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  • 1
    ISSN: 1072-8368
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Transcription factor IIIA (TFIIIA) from Xenopus laevis oocytes was the first cellular gene-specific transcription factor identified in eukaryotes1 and is the protein in which the ubiquitous zinc finger motif was first described2. TFIIIA contains nine zinc fingers2'3, binds to the internal control ...
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  • 2
    ISSN: 1072-8368
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] The S100 calcium-binding proteins are implicated as effectors in calcium-mediated signal transduction pathways. The three-dimensional structure of the S100 protein calcyclin has been determined in solution in the apo state by NMR spectroscopy and a computational strategy that incorporates a ...
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  • 3
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The HMG domain of mouse LEF-1, corresponding to residues 296-380 of the full-length protein plus an initiator methion-ine residue, was complexed with a 15-base-pair oligonucleotide duplex containing the optimal binding site from the TCR-a gene enhancer (Fig. 1). Structures were ...
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  • 4
    ISSN: 1432-2234
    Keywords: Key words: Solvation ; Electrostatics ; Generalised Born theory ; Salt effects ; Continuum solvent
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. The Poisson–Boltzmann (PB) continuum solvent model shows considerable promise in providing a description of electrostatic solvation effects in biomolecules, but it can be computationally expensive to obtain converged results for large systems. Here we examine the performance of a pairwise generalized Born approximation (GB) method on multiple conformations of a small peptide, three proteins (protein A, myoglobin, and rusticyanin) and four RNA and DNA duplexes and hairpins containing 20–24 nucleotides. Charge and dielectric radii models were adapted from the CHARMM and Amber force fields. Finite difference PB calculations were carried out with the Delphi and PEP programs, and for several examples the matrix of all pairwise interaction energies was determined. In general, this parameterization of the GB model does an excellent job of reproducing the PB solvation energies for small molecules and for groups near the surface of larger molecules. There is a systematic tendency for this GB model to overestimate the effects of solvent screening (compared to PB) for pairs of buried atoms, but individual errors tend to cancel, and a good overall account of conformational energetics is obtained. A simple extension to the GB model to account for salt effects (in the linearized Debye–Hückel approximation) is proposed that does a good job of reproducing the salt dependence of the PB calculations. In many cases, it should be possible to replace PB calculations with much simpler GB models, but care needs to be taken for systems with extensive burial of charges or dipoles.
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomolecular NMR 6 (1995), S. 341-346 
    ISSN: 1573-5001
    Keywords: Chemical shifts ; Ring currents
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary Density functional chemical shielding calculations are reported for methane molecules placed in a variety of positions near aromatic rings of the type found in proteins and nucleic acids. The results are compared to empirical formulas that relate these intermolecular shielding effects to magnetic anisotropy (‘ring-current’) effects and to electrostatic polarization of the C−H bonds. Good agreement is found between the empirical formulas and the quantum chemistry results, allowing a reassessment of the ring-current intensity factors for aromatic amino acids and nucleic acid bases. Electrostatic interactions contribute significantly to the computed chemical shift dispersion. Prospects for using this information in the analysis of chemical shifts in proteins and nucleic acids are discussed.
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  • 6
    ISSN: 1573-5001
    Keywords: conformation filter ; distance geometry ; parallel computing ; systematic search
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Two complementary approaches for systematic search in torsion angle space are described for the generation of all conformations of polypeptides which satisfy experimental NMR restraints, hard-sphere van der Waals radii, and rigid covalent geometry. The first procedure is based on a recursive, tree search algorithm for the examination of linear chains of torsion angles, and uses a novel treatment to propagate the search results to neighboring regions so that the structural consequences of the restraints are fully realized. The second procedure is based on a binary combination of torsion vector spaces for connected submolecules, and produces intermediate results in Cartesian space for a more robust restraint analysis. Restraints for NMR applications include bounds on torsion angles and internuclear distances, including relational and degenerate restraints involving equivalent and nonstereoassigned protons. To illustrate these methods, conformation search results are given for the tetrapeptide APGA restrained to an idealized β-turn conformation, an alanine octapeptide restrained to a right-handed helical conformation, and the structured region of the peptide SYPFDV.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomolecular NMR 15 (1999), S. 95-102 
    ISSN: 1573-5001
    Keywords: bond lengths ; dipolar coupling ; peptides ; quantum chemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Ab initio MP2 and density functional quantum chemistry calculations are used to explore geometries and vibrational properties of N-methylacetamide and of the alanine dipeptide with backbone angles characteristic of helix and sheet regions in proteins. The results are used to explore one-bond direct dipolar couplings for the N–H, Cα–Hα, C′–N, and Cα–C′ bonds, as well as for the two-bond C′–H interaction. Vibrational averaging affects these dipolar couplings, and these effects can be expressed as effective bond lengths that are 0.5–3% larger than the true bond lengths; bending and torsion vibrations have a bigger influence on the effective coupling than do stretching vibrations. Because of zero-point motion, these effects are important even at low temperature. Hydrogen bonding interactions at the amide group also increase the N-H effective bond length. Although vibrational contributions to effective bond lengths are small, they can have a significant influence on the extraction of order parameters from relaxation data, and a knowledge of relative bond lengths is needed when several types of dipolar couplings are to be simultaneously used for refinement. The present computational results are compared to both solid- and liquid-state NMR experiments. The analysis suggests that secondary structural elements in many proteins may be more rigid than is commonly thought.
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  • 8
    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.
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  • 9
    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.
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