence studies of ethidium-DNA complexes.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 31 (1991), S. 1351-1361 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe a 1 ns molecular dynamics simulation of an 18-residue peptide (corresponding to a portion pf the H helix of myoglobin) in water. The initial helical conformation progressively frays to a more disordered structure, with the loss of internal secondary structure generally proceeding from the C-terminus toward the N-terminus. Although a variety of mechanisms are involved in the breaking of helical hydrogen bonds, the formation of transient turn structures, with i → i + 3 hydrogen bonds, and bifurcated hydrogen-bond structures intermediate between α and turn or 310 structures is a common motif. In some cases a single water molecule is inserted into an internal hydrogen bond, but it is also common to have several water molecules involved in transient intermediates. Overall, the results provide new information about the detailed mechanisms by which helices are made and broken in aqueous solution.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 18 (1980), S. 1091-1099 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solutions to some practical problems that arise in multiple scattering calculations on large molecules are discussed. (1) Numerical instabilities near the zero of energy can be removed by rescaling the secular matrix. (2) The calculation of structure factors can be made much more efficient by the application of symmetry projection operators. (3) An energy search procedure is described that ensures that no states are inadvertently neglected. Test calculations incorporating these changes illustrate the improved numerical stability, and show decreases in computation time of 30-60%, when compared to previous codes. The procedures suggested here are applicable to both relativistic and nonrelatitistic calculations.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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