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  • 1995-1999  (1,831)
  • 1995  (1,831)
  • Biochemistry and Biotechnology  (1,318)
  • Computational Chemistry and Molecular Modeling  (513)
  • Nuclear reactions
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Years
  • 1995-1999  (1,831)
Year
  • 101
    ISSN: 0887-3585
    Keywords: overproduction ; crystallography ; X-prolyl dipeptidyl aminopeptidase ; PepX ; Lactococcus lactis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The X-prolyl dipeptidyl aminopeptidase PepX, a serine peptidase isolated originally from Lactococcus lactis subsp lactis NCDO 763, was cloned and overproduced in Escherichia coli. The enzyme was isolated in its active form in two purification steps. Crystals of PepX were grown by the hanging drop vapor diffusion method using polyethyleneglycol 4000 as precipitant at pH 5.0. The crystals are orthorhombic with cell dimensions a = 92.8 Å, b = 102.6 Å, and c = 101.6 Å, space group P21212, and probably contain one monomer of 87.5 kDa in the asymmetric unit. The crystals, very stable under X-rays, diffract to at least 2.2 Å and are suitable for high-resolution structural analysis. © 1995 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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  • 102
    ISSN: 0887-3585
    Keywords: electrostatic calculations ; DelPhi ; GRID ; structure-based drug design ; aromatic inhibitors ; influenza virus neuraminidase ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Neuraminidase (NA) is one of the two major surface antigens of influenza virus. It plays an indispensable role in the release and spread of progeny virus particles during infection. NA inhibitors reduce virus infection in animals. To improve the clinical efficacy of NA inhibitors, we have begun the design of non-carbohydrate inhibitors based on the active site structure of NA. The approach is an iterative process of ligand modeling and electrostatic calculations followed by chemical synthesis of compounds, biological testing, and NA-inhibitor complex structure determination by X-ray crystallography. A strategy has been developed to calculate Ki for newly designed inhibitors. The calculations using the DelPhi program were performed for carbohydrate inhibitors and three preliminary benzoic acid inhibitors of neuraminidase (BANA) that have been synthesized and shown to bind to the active site of NA in the crystal structure. The calculated Kis of these inhibitors have an enlightening agreement with their in vitro biological activities. This demonstrates that the calculations produce informative results on the affinity of modeled inhibitors. GRID maps were also calculated and several pockets were identified for accepting possible new ligands. The calculated Kis for newly designed ligands suggest that these potential compounds will have high inhibitory activities. © 1995 Wiley-Liss, Inc.
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  • 103
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 23 (1995), S. 285-289 
    ISSN: 0887-3585
    Keywords: immunoglobulin ; IgG ; intact antibody ; crystallization ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Attempts were made to crystallize four monoclonal antibodies, one IgG2ak and three IgG1k. Using a PEG 3350 screen combined with detergents, and developed from our experiments with an IgG2ak antibody specific for canine lymphoma cells,1,2 crystals have now been obtained of two of these four immunoglobulins, an antiphenytoin and an antiphenobarbital antibody. A complex between the antiphenobarbital antibody and its drug antigen crystallized as well. The antibody for phenytoin has, to this point, produced only clustered microcrystals, marginally suitable for X-ray analysis. Single crystals of the IgG1k antibody against phenobarbital, however, were characterized by X-ray diffraction to be primitive monoclinic, with unit cell dimensions a = 67 Å, b = 193 Å, c = 74 Å, and β = 110°. These crystals have an entire IgG1k molecule as the asymmetric unit and they diffract to at least 3.2 Å resolution. © 1995 Wiley-Liss, Inc.
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  • 104
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 23 (1995) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 105
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 23 (1995), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 106
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 23 (1995), S. ii 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 107
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 23 (1995), S. 290-293 
    ISSN: 0887-3585
    Keywords: CytB ; insecticide ; cytolytic ; purification ; crystals ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: CytB, a membrane pore-forming toxin from Bacillus thuringiensis subspecies kyushuensis, is specifically toxic to dipteran insect larvae but broadly cytolytic in vitro. It has been purified in the protoxin form from a recombinant Escherichia coli source and crystals have been obtained which diffract X-rays to at least 2.6 Å resolution. The tendency for CytB to aggregate in solution was overcome by including 50 mM of urea or 8 mM of ethanolamine during crystallization. Mutants designed to add or subtract single cysteine residues for the purpose of heavy atom derivative preparation were similarly purified and crystallized. The crystals are hexagonal bipyramids. They belong to space group P6122 (or P6522) with lattice constants a = b = 67.34 Å, c = 170.96 Å, and contain one molecule of the CytB protoxin (MW 29235) per asymmetric unit and 27% solvent by volume. © 1995 Wiley-Liss, Inc.
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  • 108
    ISSN: 0887-3585
    Keywords: carboxylate ; magnesium ; hydration ; ligand ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The first coordination shell of an Mg(II) ion in a model protein environment is studied. Complexes containing a model carboxylate, an Mg(II) ion, various ligands (NH3, H2S, imidazole, and formaldehyde) and water of hydration about the divalent metal ion were geometry optimized. We find that for complexes with the same coordination number, the unidentate carboxylate-Mg(II) ion is greater than 10 kcal mol-1 more stable than the bidentate orientation. Imidazole was found to be the most stable ligand, followed in order by NH3 formaldehyde, H2O, and H2S. © 1995 Wiley-Liss, Inc.
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  • 109
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 21 (1995), S. 237-243 
    ISSN: 0887-3585
    Keywords: domain motions ; crystal packing effects ; protein dynamics ; induced-fit ; enzyme dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics trajectories were calculated separately for each of the two molecules in the asymmetric unit of the crystal structure of the hemoprotein domain of cytochrome P450BM-3. Each simulation was 200 ps in length and included a 10 Å layer of explicit solvent. The simulated time-average structure of each P450BM-3 molecule is closer to its crystal structure than the two molecular dynamics time-averaged structures are to each other. In the crystal structure, molecule 2 has a more accessible substrate binding pocket than molecule 1, and this difference is maintained throughout the simulations presented here. In particular, the substrate docking regions of molecule 1 and molecule 2 diverge in the solution state simulations. The mouth of the substrate binding pocket is significantly more mobile in the simulation of molecule 2 than in the simulation of molecule 1. For molecule 1, the width of the mouth is only slightly larger than its X-ray value of 8.7 Å and undergoes fluctuations of about 1 Å. However, in molecule 2, the mouth of the substrate binding pocket is dramatically more open in the time-average molecular dynamics structure (14.7 Å) than in the X-ray structure (10.9 Å). Furthermore, this region of the protein undergoes large amplitude motions during the trajectory that are not seen in the trajectory of molecule 1, repeatedly opening and closing up to 7 Å. Presumably, the binding of different substrates will induce the mouth region to adopt different conformations from within the wide range of structures that are accessible. © 1995 Wiley-Liss, Inc.
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  • 110
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 21 (1995) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 111
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 21 (1995), S. 261-264 
    ISSN: 0887-3585
    Keywords: lysyl-tRNA synthetase (Thermus thermophilus) ; tRNAlys ; crystallization ; X-ray structure ; aminoacyl-tRNA synthetase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Lysyl-tRNA synthetase from Thermus thermophilus has been cocrystallized with either its cognate tRNAlYS or Escherichia coli tRNAlys using ammonium sulfate as precipitant. The crystals grow from solutions containing a 1:2.5 stoichiometry of synthetase dimer to tRNA in 18-22% ammonium sulfate in 50 mM Tris-maleate buffer at pH 7.5. Both complexes form square prismatic, tetragonal crystals with very similar unit cell parameters (a = b = 233 Å, c = 119 Å) and diffract to at least 2.7 Å resolution. However the homocomplex is of space group P4212 and the heterocomplex of space group I422. © 1995 Wiley-Liss, Inc.
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  • 112
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 21 (1995), S. 265-267 
    ISSN: 0887-3585
    Keywords: T = 3 plant virus ; cucumovirus ; protein crystallization ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Tomato aspermy virus (TAV) is a member of the T = 3 cucumovirus group, and the chrysanthemum strain (C-TAV) has been crystallized in a form suitable for X-ray structural analysis. The crystals, which grow in 14-17% ethanol at pH 8.5, are of orthorhombic space group I222 with unit cell dimensions of a = 295.1 Å, b = 320.5 Å, and c = 383.6 Å. There are two T = 3 virus particles in the unit cell, which means that they must be centered at 0,0,0 and 1/2, 1/2, 1/2 with icosahedral 222 symmetry elements coincident with crystallographic symmetry operators. The asymmetric unit of the crystals, therefore, contains one quarter of a virus particle, or 45 capsid subunits. Native diffraction data to 4 Å resolution have been collected using synchrotron radiation, though data appear to be present beyond that resolution. © 1995 Wiley-Liss, Inc.
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  • 113
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 21 (1995), S. 268-271 
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; homeodomain ; transcription factor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Embryonic development in metazoa, to a significant extent, is directed by genes which contain a conserved sequence motif named the homeobox. This sequence encodes a polypeptide called the homeodomain which has sequence specific DNA-binding activity. We report the purification, crystallization, and preliminary diffraction analysis of the Drosophila Even-skipped homeodomain (Eve HD) bound to two different oligonucleotides. Crystals of Eve HD complexed with an AT-rich sequence belong to space group P21, a = 34.06, b = 61.61, c = 39.99 Å, b=90.0°. These crystals diffract to at least 2.0 Å and both native and derivative data sets have been collected. Crystals of Eve HD complexed with a GC-rich sequence belong to space group P63, a = b = 124.52, c = 66.78 Å and diffract to 3.5 Å resolution. A native data set has been collected. © 1995 Wiley-Liss, Inc.
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  • 114
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 21 (1995), S. 307-318 
    ISSN: 0887-3585
    Keywords: Lactobacillus bulgaricus ; D-2-hydroxy acid dehydrogenase ; formate dehydrogenase ; structure prediction ; L-lactate dehydrogenase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A three-dimensional structure of the NAD-dependent D-lactate dehydrogenase of Lactobacillus bulgaricus is modeled using the structure of the formate dehydrogenase of Pseudomonas sp. as template. Both sequences share only 22% of identical residues. Regions for knowledge-based modeling are defined from the structurally conserved regions predicted by multiple alignment of a set of related protein sequences with low homology. The model of the D-LDH subunit shows, as for the formate dehydrogenase, an α/β structure, with a catalytic domain and a coenzyme binding domain. It points out the catalytic histidine (His-296) and supports the hypothetical catalytic mechanism. It also suggests that the other residues involved in the active site are Arg-235, possibly involved in the binding of the carboxyl group of the pyruvate, and Phe-299, a candidate for stabilizing the methyl group of the substrate. © 1995 Wiley-Liss, Inc.
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  • 115
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 21 (1995), S. 282-302 
    ISSN: 0887-3585
    Keywords: molecular dynamics ; configurational sampling ; glycine ; alanine ; valine and threonine dipeptides ; isobutyryl-(Ala)3-NH-methyl ; oligoalanine ; unfolding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Previous experience with the Langevin/implicit-Euler scheme for dynamics (“LI”) on model systems (butane, water) has shown that LI is numerically stable for timesteps in the 5-20 fs range but quenches high-frequency modes. To explore applications to polypeptides, we apply LI to model systems (several dipeptides, a tetrapeptide, and a 13-residue oligoalanine) and also develop a new dynamics driver approach (“DA”). The DA scheme, based on LI, addresses the important issue of proper sampling, which is unlikely to be solved by small-time step integration methods or implicit methods with intrinsic damping at room temperature, such as LI. Equilibrium averages, time-dependent molecular properties, and sampling trends at room temperature are reported for both LI and DA dynamics simulations, which are then compared to those generated by a standard explicit discretization of the Langevin equation with a 1 fs timestep. We find that LI's quenching effects are severe on both the fast and slow (due to vibrational coupling) frequency modes of all-atom polypeptides and lead to more restricted dynamics at moderate timesteps (40 fs). The DA approach empirically counteracts these damping effects by adding random atomic perturbations to the coordinates at each step (before the minimization of a dynamics function). By restricting the energetic fluctuations and controlling the kinetic energy, we are able with a 60 fs timestep to generate continuous trajectories that sample more of the relevant conformational space and also reproduce reasonably Boltzmann statistics. Although the timescale for transition may be accelerated by the DA approach, the transitional. information obtained for the alanine dipeptide and the tetrapeptide is consistent with that obtained by several other theoretical approaches that focus specifically on the determination of pathways. While the trajectory for oligoalanine by the explicit scheme over the nanosecond timeframe remains in the vicinity of the full αR-helix starting structure, and a high-temperature (6000°K) MD trajectory departs slowly from the a helical structure, the DA-generated trajectory for the same CPU time exhibits unfolding and refolding and reveals a range of conformations with an intermediate helix content. Significantly, this range of states is more consistent with spectroscopic experiments on small peptides, as well as the cooperative two-state model for helix-coil transition. The good, near-Boltzmann statistics reported for the smaller systems above, in combination with the interesting oligoalanine results, suggest that DA is a promising tool for efficiently exploring conformational spaces of biomolecules and exploring folding/unfolding processes of polypeptides. © 1995 Wiley-Liss, Inc.
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  • 116
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 299-310 
    ISSN: 0887-3585
    Keywords: prediction contest ; beta sandwich ; protein sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A secondary structure has been predicted for the protein kinase C2 regulatory domain found in homologous form in synaptotagmin, some phospholipases, and some GTP activated proteins. The proposed structure is built from seven consecutive beta strands followed by a terminal alpha helix. Considerations of overall surface exposure of individual secondary structural elements suggest that these are packed into a 2-sheet beta sandwich structure, with one of only three of the many possible folds being preferred. © 1995 Wiley-Liss, Inc.
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  • 117
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 22 (1995), S. 311-321 
    ISSN: 0887-3585
    Keywords: myoglobin ; X-ray crystallography ; molecular dynamics ; conformation analysis ; sampling ; configuration space ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The singular value decomposition (SVD) provides a method for decomposing a molecular dynamics trajectory into fundamental modes of atomic motion. The right singular vectors are projections of the protein conformations onto these modes showing the protein motion in a generalized low-dimensional basis. Statistical analysis of the right singular vectors can be used to classify discrete configurational substates in the protein. The configuration space portraits formed from the right singular vectors can also be used to visualize complex high-dimensional motion and to examine the extent of configuration space sampling by the simulation. © 1995 Wiley-Liss, Inc.
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  • 118
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 23 (1995), S. 196-203 
    ISSN: 0887-3585
    Keywords: peptide folding ; NMR ; CD ; 310-helix ; gp120 ; CD4 binding domain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A close association between the HIV surface protein gp120 and the CD4 T cell receptor initiates the viral multiplication cycle. A 15 amino acid peptide (LAV) within the CD4 binding domain of gp 120 has been shown to retain receptor binding ability. The structural behavior of the LAV peptide has been studied by CD and NMR methods in aqueous solution and upon addition of trifluoroethanol (TFE) to emulate the relatively apolar conditions at the membrane bound receptor. Previous work has shown that the LAV peptide folds into a β-pleated structure in more polar buffer/TFE mixtures, while a concerted structural change can be observed at a concentration of 60% TFE (v/v). This abrupt, cooperative refolding from a regular β-sheet to a helical secondary structure is known as “switch” behavior. Former CD experiments with LAV sequence variants have supported the assumption that four amino acids at the N-terminus (LPCR) are indispensable for the “switch.” The tetrad has a strong β-turn forming potential. The suggestion has been formulated that the tetrad can act as a nucleation site governing the refolding. The present NMR study of the LAV peptide in TFE gives evidence for a 310-helix suggesting that the tetrad adopts a type III β-turn and promotes the formation of a similar bend in the next overlapping tetrad until the sequence is restructured into a 310-helix at a critical polarity favoring intrachain hydrogen bonds. © 1995 Wiley-Liss, Inc.
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  • 119
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 204-217 
    ISSN: 0887-3585
    Keywords: α-helix ; β-helix ; β-strand ; oligomerization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Mammalian epidermal keratin molecules adopt rod-shaped conformations that aggregate to form cytoplasmic intermediate filaments. To investigate these keratin conformations and the basis for their patterns of molecular association, graphical methods were developed to relate known amino acid sequences to probable spacial configurations. The results support the predominantly α-helical conformation of keratin chains, interrupted by short non-α-helical linkages. However, it was found that many of the linkages have amino acid sequences typical of β-strand conformations. Space-filling atomic models revealed that the β-strand sequences would permit the formation of 2-chain and 4-chain cylindrical β-helices, fully shielding the hydrophobic amino acid chains that alternate with hydrophilic residues in these sequences. Because of the locations of the β-helical regions in human and mouse stratum corneum keratin chains, only homodimers of the keratins could interact efficiently to form 2-chain and 4-chain β-helices. Tetramers having the directions and degrees of overlap of constituent dimers that have been identified by previous investigators are also predicted from the interactions of β-helical motifs. Heterotetramers formed from dissimilar homodimers could combine, through additional β-helical structures, to form higher oligomers having the dimensions seen in electron microscopic studies. Previous results from chemical crosslinking studies can be interpreted to support the concept of homodimers rather than heterodimers as the basis for keratin filament assembly. © 1995 Wiley-Liss, Inc.
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  • 120
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 218-232 
    ISSN: 0887-3585
    Keywords: protein conformation ; protein stability ; sensitivity analysis ; avian pancreatic polypeptide (APP) ; molecular dynamics simulation ; OPLS/Amber force field ; continuum solvation model ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Computer simulations utilizing a classical force field have been widely used to study biomolecular properties. It is important to identify the key force field parameters or structural groups controlling the molecular properties. In the present paper the sensitivity analysis method is applied to study how various partial charges and solvation parameters affect the equilibrium structure and free energy of avian pancreatic polypeptide (APP). The general shape of APP is characterized by its three principal moments of inertia. A molecular dynamics simulation of APP was carried out with the OPLS/Amber force field and a continuum model of solvation energy. The analysis pinpoints the parameters which have the largest (or smallest) impact on the protein equilibrium structure (i.e., the moments of inertia) or free energy. A display of the protein with its atoms colored according to their sensitivities illustrates the patterns of the interactions responsible for the protein stability. The results suggest that the electrostatic interactions play a more dominant role in protein stability than the part of the solvation effect modeled by the atomic solvation parameters. © 1995 Wiley-Liss, Inc.
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  • 121
    ISSN: 0887-3585
    Keywords: human serum transferring ; iron-binding protein ; electric birefringence ; Kerr effect ; circular dichroism spectroscopy ; protein structure ; secondary structure ; tertiairy structure ; protein dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In order to investigate the secondary, tertiary, and dynamic structure of the iron-free (apo) and iron-saturated (holo) forms of human serum transferrin and its amino (N)-terminal lobe at the physiologically relevant pHs 7.4 and 5.0, we have combined ultraviolet circular dichroism (CD) spectroscopy with transient-electric birefringence (TEB) measurements. No significant changes are found in the protein's secondary structure under the different conditions studied. The tertiary structure as monitored by near-UV CD is affected by iron binding, but does not change upon decrease in pH. In contrast, TEB results indicate dramatic changes in the dynamic structure of transferrin both upon binding of iron and decrease of pH. In apotransferrin freedom of movement is found for the lobes with respect to each other, and for the domains within the lobes. The interlobal flexibility is considerably enhanced at the lower pH. Holotransferrin is found to behave as a rigid molecule. © 1995 Wiley-Liss, Inc.
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  • 122
    ISSN: 0887-3585
    Keywords: Pyrococcus woesei ; pullulanase ; thermostable enzyme ; X-ray diffraction ; crystallization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The thermostable amylopullulanase from Pyrococcus woesei was crystallized. Crystals, suitable for a crystallographic analysis up to a size of 0.6 mm in their longest dimension, have been obtained by the vapor diffusion method in a solution containing polyethyleneglycol 4000 (PEG 4000), isopropanol, and Tris/Cl- buffer pH 7.5. Crystals grown under these conditions form hexagonal rods and diffract to a maximum resolution of 3 Å. The crystals belong to the trigonal lattice type with the spacegroup P3121 or P3221, respectively, have the cell dimensions a = b = 96.8 Å, c = 196.2 Å, α = β = 90°,γ = 120°. The crystals have a theoretical packing density of 2.7 Å3/Da, assuming one molecule with a molecular weight of 88.8 kDa in the asymmetric unit. Furthermore the self-rotation analysis of the dataset revealed only crystallographic symmetries. The merged native data of two crystals resulted in a 88% complete dataset. © 1995 Wiley-Liss, Inc.
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  • 123
    ISSN: 0887-3585
    Keywords: C-type lectin ; crystallization database ; incomplete factoriel experiments ; pancreatic stone protein ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of human lithostathine, a pancreatic glycoprotein which inhibits the growth and nucleation of calcium carbonate crystals, were grown using PEG 4000 as the precipitating agent. The crystals belong to the hexagonal space group P61 (or its enantiomorph P65) and diffract to 1.55 Å resolution. There is one molecule in the asymmetric unit and the crystals have 39% solvent. © 1995 Wiley-Liss, Inc.
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  • 124
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 598-603 
    ISSN: 0887-3585
    Keywords: inosine monophosphate dehydrogenase ; Tritrichomonas foetus ; crystallization ; X-ray diffraction ; purine ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Inosine-5′-monophosphate dehydrogenase (IMPDH) from the protozoan parasite Tritrichomonas foetus has been expressed in E. coli and crystallized. Crystals were grown to 0.1 mm in each dimension in 18 to 72 h using ammonium sulfate and low-molecular-weight polyethylene glycols. The crystals belong to the cubic space group P432 with unit cell edge = 157.25 Å. The enzyme is a homotetramer with each monomer having a molecular weight of 55,534 Da. There is one monomer per asymmetric unit, based on a volume/mass ratio of 2.7 Å3/Da and self-rotation analysis. The crystals are adequately stable to allow a complete data set to be collected from a single crystal. Complete native data sets have been collected to 2.3 Å resolution at 4°C using synchrotron radiation. High-quality complete data extending to 3.0 Å resolution have been collected from crystals of four putative derivatives, and the data appear to be isomorphous with that of the native crystals in each case. Efforts to solve the derivatives for use in MIR phasing are underway. © 1995 Wiley-Liss, Inc.
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  • 125
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 607-609 
    ISSN: 0887-3585
    Keywords: Bacillus subtilis ; ferrochelatase ; X-ray diffraction ; crystallization ; heme synthesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Bacillus subtilis ferrochelatase (EC 4.99.1.1), the final enzyme in protoheme IX biosynthesis, was produced with an inducible T7 RNA polymerase expression system in Escherichia coli and purified from the soluble cell fraction. It was crystallized from polyethylene glycol solution using the microseeding technique. The crystals diffract to a minimum Bragg spacing of 2.1 Å. The space group is P42 with unit cell dimensions a = b = 50.2 Å, c = 120.1 Å. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 613-613 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 127
    ISSN: 0887-3585
    Keywords: immunoglobulin ; κ-chain ; X-ray diffraction ; bacterial cell wall ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Protein L is a multi domain cell wall constituent of certain strains of Peptostreptococcus magnus which binds to the variable domain of immunoglobulin κ-light chains. A single immunoglobulin-binding domain of Mr = 9000 from this protein has been isolated and crystallized. The crystals are of space group P42212, with cell dimensions a = b = 66.9 Å, c = 68.3 Å, and diffract to at least 2.2 Å resolution. The asymmetric unit of the crystal contains two molecules of the protein L domain, related by a noncrystallographic 2-fold axis, as revealed by a self-rotation function calculated with native diffraction data. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 32-37 
    ISSN: 0887-3585
    Keywords: circular dichroism ; parallel β-sheet ; parallel β-helix ; pectate lyase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The pectate lyases, PelC and PelE, have an unusual folding motif, known as a parallel β-helix, in which the polypeptide chain is coiled into a larger helix composed of three parallel β-sheets connected by loops having variable lengths and conformations. Since the regular secondary structure consists almost entirely of parallel β-sheets these proteins provide a unique opportunity to study the effect of parallel β-helical structure on circular dichroism (CD). We report here the CD spectra of PelC and PelE in the presence and absence of Ca2+, derive the parallel β-helical components of the spectra, and compare these results with previous CD studies of parallel β-sheet structure. The shape and intensity of the parallel β-sheet spectrum is distinctive and may be useful in identifying other proteins that contain the parallel β-helical folding motif. © 1995 Wiley-Liss, Inc.
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  • 129
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 38-48 
    ISSN: 0887-3585
    Keywords: difference-distance matrix ; hemoglobin rigid core ; structure search ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A rigid domain, defined here as a tertiary structure common to two or more different protein conformations, can be identified numerically from atomic coordinates by finding sets of residues, one in each conformation, such that the distance between any two residues within the set belonging to one conformation is the same as the distance between the two structurally equivalent residues within the set belonging to any other conformation. The distance between two residues is taken to be the distance between their respective α carbon atoms. With the methods of this paper we have found in the deoxy and oxy conformations of the human hemoglobin α1β1 dimer a rigid domain closely related to that previously identified by Baldwin and Chothia (J. Mol. Biol. 129:175-220,1979). We provide two algorithms, both using the difference-distance matrix, with which to search for rigid domains directly from atomic coordinates. The first finds all rigid domains in a protein but has storage and processing demands that become prohibitively large with increasing protein size. The second, although not necessarily finding every rigid domain, is computationally tractable for proteins of any size. Because of its efficiency we are able to search protein conformations recursively for groups of non-intersecting domains. Different protein conformations, when aligned by superimposing their respective domain structures; can be examined for structural differences in regions complementing a rigid domain. © 1995 Wiley-Liss, Inc.
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  • 130
    ISSN: 0887-3585
    Keywords: BPTI ; structure refinement ; time-averaged NOE restraints ; protein dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structural and dynamic properties of bovine pancreatic trypsin inhibitor (BPTI) in aqueous solution are investigated using two molecular dynamics (MD) simulations: one of 1.4 ns length and one of 0.8 ns length in which atom-atom distance bounds derived from NMR spectroscopy are included in the potential energy function to make the trajectory satisfy these experimental data more closely. The simulated properties of BPTI are compared with crystal and solution structures of BPTI, and found to be in agreement with the available experimental data. The best agreement with experiment was obtained when atom-atom distance restraints were applied in a time-averaged manner in the simulation. The polypeptide segments found to be most flexible in the MD simulations coincide closely with those showing differences between the crystal and solution structures of BPTI. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 63-72 
    ISSN: 0887-3585
    Keywords: enzyme ; structure ; function ; thermostability ; proteolysis ; drug resistance ; β-lactams ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The stability properties of six natural mutants of the TEM-1 β-lactamase have been studied. The glutamate to lysine substitution at positions 104 and 240 stabilize the enzyme. Conversely, the G238S mutant's decreased stability might reflect an altered conformation of the active site and thus be related to the modified substrate profile. The relative stability of the R164S and R164H mutants is explained by the formation of a hydrogen bond between these residues and Asp-179 conferring a somewhat different structure to the omega loop and thus also explaining the extended substrate profile of these mutants. The loss of stability of the R164H mutant with increasing pH values can be explained by the titration of a hydrogen bond between the Nδ of His-164 and the Oδ of Asp-179. The properties of the G238S+E104K double mutant which is the most active against third-generation cephalosporins result from a balance of destabilizing and stabilizing substitutions, and their effects seem to be additive. The behavior of the R164S + E240K mutant might be explained on the basis of a similar compensation phenomenon. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 132-140 
    ISSN: 0887-3585
    Keywords: protein folding ; protein stability ; mutational effects ; φ, ψ distribution ; Ramachandran map ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Changes in amino acid side chains have long been recognized to alterthe range and distribution of φ, ψ angles found in the main chain of polypeptides. Altering the range and distribution of φ, ψ angles also alters the conformational entropy of the flexible denatured state and may thus stabilize or destabilize it relative to the comparatively conformationally rigid native state. A database of 12,320 residues from 61 nonhomologous, high resolution crystal structures was examined to determine the φ, ψ conformational preferences of each of the 20 amino acids. These observed distributions in the native state of proteins are assumed to also reflect the distributions found in the denatured state. The distributionswere used to approximate the energy surface for each residue, allowing the calculation of relative conformational entropies for each residue relative to glycine. In the most extreme case, replacement of glycine by proline, conformational entropy changes will stabilize the native state relative to the denatured state by -0.82 ± 0.08 kcal/mol at 20°C. Surprisingly, alanine is found to be the most ordered residue other than proline. This unexpected result is a result of the high percentage of alanines found in helical conformations. This either indicates that the observed distributions in the native state do not reflect the distributions in the denatured state, or that alanine is much more likely to adopt a helical conformation in the denatured state than residues with longer side chains. Among those residues with φ, ψ angles compatible with helix incorporation the percentage of alanines actually in helices is very similar to other residues. This and the consistent ordering of alanine relative to other residues regardless of secondary structure are evidence that φ, ψ distributions in native states reflect those in the denatured states. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 354-357 
    ISSN: 0887-3585
    Keywords: crystallography ; calcium-binding protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Bipyramidal crystals of the recombinant calmodulin from Trypanosoma brucei rhodesiense were obtained by vapor diffusion against 55% (v/v) 2-methyl-2,4-pentanediol in 0.05 M cacodylate buffer, pH 5.6. When few nucleation events occurred, crystals grew to 0.25 × 0.25 × 1.20 mm. The space group of the crystal is I4122, with unit cell dimensions a = b = 56.88 Å, c = 230.11 Å, α = β = γ = 90°, z = 16. The molecular mass and volume of the unit cell suggest that there is one molecule in the asymmetric unit. The I/σ(I) ratio for data at 3.0 Å resolution was 3.67, indicating that the final structure can be refined at higher resolution. Molecular replacement methods and the PC-refinement technique have not yet yielded the structure under a variety of search conditions. We are currently investigating the multiple isomorphous replacement approach to determine this crystal structure. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 245-258 
    ISSN: 0887-3585
    Keywords: bacterial muramidase ; peptidoglycan ; structure comparison ; sequence motifs ; structure/function relationships ; evolutionary relationships ; X-ray structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The 70-kDa soluble lytic transglycosylase (SLT70) from Escherichia coli is a bacterial exo-muramidase that cleaves the cell wall peptidoglycan, producing 1,6-anhydro-muropeptides. The X-ray structure of SLT70 showed that one of its domains is structurally related to lysozyme, although there is no obvious similarity in amino acid sequence. To relate discrete structural features to differences in reaction mechanism and substrate/product specificity, we compared the threedimensional structure of the catalytic domain of SLT70 with the structures of three typical representatives of the lysozyme superfamily: chicken-type hen egg-white lysozyme, goosetype swan egg-white lysozyme, and phage-type lysozyme from bacteriophage T4. We find a particularly close relationship between the catalytic domain of SLT70 and goose-type lysozyme, with not only a significant similarity in overall structure, but even a weak homology in amino acid sequence. This finding supports the notion that the goose-type lysozyme takes up a central position in the lysozyme superfamily and that it is structurally closest to the lysozyme ancestors. The saccharide-binding groove is the most conserved part in the four structures, but only two residues are absolutely preserved: the “catalytic” glutamic acid and a structurally required glycine. The “catalytic” aspartate is absent in SLT70, a difference that can be related to a different mechanism of cleavage of the β-1,4-glycosidic bond. The unique composition of amino acids at the catalytic site, and the observation of a number of differences in the arrangements of secondary structure elements, define the catalytic domain of SLT70 as a novel class of lysozymes. Its fold is expected to be exemplary for other bacterial and bacteriophage muramidases with lytic transglycosylase activity. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 21 (1995) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 136
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 1-10 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; protein phosphatase ; evolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A bona fide consensus prediction for the secondary and supersecondary structure of the serine-threonine specific protein phosphatases is presented. The prediction includes assignments of active site segments, an internal helix, and a region of possible 310 helical structure. An experimental structure for a member of this family of proteins should appear shortly, allowing this prediction to be evaluated. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 11-21 
    ISSN: 0887-3585
    Keywords: phage display ; protein stability ; genetic selection ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method has been developed to select proteins that are thermodynamically destabilized yet still folded and functional. The DNA encoding the B1 IgG-binding domain from Group G Streptococcus (Strp G) has been fused to gene III of bacteriophage M13. The resulting fusion protein is displayed on the surface of the phage thus enabling the phage to bind to IgG molecules. In addition, these phage exhibit a small plaque phenotype that is reversed by mutations that destabilize the Strp G domain. By selecting phage with large plaque morphology that retain their IgG-binding function, it is possible to identify mutants that are folded but destabilized compared with wild-type Strp G. Such mutants can be divided into three general categories: (1) those that disrupt packing of hydrophobic side chains in the protein interior; (2) those that destabilize secondary structure; and (3) those that alter specific hydrogen bonds involving amino acid side chains. A number of the mutants have been physically characterized by circular dichroism and nuclear magnetic resonance and have been shown to have structures similar to wild-type Strp G but stabilities that were decreased by 2-5 kcal/mol. © 1995 Wiley-Liss, Inc.
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  • 138
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 22-29 
    ISSN: 0887-3585
    Keywords: solvation ; electrostatic interaction ; proton transfer ; ab initio quantum mechanical ; semiempirical quantum mechanical ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The energies of binding of seven ligands by p-hydroxybenzoate hydroxylase (PHBH) were calculated theoretically. Direct enzyme-ligand interaction energies were calculated using the ab initio quantum mechanical model assembly of the active site at the 3-21G level. Solvation energies of the ligands needed in the evaluation of the binding energies were calculated with the semiempirical AM1-SM2 method and the long-range electrostatic interaction energies between the ligands and the protein matrix classically using the static charge distributions of the ligands and the protein. Energies for proton-transfer between the ligands OH or SH substituent at position 4 and the active-site tyrosine within the ab initio model assemblies were calculated and compared to the corresponding pKas in aqueous solution. Excluding 3,4-dihydroxybenzoate, the natural product of PHBH, a linear relationship between the calculated binding energies and the experimental binding free energies was found with a correlation coefficient of 0.90. Contributions of the direct enzyme-ligand interaction energies, solvation energies and the long-range electrostatic interaction energies to the calculated binding energies were analyzed. The proton-transfer energies of the ligands with substituents ortho to the ionized OH were found to be perturbed less in the model calculations than the energies of their meta isomers as deduced from the corresponding pKas. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 30-39 
    ISSN: 0887-3585
    Keywords: protein-protein interaction ; protein-DNA interaction ; microcalorimetry ; heat capacity changes ; entropy ; accessible surface area ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The affinity of two molecules for each other and its temperature dependence are determined by the change in enthalpy, free enthalpy, entropy, and heat capacity upon dissociation. As we know the forces that stabilize-protein-protein or protein-DNA association and the three-dimensional structures of the complex, we can in principle derive values for each one of these parameters. The calculation is done first in gas phase by molecular mechanics, then in solution with the help of hydration parameters calibrated on small molecules. However, estimates of enthalpy and entropy changes in gas phase have excessively large error bars even under the approximation that the components of the complex associate as rigid bodies. No reliable result can be expected at the end. The fit to experimental values derived from binding and calorimetric measurements is poor, except for the dissociation heat capacity. This parameter can be attributed mostly to the hydration step and it correlates with the size of the interface. Many protein-protein complexes have interface areas in the range 1200-2000 Å2 and only small conformation changes, so the rigid body approximation applies. It is less generally valid in protein-DNA complexes, which have interfaces covering 2200-3100 Å2, large dissociation heat capacities, and affect both the conformation and the dynamics of their components. © 1995 Wiley-Liss, Inc.
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  • 140
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 403-414 
    ISSN: 0887-3585
    Keywords: modeling by homology ; protein structure prediction ; loop modeling ; side-chain placement ; Monte Carlo procedure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Five models have been built by the ICM method for the Comparative Modeling section of the Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. The targets have homologous proteins with known three-dimensional structure with sequence identity ranging from 25 to 77%. After alignment of the target sequence with the related three-dimensional structure, the modeling procedure consists of two subproblems: side-chain prediction and loop prediction. The ICM method approaches these problems with the following steps: (1) a starting model is created based on the homologous structure with the conserved portion fixed and the noncon-served portion having standard covalent geometry and free torsion angles; (2) the Biased Probability Monte Carlo (BPMC) procedure is applied to search the subspaces of either all the nonconservative side-chain torsion angles or torsion angles in a loop backbone and surrounding side chains. A special algorithm was designed to generate low-energy loop deformations. The BPMC procedure globally optimizes the energy function consisting of ECEPP/3 and solvation energy terms. Comparison of the predictions with the NMR or crystallographic solutions reveals a high proportion of correctly predicted side chains. The loops were not correctly predicted because imprinted distortions of the backbone increased the energy of the near-native conformation and thus made the solution unrecognizable. Interestingly, the energy terms were found to be reliable and the sampling of conformational space sufficient. The implications of this finding for the strategies of future comparative modeling are discussed. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 431-445 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; secondary structure ; evaluation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The results of a protein structure prediction contest are reviewed. Twelve different groups entered predictions on 14 proteins of known sequence whose structures had been determined but not yet disseminated to the scientific community. Thus, these represent true tests of the current state of structure prediction methodologies. From this work, it is clear that accurate tertiary structure prediction is not yet possible. However, protein fold and motif prediction are possible when the motif is recognizably similar to another known structure. Internal symmetry and the information inherent in an aligned family of homologous sequences facilitate predictive efforts. Novel folds remain a major challenge for prediction efforts. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 446-453 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two bona fide consensus predictions of secondary and tertiary structure in a protein family, made and announced before experimental structures were known, are evaluated in light of the subsequently determined experimental structures. The first, for phospho-β-galactosidase, identified the core strands of an 8-fold α-β barrel, and identified the 8-fold α-β barrel itself, which was found in the subsequently determined experimental structure to be the core folding domain. The second, for synaptotagmin, identified seven out of eight β-strands in the structure correctly, missing only a noncore strand. Three preferred “topologies” were selected from several hundred thousand possible topologies of these seven predicted strands using a rule-based analysis. The subsequently determined experimental structure showed that these seven strands in synaptotagmin adopt one of the three preferred topologies. We were unable, however, to identify the correct topology from among these three topologies. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 100-109 
    ISSN: 0887-3585
    Keywords: protein structure ; RNA structure ; lattice model ; chain connectivity ; self-avoiding ; dynamic programming ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An algorithm based on dynamic programming gives the lattice models having the minimal RMS deviations from the actual folds of protein (RNA, etc.) chains for a given lattice and a given orientation of the macromolecule relative to the lattice. The algorithm is applicable for 3-D lattices of any kind. The accuracy of the lattice approximation increases when the distance between neighbor chain links is not rigidly fixed. Special repulsive potentials facilitate generation of self-avoiding lattice chains. The results of model building show the efficiency and precisionof this proposed general method when compared with others. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 81-99 
    ISSN: 0887-3585
    Keywords: protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We describe LINUS, a hierarchic procedure to predict the fold of a protein from its amino acid sequence alone. The algorithm, which has been implemented in a computer program, was applied to large, overlapping fragments from a diverse test set of 7 X-ray-elucidated proteins, with encouraging results. For all proteins but one, the overall fragment topology is well predicted, including both secondary and supersecondary structure. The algorithm was also applied to a molecule of unknown conformation, groES, inwhich X-ray structure determination is presently ongoing. LINUS is an acronym for Local Independently Nucleated Units of Structure. The procedure ascends the folding hierarchy in discrete stages, with concomitant accretion of structure at each step. The chain is represented by simplified geometry and folds under the influence of a primitive energy function. The only accurately described energetic quantity in this work is hard sphere repulsion-the principal forceinvolved in organizing protein conformation [Richards, F. M. Ann. Rev. Biophys. Bioeng. 6:151-176, 1977]. Among other applications, the method is a natural tool for use in the human genome initiative. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 22 (1995), S. 110-118 
    ISSN: 0887-3585
    Keywords: protein folding ; guanidine hydrochloride denaturation ; molten globule ; folding/unfolding kinetics ; proline isomerization ; slow-folding forms ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The TEM-1 β-lactamase is a globular protein containing 12 proline residues. The folding mechanism of this enzyme was investigated by kinetic and equilibrium experiments with the help of fluorescence spectroscopy and circular dichroism. The equilibrium denaturation of the protein induced by guanidine hydrochloride occurs in two discrete steps, indicating the existence of a thermodynamically stable intermediate state. Thisstate is 5.2 ± 0.4 kcal/mol less stable than the native conformation and 5.7 ± 0.2 kcal/mol more stable than the fully denaturedprotein. This intermediate state exhibits a high content of native secondary structure elements but is devoid of specific tertiary organization; its relation to the “molten globule” is discussed. Refolding kinetic experimentsrevealed the existence of a transient intermediate conformation between thethermodynamically stable intermediate and the native protein. This transient intermediate appears rapidly during the folding reaction. It exhibits a secondary structure content very similar to that of the native protein and has also recovered a significant amount of tertiary organisation. The final refolding step of the TEM-1 β-lactamase, leading to the native enzyme, is dominated by two major slow kinetic phases which probablyreflect a very complex process kinetically limited by proline cis/transisomerization. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 472-490 
    ISSN: 0887-3585
    Keywords: drug design ; FKBP ; FK506 ; immunophilin ; MCSS ; DLD ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An automated method for the dynamic ligand design (DLD) for a binding site of known structure is described. The method can be used for the creation of de novo ligands and for the modification of existing ligands. The binding site is saturated with atoms (sp3 carbon atoms in the present implementation) that form molecules under the influence of a potential function that joins atoms to each other with the correct stereochemistry. The resulting molecules are linked to precomputed functional group minimum energy positions in the binding site. The generalized potential function allows atoms to sample a continuous parameter space that includes the Cartesian coordinates and their occupancy and type, e.g., the method allows change of an sp3 carbon into an sp2 carbon or oxygen. A parameter space formulated in this way can then be sampled and optimized by a variety of methods. In this work, molecules are generated by use of a Monte Carlo simulated annealing algorithm. The DLD method is illustrated by its application to the binding site of FK506 binding protein (FKBP), an immunophilin. De novo ligands are designed and modification of the immunosuppressant drug FK506 are suggested. The results demonstrate that the dynamic ligand design approach can automatically construct ligands which complement both the shape and charge distribution of the binding site. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 161-164 
    ISSN: 0887-3585
    Keywords: homeodomain ; protein-DNA interactions ; X-ray diffraction ; cocrystals ; MATa1 ; MATα2 ; a1 ; α2 ; yeast ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals have been obtained of a ternary complex containing the yeast a1/α2 homeodomain heterodimer bound to a 21-base pair DNA site containing two 5′ overhanging bases at each end. The crystals are grown from cobaltic hexamine and form in space group P61 or P65 with a = b = 133 Å, c = 45.4 Å. Crystals that are flash-frozen at -179°C diffract to 2.7 Å along the c-axis and to 2.4 Å in perpendicular directions. The crystals contain one protein-DNA complex in the crystallographic asymmetric unit. © 1995 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 130-139 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The roles of Ser-235 and helix-8′ (residues 235-242) in the functional binding and turnover of phosphorylated substrates by the α-subunit of the E. coli tryptophan synthase (TSase) α2β2-holoenzyme complex are examined. Previous crystallographic analyses indicated that this region was one of several near the phosphate moiety of the physiological substrate, indole-3-glycerol phosphate (IGP). The peptidyl amido group of Ser-235 was suggested to H-bond to the phosphate group; a helix macrodipole binding role was suggested for helix-8′. The activities and substrate Kms of mutant α-subunits altered in this region by site-specific mutagenesis are reported here. Substitutions at Ser-235 by an acidic (glutamic acid, mutant SE235), basic (lysine, mutant SK235), or a nonpeptidyl amido-containing residue (proline, mutant SP235) exhibit 40- to 180-fold Km increases for IGP and D-glyceraldehyde-3-phosphate; no Km defects for indole were observed. kcat values for SP235, SE235, and SK235 are 100, 70, and 40%, respectively, of the wild-type value. Steric considerations may explain the results with the SE235 and SK235 mutant α-subunits; however, the SP235 results are consistent with the suggested phosphate binding role for the Ser-235 peptidyl amide group during catalysis. A helix-8′ dipole role was explored following proline substitutions separately at the first six (of eight) residues. Proline substitutions at positions-1 through -4 in helix-8′ have normal indole Kms and catalytic activities in all four TSase reactions, suggesting no major global structural changes in these proteins. By these criteria, substitutions at positions-5 and -6 lead to significant structural alterations. Km increases for phosphorylated substrates are substantial (up to 40-fold) and are dependent upon the presence of L-serine at the β-subunit active site. In the absence of L-serine, substitution only at the first position results in binding defects; in the presence of L-serine, substitutions at the first, second and third positions show binding defects of decreasing magnitude, sequentially. Substitutions at the fourth and fifth position have no effect on substrate binding. It is suggested that during catalysis a helix dipole effect on binding may be exerted but only via inter-subunit-induced conformational changes due to ligand (L-serine) binding to the β-subunit. © 1995 Wiley-Liss, Inc.
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  • 149
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    Proteins: Structure, Function, and Genetics 21 (1995) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
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  • 150
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 149-160 
    ISSN: 0887-3585
    Keywords: CTD structure ; peptide conformation by NMR ; transcription ; β-turns ; tandem repeats ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The conformation of the repeating heptapeptide unit of the carboxyl-terminal domain of RNA Polymerase II, Y1S2P3T4S5P6S7 has been examined using nuclear magnetic resonance spectroscopy and circular dichroism. Nuclear Overhauser effects and CD spectra for the synthetic 56-residue peptide H2N-(S2P3T4S5P6S7Yl)8-COOH in water indicate that the peptide is largely unordered. A small population of folded molecules is observed to contain β-turns located at Ser2-Pro3-Thr4-Ser5 (SPTS) and Ser5-Pro6-Ser7-Tyr1 (SPSY). CD and NMR results in 90% TFE also indicate an equilibrium population of structures, but the fraction of turns is higher. Similarities of nuclear Overhauser effects in water and in 90% TFE suggest that the structures in TFE are biologically relevant. Based on these observations, the average structure of a single conformer of the heptapeptide repeat in 90% TFE was obtained by a distance geometry-simulated annealing method, using distance restraints extracted from nuclear Overhauser data. NMR spectra of the 56-mer show signals corresponding to only one repeat indicating that each repeat is in an identical environment. Thus it is possible to obtain an average structure of the heptapeptide repeat from NOE data on the 56-mer. Twenty-seven final structures were calculated and the root mean square deviations between the 27 structure and the mean coordinates was 1.52 Å for the backbone and 2.2 Å for all nonhydrogen atoms. The heptapeptide repeat consists of two overlapping β-turns which are potentially stabilized by hydrogen bonds. The hydroxyl side chains of Ser2, Ser5, Thr4, and Ser7 all appear to be equally exposed for potential phosphorylation. The tyrosyl side chain of each repeat is folded inwards to the backbone and can potentially hydrogen bond to the carbonyl oxygen of the tyrosine in the preceding repeat. Iteration of the average structure of the heptapeptide repeat results in a model of the carboxyl-terminal domain with a regular but unusual secondary structure consisting of a series of staggered β-turns. © 1995 Wiley-Liss, Inc.
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  • 151
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 127-129 
    ISSN: 0887-3585
    Keywords: inverse folding ; polar fraction ; potential of mean force ; Boltzmann device ; sequence-structure alignment ; conformation recognition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: On the study of protein inverse folding problem, one goal is to find simple and efficient potential to evaluate the compatibility between structure and a given sequence. We present here a novo empirical mean force potential to address the importance of electrostatic interactions in protein inverse folding study. It is based on protein main chain polar fraction and constructed in a way similar with Sippl's from a database of 64 known independent three-dimensional protein structures. This potential was applied to recognize the protein native conformations among a conformation pool. Calculated results show that this potential is powerful in picking out native conformations, in addition it can also find structure similarity between proteins with low sequence similarity. The success of this new potential clearly shows the importance of electrostatic factors in protein inverse folding studies. © 1995 Wiley-Liss, Inc.
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  • 152
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 73-82 
    ISSN: 0887-3585
    Keywords: protein folding ; protein structure ; genetic algorithms ; Monte Carlo simulations ; ring closure ; dihedral angles ; structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have enhanced genetic algorithms and Monte Carlo methods for simulation of protein folding by introducing “local moves” in dihedral space. A local move consists of changes in backbone dihedral angles in a sequential window while the positions of all atoms outside the window remain unchanged. We find three advantages of local moves: (1) For some energy functions, protein conformations of lower energy are found; (2) these low energy conformations are found in fewer steps; and (3) the simulations are less sensitive to the details of the annealing protocol. To distinguish the effectiveness of local move algorithm from the complexity of the energy function, we have used several different energy functions. These energy functions include the Profile score (Bowie et al., Science 253:164-170, 1991), the knowledge-based energy function used by Bowie and Eisenberg 1994 (Proc. Natl. Acad. Sci. U.S.A. 91:4434-4440, 1994), two energy terms developed as suggested by Sippl and coworkers (Hendlich et al., J. Mol. Biol. 216:167180, 1990), and AMBER (Weiner and Kollman, J. Comp. Chem. 2:287-303, 1981). Besides these energy functions we have used three energy functions that include knowledge of the native structures: the RMSD from the native structure, the distance matrix error, and an energy term based on the distance between different residue types called DBIN. In some of these simulations the main advantage of local moves is the reduced dependence on the details of the annealing schedule. In other simulations, local moves are superior to other algorithms as structures with lower energy are found. © 1995 Wiley-Liss, Inc.
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  • 153
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 83-96 
    ISSN: 0887-3585
    Keywords: ROP protein ; 4-α-helix-bundle ; protein stability ; cavity mutations ; heat capacity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structural and energetic perturbations caused by cavity-creating mutations (Leu-41 → Val and Leu-41 → Ala) in the dimeric 4-α-helical-bundle protein ROP have been characterized by CD spectroscopy and differential scanning calorimetry (DSC). Deconvolution of the CD spectra showed a decrease in α -helicity as a result of the amino acid exchanges that follows qualitatively the overall decrease in conformational stability. Transition enthalpies are sensitive probes of the energetic change associated with point mutations. ΔH0 values at the respective transition temperatures, T1/2 (71.0, 65.3, and 52.9°C at 0.5 mg/ml) decrease from 580 ± 20 to 461 ± 20 kJ/(mol of dimmer) and 335 ± 20 kJ/(mol of dimmer) for wildtype ROP (Steif, C., Weber, P., Hinz, H.-J., Flossdorf, J., Cesareni, G., Kokkinidis, M. Biochemistry 32:3867-3876, 1993), L41V, and L41A, respectively. The conformational stabilities at 25°C expressed by the standard Gibbs energies of denaturation, ΔGD0, are 71.7, 61.1, and 46.1 kJ/(mol of dimmer). The corresponding transition enthalpies have been obtained from extrapolation using the cpD(T)and cpN(T) functions. Their values at 25°C are 176.3, 101.9, and 141.7 kJ/(mol of dimmer) for wild-type ROP, L41V, and L41A, respectively. When the stability perturbation resulting from the cavity creating mutations is referred to the exchange of 1 mol of CH2 group, the average ΔΔGD0 value is -5.0 ± 1 kJ/(mol of CH2 group). This decrease in conformation stability suggests that dimeric ROP exhibits the same susceptibility to Leu → Yal and Leu → Ala exchanges as small monomeric proteins. Careful determinations of the partial specific heat capacities of wild-type and mutated protein solutions suggest that the mutational effects are predominantly manifested in the native rather than the unfolded state. © 1995 Wiley-Liss, Inc.
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  • 154
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 226-236 
    ISSN: 0887-3585
    Keywords: doeking ; Monte Carlo ; LexA repressor ; DNA binding domain ; protein-DNA interaction ; solution structure ; molecular recognition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A structural model for the interaction of the LexA repressor DNA binding domain (DBD) with operator DNA is derived by means of Monte Carlo docking. Protein-DNA complexes were generated by docking the LexA repressor DBD NMR solution structure onto both rigid and bent B-DNA structures while giving energy bonuses for contacts in agreement with experimental data. In the resulting complexes, helix III of the LexA repressor DBD is located in the major groove of the DNA and residues Asn-41, Glu-44, and Glu-45 form specific hydrogen bonds with bases of the CTGT DNA sequence. Ser-39, Ala-42, and Asn-41 are involved in a hydrophobic interaction with the methyl group of the first thymine base. Residues in the loop region connecting the two β-sheet strands are involved in nonspecific contacts near the dyad axis of the operator. The contacts observed in the docked complexes cover the entire consensus CTGT half-site DNA operator, thus explaining the specificity of the LexA repressor for such sequences. In addition, a large number of nonspecific interactions between protein and DNA is observed. The agreement between the derived model for the LexA repressor DBD/DNA complex and experimental biochemical results is discussed. © 1995 Wiley-Liss, Inc.
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  • 155
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    Proteins: Structure, Function, and Genetics 21 (1995), S. 256-260 
    ISSN: 0887-3585
    Keywords: α/β - barrel ; α/β - hyperboloid - 8 ; three-dimensional structure ; local tight packing of hydrophobic groups ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An analysis of possible tight packing of hydrophobic groups simultaneously at the both surfaces of β-hyperboloid-8 was conducted. This analysis shows that the disposition of amino acid side chains at the real β-structure's surface is unique. If we sign the mean distance between adjacent β-strands as “a,” and the mean distance along β-strand between Cα atoms, whose side chains are directed to one side of the β-sheet, as “b,” the ratio b/a = √2 very precisely. This ratio ensures the most efficient packing of side hydrophobic groups at the outer surface of β-hyperboloid-8, forming, at the same time, the second by efficiency packing at its inner surface. © 1995 Wiley-Liss, Inc.
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  • 156
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 295-300 
    ISSN: 0887-3585
    Keywords: automatic prediction of protein secondary structure and solvent accessibility ; neural networks ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Accuracy of predicting protein secondary structure and solvent accessibility from sequence information has been improved significantly by using information contained in multiple sequence alignments as input to a neural 'network system. For the Asilomar meeting, predictions for 13 proteins were generated automatically using the publicly available prediction method PHD. The results confirm the estimate of 72% three-state prediction accuracy. The fairly accurate predictions of secondary structure segments made the tool useful as a starting point for modeling of higher dimensional aspects of protein structure. © 1995 Wiley-Liss, Inc.
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  • 157
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 318-326 
    ISSN: 0887-3585
    Keywords: evaluation ; comparative protein modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin that were calculated by MODELLER, a program for comparative protein modeling by satisfaction of spatial restraints. The models have good stereochemistry and are at least as similar to the crystallographic structures as the closest template structures. The largest errors occur in the regions that were not aligned correctly or where the template structures are not similar to the correct structure. These regions correspond predominantly to exposed loops, insertions of any length, and non-conserved side chains. When a template structure with more than 40% sequence identity to the target protein is available, the model is likely to have about 90% of the mainchain atoms modeled with an rms deviation from the X-ray structure of ≈ 1 Å, in large part because the templates are likely to be that similar to the X-ray structure of the target. This rms deviation is comparable to the overall differences between refined NMR and X-ray crystallography structures of the same protein. © 1995 Wiley-Liss, Inc.
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  • 158
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 327-336 
    ISSN: 0887-3585
    Keywords: correlated structural changes ; eosinophil-derived neurotoxin ; cellular retinoic acid-binding protein ; histidine-containing phosphocarrier protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Comparative models of three proteins have been built using a variety of computational methods, heavily supplemented by visual inspection. We consider the accuracy obtained to be worse than expected. A careful analysis of the models shows that a major reason for the poor results is the interconnectedness of the structural differences between the target proteins and the template structures they were modeled from. Side chain conformations are often determined by details of the structure remote in the sequence, and can be influenced by relatively small main chain changes. Almost all of the regions of substantial main chain conformational change interact with at least one other such region, so that they often cannot be modeled independently. Visual inspection is sometimes effective in correcting errors in sequence alignment and in spotting when an alternative template structure is more appropriate. We expect some improvements in the near future through the development of structure-based sequence alignment tools, side chain interconnectedness rotamer choice algorithms, and a better understanding of the context sensitivity of conformational features. © 1995 Wiley-Liss, Inc.
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  • 159
    ISSN: 0887-3585
    Keywords: molecular model ; comparative model ; homology model ; structure prediction ; calculated structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In spite of the tremendous increase in the rate at which protein structures are being determined, there is still an enormous gap between the numbers of known DNA-derived sequences and the numbers of three-dimensional structures. In order to shed light on the biological functions of the molecules, researchers often resort to comparative molecular modeling. Earlier work has shown that when the sequence alignment is in error, then the comparative model is guaranteed to be wrong. In addition, loops, the sites of insertions and deletions in families of homologous proteins, are exceedingly difficult to model. Thus, many of the current problems in comparative molecular modeling are minor versions of the global protein folding problem. In order to assess objectively the current state of comparative molecular modeling, 13 groups submitted blind predictions of seven different proteins of undisclosed tertiary structure. This assessment shows that where sequence identity between the target and the template structure is high (〉 70%), comparative molecular modeling is highly successful. On the other hand, automated modeling techniques and sophisticated energy minimization methods fail to improve upon the starting structures when the sequence identity is low (∼30%). Based on these results it appears that insertions and deletions are still major problems. Successfully deducing the correct sequence alignment when the local similarity is low is still difficult. We suggest some minimal testing of submitted coordinates that should be required of authors before papers on comparative molecular modeling are accepted for publication in journals. © 1995 Wiley-Liss, Inc.
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  • 160
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 337-355 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; fold recognition ; threading ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: This paper evaluates the results of a protein structure prediction contest. The predictions were made using threading procedures, which employ techniques for aligning sequences with 3D structures to select the correct fold of a given sequence from a set of alternatives. Nine different teams submitted 86 predictions, on a total of 21 target proteins with little or no sequence homology to proteins of known structure. The 3D structures of these proteins were newly determined by experimental methods, but not yet published or otherwise available to the predictors. The predictions, made from the amino acid sequence alone, thus represent a genuine test of the current performance of threading methods. Only a subset of all the predictions is evaluated here. It corresponds to the 44 predictions submitted for the 11 target proteins seen to adopt known folds. The predictions for the remaining 10 proteins were not analyzed, although weak similarities with known folds may also exist in these proteins. We find that threading methods are capable of identifying the correct fold in many cases, but not reliably enough as yet. Every team predicts correctly a different set of targets, with virtually all targets predicted correctly by at least one team. Also, common folds such as TIM barrels are recognized more readily than folds with only a few known examples. However, quite surprisingly, the quality of the sequence-structure alignments, corresponding to correctly recognized folds, is generally very poor, as judged by comparison with the corresponding 3D structure alignments. Thus, threading can presently not be relied upon to derive a detailed 3D model from the amino acid sequence. This raises a very intriguing question: how is fold recognition achieved? Our analysis suggests that it may be achieved because threading procedures maximize hydrophobic interactions in the protein core, and are reasonably good at recognizing local secondary structure. © 1995 Wiley-Liss, Inc.
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  • 161
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 356-369 
    ISSN: 0887-3585
    Keywords: structure prediction ; fold recognition ; protein threading ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present an analysis of 10 blind predictions prepared for a recent conference, “Critical Assessment of Techniques for Protein Structure Prediction.”1 The sequences of these proteins are not detectably similar to those of any protein in the structure database then available, but we attempted, by a threading method, to recognize similarity to known domain folds. Four of the 10 proteins, as we subsequently learned, do indeed show significant similarity to then-known structures. For 2 of these proteins the predictions were accurate, in the sense that a similar structure was at or near the top of the list of threading scores, and the threading alignment agreed well with the corresponding structural alignment. For the best predicted model mean alignment error relative to the optimal structural alignment was 2.7 residues, arising entirely from small “register shifts” of strands or helices. In the analysis we attempt to identify factors responsible for these successes and failures. Since our threading method does not use gap penalties, we may readily distinguish between errors arising from our prior definition of the “cores” of known structures and errors arising from inherent limitations in the threading potential. It would appear from the results that successful substructure recognition depends most critically on accurate definition of the “fold” of a database protein. This definition must correctly delineate substructures that are, and are not, likely to be conserved during protein evolution. © 1995 Wiley-Liss, Inc.
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  • 162
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 370-375 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; prediction experiment ; sequence structure compatibility ; fold recognition ; threading ; urease ; pyruvate phosphate dikinase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A protein fold recognition method was tested by the blind prediction of the structures of a set of proteins. The method evaluates the compatibility of an amino acid sequence with a three-dimensional structure using the four evaluation functions: side-chain packing, solvation, hydrogen-bonding, and local conformation functions. The structures of 14 proteins containing 19 sequences were predicted. The predictions were compared with the experimental structures. The experimental results showed that 9 of the 19 target sequences have known folds or portions of known folds. Among them, the folds of Klebsiella aerogenes urease β subunit (KAUB) and pyruvate phosphate dikinase domain 4 (PPDK4) were successfully recognized; our method predicted that KAUB and PPDK4 would adopt the folds of macromomycin (Ig-fold) and phosphoribosylanthra-nilate isomerase:indoleglycerol-phosphate synthase (TIM barrel), respectively, and the experimental structure revealed that they actually adopt the predicted folds. The predictions for the other targets were not successful, but they often gave secondary structural patterns similar to those of the experimental structures. © 1995 Wiley-Liss, Inc.
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  • 163
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 376-386 
    ISSN: 0887-3585
    Keywords: knowledge based potentials ; molecular modeling ; prediction of protein structure ; protein function ; genome projects ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The prediction experiment reveals that fold recognition has become a powerful tool in structural biology. We applied our fold recognition technique to 13 target sequences. In two cases, replication terminating protein and prosequence of subtilisin, the predicted structures are very similar to the experimentally determined folds. For the first time, in a public blind test, the unknown structures of proteins have been predicted ahead of experiment to an accuracy approaching molecular detail. In two other cases the approximate folds have been predicted correctly. According to the assessors there were 12 recognizable folds among the target proteins. In our postprediction analysis we find that in 7 cases our fold recognition technique is successful. In several of the remaining cases the predicted folds have interesting features in common with the experimental results. We present our procedure, discuss the results, and comment on several fundamental and technical problems encountered in fold recognition. © 1995 Wiley-Liss, Inc.
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  • 164
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 398-402 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; β-strand ; potential of mean force ; Hidden Markov model ; multiple sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Protein structure predictions were submitted for 9 of the target sequences in the competition that ran during 1994. Targets sequences were selected that had no known homology with any sequence of known structure and were members of a reasonably sized family of related but divergent sequences. The objective was either to recognize a compatible fold for the target sequence in the database of known structures or to predict ab initio its rough 3D topology. The main tools used were Hidden Markov models (HMM) for fold recognition, a β- strand pair potential to predict β-sheet topology, and the PHD server for secondary structure prediction. Compatible folds were correctly identified in a number of cases and the β-strand pair potential was shown to be a useful tool for ab initio topology prediction. © 1995 Wiley-Liss, Inc.
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  • 165
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 387-397 
    ISSN: 0887-3585
    Keywords: protein structure prediction ; threading ; protein sequence analysis ; protein folding ; computational methods ; dynamic programming algorithms ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Analysis of the results of the recent protein structure prediction experiment for our method shows that we achieved a high level of success, Of the 18 available prediction targets of known structure, the assessors have identified 11 chains which either entirely match a previously known fold, or which partially match a substantial region of a known fold. Of these 11 chains, we made predictions for 9, and correctly assigned the folds in 5 cases. We have also identified a further 2 chains which also partially match known folds, and both of these were correctly predicted. The success rate for our method under blind testing is therefore 7 out of 11 chains. A further 2 folds could have easily been recognized but failed due to either overzealous filtering of potential matches, or to simple human error on our part. One of the two targets for which we did not submit a prediction, prosubtilisin, would not have been recognized by our usual criteria, but even in this case, it is possible that a correct prediction could have been made by considerin a combination of pairwise energy and solvation energy Z-scores. Inspection of the threading alignments for the (αβ)8 barrels provides clues as to how fold recognition by threading works, in that these folds are recognized by parts rather than as a whole. The prospects for developing sequence threading technology further is discussed. © 1995 Wiley-Liss, Inc.
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  • 166
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    Proteins: Structure, Function, and Genetics 23 (1995), S. 415-421 
    ISSN: 0887-3585
    Keywords: model building by homology ; position specific rotamers ; model evaluation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this study we concentrate on replacing side chains as a subtask of model building by homology. Two problems arise. How to determine potential low energy rotamers? And how to avoid the combinatorial explosion that results from the combination of many residues for which multiple good rotamers are predicted? We attempt to solve these problems by choosing position-specific rather than generalized rotamers and by sorting the residues that have to be modelled as a function of their freedom in rotamer space. The practical advantages of our method are the quality of the models for cases of high backbone similarity, the small amount of human intervention needed, and the fact that the method automatically estimates the reliability with which each residue has been modeled. Other methods described in this issue are probably more suitable if large backbone rearrangements or loop insertions and deletions need to be modeled. © 1995 Wiley-Liss, Inc.
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  • 167
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    Journal of Molecular Recognition 8 (1995), S. 167-168 
    ISSN: 0952-3499
    Keywords: MSH ; melanoma ; receptor ; MC1 ; up-regulation ; down-regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 168
    ISSN: 0952-3499
    Keywords: human immunodeficiency virus (HIV-1) ; envelope glycoprotein gp120 ; V3 loop ; porphyrin binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Several porphyrin derivatives were reported to have anti-HIV-1 activity. Among them, meso-teta(4-carboxyphenyl)porphine (MYCPP) and other carboxyphenyl derivatives were the most potent inhibitors (EC50 〈 0.7 μM). MTCPP bound to the HIV-1 enveloope glycoprotein gp120 and to full-length V3 loop peptides corresponding to several HIV-1 isolates but not to other peptides from gp120+gp41. However, it remained possible that MTCPP bound to HIV-1 envelop glycoprotein gp120 and to full-length V3 loop peptides corresponding to several HIV-1 isolates but not to other peptides from gp120+gp41. However, it remained possible that MTCPP bound to regions on gp120 which cannot be mimicked by peptides. Further characterization of the binding domain for MTCPP is important for understanding the antiviral activity of porphyrins and for the design of anit-HIV-1 drugs interfering with functions of the virus envelope. Results presented here show that: (i) deletion of the V3 loop from the gp120 sequence resulted in drastically diminished MTCPP binding, suggesting that the V3 loop is the dominant if not the only target site on gp120; (ii) this site was only partially mimicked by full-length V3 loop peptides; (iii) MTCPP binding to the gp120 V3 loop elicited allosteric effects resulting in decreased accessibility of the CD4 receptor binding site; (iv) the binding site for MTCPP lies within the central portion of the V3 loop (KSIHIGPGRAFY for the HIV-1 subtype B consensus sequence) and does not involve directly the GPG apex of the loop. These results may help in designing antiviral compounds with improved activity.
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  • 169
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    Journal of Molecular Recognition 8 (1995), S. 3-8 
    ISSN: 0952-3499
    Keywords: enkaphalin ; dynorphin ; naltrexamine ; somatostatin ; substance P ; opioid receptors ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Conformations of regulatory peptides interacting lipid membranes were compared with those of chemically constrained molecules that react-selectively with different receptor classes. Striking similarities in the topochemistry of molecules with similar activity were observed, The membrane-induced topomers were almost congruent with the topomers that are selectively recognized by the same receptors. Finally, the ideas developed in the membrane compartments theory allow a quantitative prediction of receptor preference are compatible with our present knowledge of receptor structure.
    Additional Material: 6 Ill.
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  • 170
    ISSN: 0952-3499
    Keywords: phospholipase A2 ; snake venom ; molecular evolution ; cDNA ; gene ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: As a step towards understanding the structure and function of phospholipases A2 (PLA2s), five cDNAs encoding Trimeresurus flavoviridis venom gland PLA2 isozymes have been sequenced. They revealed that the 5′ and 3′ un translated regions are much more homologous than the protein-coding regions and that mbase substitutions have occurred at similar rates for the three positions of codons in the protein-coding regions. Such novel findings are of great interest from the viewpoint of molecular evolution. To gain a further insight into this evolutional phenomenon, we have isolated and sequenced six T. flavoviridis PLA2 isozyme genes. Each gene consisted of four exons and three introns and encoded protein of 138 amino-acid residues, including the signal sequence of 16 amino-acid residues. The introns were much more homologous than the protein-coding regions of exons except for the signal peptide-coding region of the first exon. The absence of apparent functional role in the introns suggested that the protein-coding regions, expect for the signal peptide-coding domains, have evolved at greater substitution rates than introns. The fact that the numbers of nucleotide substitutions per non-synonymous site are close to or larger than the number of nucleotide substitutions per synonymous site for relevant pairs of genes revealed that Darwinian-type accelerated substitutions have occurred in the protein-coding regions of exons. This is compatible with the presence of PLA2 species with diverse physiological activities in the venom.
    Additional Material: 6 Ill.
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  • 171
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    Journal of Molecular Recognition 8 (1995), S. 327-333 
    ISSN: 0952-3499
    Keywords: citrate synthase ; TCA cycle ; 13C NMR ; allosteric control ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: This study examined the organization of the Krebs tricarboxylic acid (TCA) cycle by metabolic engineering and high-resolution 13C NMR. The oxidation of [1,2,3-13C]propionate to glutamate via the TCA cycle was measured in wild-type (WT) and a citrate synthase mutant (CS-) strain of Escherichia coli transformed with allosteric E. coli citrate synthase (ECCS) or non-allosteric pig citrate synthase (PCS). The 13C fractional enrichment in glutamate C-2, C-3, and C-4 in ECCS and PCS were similar; although quantitative differences in total citrate synthase activity and total C-4 labeling of glutamate were observed in ECCS and PCS. Allosteric ECCS cells contained 10-fold less total enzyme activity than PCS but only 50% less total labeling in glutamate C-4 and equivalent doubling times. The observed spectra were mathematically fitted using an iterative procedure(TCACALC) and yielded an acetate/succinyl-CoA flux ratio of 10 for both ECCS and PCS, a result that is in agreement with the isotopomer analyses of the 13C spectra of cells presented with [3-13C] propionate or [2-13C]propionate. The results are consistent with the presence of an allosteric citrate synthase in ECCS and a non-allosteric citrate synthase in PCS. The former maintains TCA cycle flux via alternative propionate pathways activated by positive allosteric mechanisms and the latter via elevated enzyme levels.
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  • 172
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    Journal of Molecular Recognition 8 (1995), S. 1-2 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 173
    ISSN: 0952-3499
    Keywords: 13C NMR ; 2,2,2, trifluoroethane sulfonyl chloride ; carbonyldiimidazole ; alkyl agarose ; alkyl silica ; immobilized alkylamines ; immobilized alkane thiols ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A major problem in affinity technology is the analysis of the synthesized solid supports, since liquid phase methodology can generally not be applied. Recently we reported a novel reaction sequence for the 2,2,2-trifluoroethanesulfonyl chloride (tresyl chloride) coupling of nucleophiles [Demiroglou et al. (1994) Angew. Chem. Int. Ed. Engl. 33, 120-123] to agarose and concluded that previously proposed structures could not be correct. However it was not possible for us to conclusively define the new reaction products because the agarose derivatives could not be solubilized for customary liquid state 13C NMR analysis. Therefore in this paper solid state 13C CP/MAS NMR spectroscopy is applied for the first time to the polysacharide agarose. Using alkyl agarose derivatives prepared by the carbonyldiimidazol method as control we found that reliable spectra in agreement with the published reaction mechanism could be obtained. The method was then applied to the novel reaction products of the tresyl chloride reaction. From the solid state 13C NMR spectra and other quantitative data it is concluded that a β-sulfonyl carboxylic acid is generated during alkaline hydrolysis of tresyl agarose and that alkyl amines are coupled by a β-sulfonyl amide bond in an elimination-addition reaction in the absence of SO-and SC-scission of the tresyl group. In the case of alkane thiol coupling the absence of SC-scission cannot be demonstrated indicating either a different reaction mechanism or possibly a mixture of reaction products.
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  • 174
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    Journal of Molecular Recognition 8 (1995), S. 63-66 
    ISSN: 0952-3499
    Keywords: MHC ; T-cell receptor ; T-cell activation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Antigen-specific T-cell activation requires the formation of a transient cell-cell conjugate between a T cell and an appropriate antigen presenting cell (APC). Focal aggregation of T-cell receptor (TCR) molecules at the T-cell-APC membrane interface accompanies formation of multiple non-covalent intercellular bridges consisting of TCRs on the T cell and cognate MHC-peptide complexes on the APC. Enhanced adhesiveness and T-cell activation follow the T-cell signalling that results from crosslinking of T-cell receptors (TCR). Models of AT-cell activation propose that the APC and activated T cell separate following a decline in the enhanced adhesiveness. The rate of intercellular TCR-(MHC-peptide) complexes formed during T-cell activation is unknown. Based on the reported CD4-positive T-cell internalization of the peptide moiety of preformed cognate MHC II-peptide complexes, it is proposed here that translocation of the peptide moiety leads to destabilization and decomposition of intercellular trimolecular TCR-(MHC-peptide) complexes in the T-cell-APC interface. This decomposition accompanies or results in the decline in enhanced adhesiveness leading to separation of the APC and activated T cell.
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  • 175
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    Journal of Molecular Recognition 8 (1995), S. 95-99 
    ISSN: 0952-3499
    Keywords: BIAcore ; lectin ; glycoprotein ; kinetics ; surface plasmon resonance ; oligosaccharide ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A simple and rapid analytical method for detecting interaction between loigosaccharides of glycoproteins and different lectins was studies by surface plasmon resonance using a biosensor (BIA coreTM). The interactions of three lectins, Smambucus Sieboldiana agglutinin (SSA), Ricinus communis agglutinin I (RCA I) and Concanavalin A (Con A) for fetuni and digested fetuins wiht glycosidases, asialo-, agalacto-, and aglucosamino-fetuin, were investigated as a model system. These fetuins were immobilized to the matrix of the sensor chip and the lectins were injected into the sensor chip cartridge. The association and dissociation reactions could be monitored as resonance signals in real time. The interactions with lectins significantly changed as the oligosaccharides of fetuins were trimmed. The interactions between fetuin and SSA, asialofetuin and RCAI, and aglucosaminofetuin and Con A show the highest affinity properties, respectively. The association constants of these lectins were estimated to be 1.4 × 107, 1.9 × 108 and 5.3 × 107 (M-1), respectively. These results suggested that the interactions between lectins and glycoproteins could be well defined in real time and kinetically, and that the partial structure of oligosaccharides of glycoproteins can be estimated by determination of the interactions with various lectins after glycosidase digestions using the biosensor.
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  • 176
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    Journal of Molecular Recognition 8 (1995), S. 111-115 
    ISSN: 0952-3499
    Keywords: immunoadsorbent ; stability ; antibodies release ; therapeutic use ; apolipoprotein B ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Various matrices were reacted with four different activation reagents, in order to prepare immuno-adsorbents for the selective removal of low-density lipoproteins from blood plasma of patients affected by hypercholesterolaemia. The resulting immuno-adsorbents were compared to that obtained earlier with cyanogen bromide activation, in terms of coupling yield, adsorption capacity and moreover stability towards the various chemical and biochemical conditions to which they are submitted during their handling. Tresyl chloride-activated Sepharose 6 Fast Flow turns out to afford optimal stability in the whole pH range tested.
    Additional Material: 4 Ill.
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  • 177
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    Journal of Molecular Recognition 8 (1995), S. 139-145 
    ISSN: 0952-3499
    Keywords: lipase ; bio-assay ; biosensor ; hybridisation ; Candida ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Radiolabelled polynucleotide probes have been employed extensively for the detection of complementary nucleic acids by specific hybridization. Within the last few years, various methods have been developed using enzyme-labelled probes to avoid unstable and hazardous isotopes. These assays, based on photometry, fluorescenec, and chemiluminescence, have helped to overcome the use of radioactive probes.To increase the performance of a non-radioactive DNA detection system, the labelling enzyme should remain stable under hybridization conditions which allow the formation of a 15-25 bp long DNA-DNA duplex (Tm = 50-70°C). Therefore, the use of unstable phosphatase and peroxidase conjugates must be avoided due to the composition of the hybridization mixture and the high temperature. By screening various hydrolytic enzymes to fit the special demands, fungal lipases turned out to be the most practical. They offer high sensitivity due to an extremely high turnover number, stability at room temperature for several years, thermostability under working conditions and an easy design of various chromogenic, fluorescent and electrochemical active substrates.Several types of silanized, oxidized and unmodified metal sensors and also standard microtitre plates modified with amino groups were used for the immobilization of oligonuleotides. A sandwich hybridization using the lipase-labelled oligonucleotide probe and a terminal immobilized capture DNA on a microtitre plate or sensor surface combined with a rapid hybridization in solution simplifies and improves the performance of the DNA detection system.
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  • 178
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    Journal of Molecular Recognition 8 (1995), S. 164-166 
    ISSN: 0952-3499
    Keywords: receptors ; insulin ; oncogenes ; phosphorylation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 4 Ill.
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  • 179
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    Journal of Molecular Recognition 8 (1995), S. 162-163 
    ISSN: 0952-3499
    Keywords: estradiol receptor ; transcription ; hormone binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 1 Ill.
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  • 180
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    Journal of Molecular Recognition 8 (1995), S. 132-138 
    ISSN: 0952-3499
    Keywords: ferrocene ; cyclodextrin ; inclusion complex ; biosensor ; glucose oxidase ; biocatalysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Inclusion complexes of 1,1′-dimethylferrocene (DMFe) with α-, 2-hydroxypropyl-β- or γ- cyclodextrins were formed in aqueous systems. For the first time, the interacting DMFe-cyclodextrin systems have been characterized using cyclic voltammetry which enabled the estimation of the complexation order, the formation constant and the diffusivity. Cyclic voltammetry was performed at a stationary electrode, yielding complexation ration of 1:2 for DMFe with α-cyclodextrin and 1:1 with the other two cyclodextrins, as expected from the known cavity dimensions for the cyclodextrins. Formation constants of 4.4 × 104 M-2, 1.2 × 103 M-1 and 2.9 × 102 M-2 were than determined for the complexes between DMFe and the α-, β-, and γ-cyclodextrins, respectively, in relative agreement with the literature. The maximum complexation efficiency, diffusivity and solubility were observed for the DMFe:2-hydroxypropyl-β-cyclodextrin inclusion complex, which, combined with cost factors, resulted in the selection of this form for bioelectrocatalysis studies. The efficiency of the complex as a mediator for the glucose: glucose oxidase system was determined by measuring the rate constant (kS) for reaction of the oxidized DMFe with the reduced enzyme. The kS value decreased from 3.4 × 104 M-1 s-1 to 1.9 × 104 M-1 s-1 with an increase in 2-hydroxypropyl-β-cyclodextrin concentration from 4mM. In this range, the ks value is similar to that of free ferrocene, implying a high efficiency of the DMFe:2-hydroxypropyl-β-cyclodextrin inclusion complex.
    Additional Material: 6 Ill.
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  • 181
    ISSN: 0952-3499
    Keywords: acetylcholine receptor ; phage epitope library ; monoclonal antibodies ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 182
    ISSN: 0952-3499
    Keywords: basic fibroblast growth factor ; phage-epitope library ; monoclonal antibodies ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 183
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    Journal of Molecular Recognition 8 (1995), S. 185-195 
    ISSN: 0952-3499
    Keywords: lipocalin ; protein fold ; structural polarity ; ligand binding ; macromolecular complex ; cell binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The lipocalins, a diverse family of small extracellular ligand proteins, display a remarkable range of different molecular properties. While their binding of small hydrophobic molecules, and to a lesser extent their binding to cell surface receptors, is well known, it is shown here that formation of macromolecular complexes is also a common feature of this family. Analysis of known crystallographic structures reveals that the lipocalins process a conserved common structure: an antiparallel β-barrel with a repeated +1 topology. Comparisons show that within this overall similarity the structure of individual proteins is specifically adapted to bind their particular ligands, forming a binding site from an internal cavity (within the barrel) and/or an external loop scaffold, which gives rise to different binding modes that reflects the need to accommodate ligands of different shape, size, and chemical structure. The architecture of the lipocalin fold suggests that the both the ends and sides of this barrel are topologically distinct, differences also apparent in analyses of structural and sequence variation within the family. These different can be linked to experimental evidence suggesting a possible functional dichotomy between the two ends of the lipocalin fold. The structurally invariant end of the molecule may be implicated in general binding small ligands and forming macromolecular complexes via an exposed binding surface.
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  • 184
    ISSN: 0952-3499
    Keywords: cell surface ; molecular pattern ; energy transfer ; fluorescence ; flow cytometry ; transmembrane potential ; intercellular communication ; MHC ; antigen presentation ; intercellular communication ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular recognition processes between cell surface elements are discussed with special reference to cell surface pattern formation of membrane-bound integral proteins. The existence, as detected by flow cytometric resonance energy transfer (Appendix), and significance of cell surface patterns involving the interleukin-2 receptor, the T-cell receptor-CD3 system, the intercellular adhesion molecule ICAM-1, and the major histocompatilibilty complex class I and II molecules in the plasma membrane of lymphocytes are described. The modulation of antigen presentation by transmembrane potential changes is discussed, and a general role of transmembrane potential changes, and therefore of icon channel activities, adduced as one of the major regulatory mechanisms of cell-cell communications. A general role in the mediation and regulation of intercellular interactions is suggested for cell-surface macromolecular patterns. The dynamic pattern of protein and lipid molecules in the plasma membrane is generated by the genetic code, but has a remarkable flexibility and may be one of the major instruments of accomodation and recognition processes at the cellular level.
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  • 185
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    Journal of Molecular Recognition 8 (1995), S. 146-150 
    ISSN: 0952-3499
    Keywords: biosensor ; photostructuring ; glutamine sensor ; electrochemical detection ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: This article details a new type of biosensor for the simultaneous analysis of glucose, glutamate and glutamate and glutamine in complex biological fluids like fermentation broths and blood. Simultaneous analysis was made possible by the application of different enzyme layers onto different electrodes of one photostructurized sensoe. Photostructuring was done by means of a new developed photopolymer. Preparation of the photopolymer and the enzyme layers as well as the characterization of the sensors thus constructed with respect to linearity., response time and sensitivity are described.
    Additional Material: 9 Ill.
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  • 186
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    Journal of Molecular Recognition 8 (1995), S. 151-156 
    ISSN: 0952-3499
    Keywords: cell-free translation ; phase partitioning ; protein synthesis ; dextran-PEG two phase system ; rabbit reticulocyte lysate ; wheat germ extract ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Protein synthesis in an aqueous two-phase system is reported here as a novel type of extractive bioconversion. Translation of BMV RNA was studied using either rabbit reticulocyte lysate or wheat-germ extract in aqueous dextran-PEG systems. Both polymers inhibited protein synthesis and the translation system partitioned into both phases. In the rabbit reticulocyte two-phase system, protein synthesis reached 30% of that in free solution, while in wheat in wheat-germ extract it was 60% of that in free solution. Protein was found mainly in the dextran (lower) phase but its partitioning was related to the polymer concentration, and molecular weight, as well as the ionic strength of the system. Protein synthesis was highly influenced by PEG concentration, potassium chloride concentration, and dextran molecular weight.
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  • 187
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    Journal of Molecular Recognition 8 (1995), S. 161-161 
    ISSN: 0952-3499
    Keywords: IgE antibodies ; multispecificity ; computer-aided molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 188
    ISSN: 0952-3499
    Keywords: ganglioside GM1 ; glycolipid ; oligosaccharide ; NMR ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The solution dynamics of the oligosaccharide moiety of ganglioside GM1 have been determined by use of a combination of 1H rotating frame Overhauser effect measurements and restrained molecular dynamics simulations, It is found that the Galβ1-3 and NeuNAc moieties which are primarily recognized by cholera toxin both exhibit considerable torsional flexibility about their respective glycosidic linkages. A comparison with the bound state conformation of the ganglioside in association with cholera toxin B-pentamer, shows that a low energy conformation of the oligosaccharide, which closely approximates the globel minimum, is selected upon binding.
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  • 189
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    Journal of Molecular Recognition 8 (1995) 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 190
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    Journal of Molecular Recognition 8 (1995), S. 171-177 
    ISSN: 0952-3499
    Keywords: drug allergy ; penicillin allergens ; flucloxacillin ; beta-lactam allergens ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Unlike studies on the antigenicity of penicillins in laboratory animals, limited information is available on the allergenicity of penicillins in man, especially with regard to fine structural allergenic differences between the many different penicillins. Inconsistent with the earlier conclusions of others, our studies suggest that side-chain structures to flucloxacillin-reactive IgE antibodies. Quantitative hapten inhibition studies revealed potent inhibition by flucloxacillin and three structurally related penicillins: oxacillin, cloxacillin and dicloxacillin. Analysis of the results showed that the side-chain group of flucloxacillin, 3-2(-chloro-6-fluorophenyl)-5-methyl-4-isoxazolyl, is recognized by some antibodies and that the 5-methyl-3-phenyl-4-isoxazolyl group, with or without halogen substituents, accounts for the reactivity of other antibodies and for the cross-reactions seen with some other penicillins. Since it is the side-chain group that distinguishes the many different types of penicillin, and since IgE antibodies in many of the allergic reactions recognize the side-chain groups, it is becoming clear that specific assays are required for the detection of IgE antibodies to each of the different penicillins.
    Additional Material: 4 Ill.
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  • 191
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    Journal of Molecular Recognition 8 (1995), S. 179-183 
    ISSN: 0952-3499
    Keywords: uterine oxytocin receptors ; longitudinal muscle membranes ; pregnant rat ; positive cooperativity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Receptors of oxytocin were found to occur in the membrane fraction obtained from longitudinal muscle of pregnant rat uterus. The affinity of the membrane receptor for oxytocin increased through an increase in the association rate and a decrease in the dissociation rate during gestation. The membrane oxytocin receptor concentrations rose almost three-fold from Day 15 to Day 21. A transition of oxytocin receptors from a single class of independent sites to site-site interacted multiple binding sites, which most likely exhibit positive cooperativity during the last seven days of gestation, was observed. These results suggest that changes in the dynamics of uterine oxytocin receptors also play an important role in the onset of labor.
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  • 192
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    Journal of Molecular Recognition 8 (1995), S. 211-236 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 193
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    Journal of Molecular Recognition 8 (1995) 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 194
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    Journal of Molecular Recognition 8 (1995), S. 247-257 
    ISSN: 0952-3499
    Keywords: APP ; heparin binding site ; zinc binding site ; processing of APP ; βA4 amyloid formation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Alzheimer's disease βA4 amyloid precursor protein (APP) has been shown to be involved in a diverse set of biological protein precursor-like proteins (APLP1 and APLP2) belong to a superfamily of proteins that are probably functionally related. In order to characterize the cell adhesion properties of APP the brain specific isoform APP695 was purified and used to assess the binding to herparin, a structural and functional analogue of the glycosaminoglycan heparan sulfate. We show that APP binds in a time dependent and saturable manner to heparin. The salt concentration of 620 mM at which APP elutes from heparin Sepharose is greater than physiological. Tha apparent equilibrium constant for dissociation was determined to be 300 pM for APP binding to heparin Sepharose. A high affinity heparin binding site was identified within a region conversed in rodent and human APP, APLP1 and APLP2. This binding site was located between residues 316-337 of APP695 which is within the carbohydrate domain of APP. We also demonstrate an interaction between this heparin binding site and the zinc(II) binding site which is conserved in all members of the APP superfamily. We show by using an automated surface plasmon resonance biosensor (BIAcore, Pharmacia) that the affinity for heparin is increased two- to four-fold in the presence of micromolar zinc(II). The identification of zinc-enhanced binding of APP to heparin sulfate side chains of proteoglycans offers a molecular link between zinc(II), as a putative environmental toxin for Alzheimer's disease, and aggregation of amyloid βA4 protein.
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  • 195
    ISSN: 0952-3499
    Keywords: Antibodies ; fluorescein ; dynamic ligand stabilization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The ability of antibodies to specifically select and stabilize through binding one or more isomers of highly dynamic ligands remains a relatively unexplored immunochemical problem. The experimental strategy employed in this study was to elicit homogeneous antibodies to polyarmatic fluorescein which exists in one isomeric form. The binding properties of a monoclonal rat antifluorescein antibody specific to a given isomer were quantitatively studied to determine the capacity ot bind dynamic analogues of fluorescein which exists in multiple isomers. To generate monoclonal anti-fluorescein antibodies that reacted with specific dynamia analogues of fluorescein posessing unconjugated aromatic ring systems, immune spleenocytes from Lou/M rats immunized with FITC(I)-KLH were fused with Balb/c SP2/0-Ag14 murine myeloma cells forming rat-mouse hybridomas. Cell line P2A12-1-C8 was selected for further characterization from the original 23 stable rat hybrids, since it produced a monoclonal antibody with a binding affinity 2.0 × 1010/M for fluorescein based on dissociation rate measurements. P2A12-1-C8 exhibited significant reactivity with HPF and phenol red, which are dynamic structural analogues of the homologous florescein ligand. No reactivity was demonstrated with phenolphthalein, which based on relative chemical structures was expected to be more reactive than phenol red. Computer-based molecular modeling and energy minimization studies of fluorescein, HPF, phenol red, and phenolphthalein showed that in terms of the most energetically favotable orientation of the three aromatic rings, phenol red more closely simulated fluorescein than phenolphthalein. The results were analyzed in terms of the mechanisms of dynamic ligand stabilization and binding involving accommodation of specific ligand isomers by energetically permissible conformational states exhibited by an antibody active site. Thus, antibody reactivity of an anti-fluorescein antibody with phenol red and phenolphthalein was dicated more by ligand dynamics and aromatic orientation than by chemical structure similarities.
    Additional Material: 5 Ill.
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  • 196
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    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 8 (1995), S. 279-279 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 197
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    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 8 (1995) 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 198
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    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 8 (1995), S. 281-289 
    ISSN: 0952-3499
    Keywords: S1 nuclease ; immunoaffinity purification ; cysteine 25 ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A simple procedure, involving heat treatment, gel filtration on Sephadex G-100 followed by chromatography on anti-S1 nuclease antibodies bound to Sepharose, was developed for purification of S1 nuclease to homogeneity with an overall yield of 72%. S1 nuclease was rapidly inactivated, at pH 6.0 and 37°C, in presence of o-phthalaldehyde. Kinetic analysis of o-phthalaldehyde mediated inactivation showed that the reaction followed pseudo-first-order kinetics and the loss of enzyme activity was due to the formation of a single isoindole derivative per molecule of the enzyme. Absorbance and fluorescence spectrophotometric data also gave similar results. The isoindole derivative formation, as a result of o-phthalaldehyde treatment is known to occur through crosslinking of the thiol group of cysteine and the ε-amino group of lysine, situated in close proximity in the native enzyme. Since, modification of only available cysteine residue (Cys 25) did not affect the catalytic activity of the enzyme, the o-phthalaldehyde mediated inactivation of S1 nuclease is due to the modification of lysine. Substrates of S1 nuclease, namely ssDNA, RNA and 3′ AMP, could protect the enzyme against o-phthalaldehyde mediated inactivation. Moreover, the modified enzyme (having very little catalytic activity) showed a significant decrease in its ability to bind 5′ AMP, a competitive inhibitor of S1 nuclease, suggesting that the modification has occurred at the substrate binding site. The above results point towards the presence of cysteine 25 in close proximity to the substrate binding site.
    Additional Material: 5 Ill.
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  • 199
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    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 8 (1995), S. 290-303 
    ISSN: 0952-3499
    Keywords: databases ; graph matching ; pharmacophoric patterns ; similarity searching ; substructure searching ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: This paper provides an overview of the research that has been carried out in Sheffield over the last decade into searching techniques for databases of three-dimensional (3D) chemical structures. A 3D structure or query pattern is represented by a labelled graph, in which the nodes and the edges of the graph are used to represent atoms and the associated inter-atomic distances, respectively. The presence of a pharmacophore in each of the structures in a database can then be tested by means of a subgraph isomorphism algorithm, the computational requirements of which are minimized by the use of an initial screening procedure that eliminates the majority of the structures from the subgraph-isomorphism search. Analogous graph-based representation and searching methods can also be used with flexible 3D structures: in this case, the edges of the graphs represent inter-atomic distance ranges and a final conformational search needs to be carried out for those molecules that match the query pharmacophore in the subgraph-isomorphism search. The paper also reviews related work on the automatic identification of pharmacophoric patterns and on 3D similarity searching.
    Additional Material: 6 Ill.
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  • 200
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    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 8 (1995) 
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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