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  • 1985-1989  (1,250)
  • 1965-1969
  • 1988  (1,250)
  • Biochemistry and Biotechnology  (680)
  • Engineering General  (570)
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  • 1985-1989  (1,250)
  • 1965-1969
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  • 1
    Electronic Resource
    Electronic Resource
    Two trifluoperazine-binding sites on calmodulin predicted from comparative molecular modeling with troponin-C (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 1-17 
    Details
    ISSN: 0887-3585
    Keywords: computer modeling ; trifluoperazine ; conformational change ; calcium binding proteins ; hydrophobic binding interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Among the known regulatory proteins that are conformationally sensitive to the binding of calcium ions, calmodulin and troponin-C have the greatest primary sequence homology. This observation has led to the conclusion that the most accurate predicted molecular model of calmodulin would be based on the X-ray crystallographic coordinates of the highly refined structure of turkey skeletal troponin-C. This paper describes the structure of calmodulin built from such a premise. The resulting molecular model was subjected to conjugate gradient energy minimization to remove unacceptable intramolecular non-bonded contacts. In the analysis of the resulting structure, many features of calmodulin, including the detailed conformation of the Ca2+-binding loops, the amino- and carboxy-terminal hydrophobic patches of the Ca2+-bound form, and the several clusters of acidic residues can be reconciled with much of the previously published solution data. Calmodulin in missing the N-terminal helix characteristic of troponin-C. The deletion of three residues from the central helical linker (denoted D/E in troponin-D) shortens the molecule and changes the orientation of the two domains of calmodulin by 60° relative to those in troponin-C. The molecular model has been used to derive two possible binding sites for the antipsychotic drug trifluoperazine, a potent competitive inhibitor of calmodulin activity.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030102
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  • 2
    Electronic Resource
    Electronic Resource
    Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: Application to the DNA binding domain of lac repressor from Escherichia coli (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 209-218 
    Details
    ISSN: 0887-3585
    Keywords: distance-restrained molecular dynamics ; 2D NOE-spectroscopy ; tertiary structure ; solution conformations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The technique of two-dimensional nuclear magnetic resonance (2D-NMR) has recently assumed an active role in obtaining information on structures of polypeptides, small proteins, sugars, and DNA fragments in solution. In order to generate spatial structures from the atom-atom distance information obtained by the NMR method, different procedures have been developed. Here we introduce a combined procedure of distance geometry (DG) and molecular dynamics (MD) calculations for generating 3D structures that are consistent with the NMR data set and have reasonable internal energies. We report the application of the combined procedure on the lac repressor DNA binding domain (headpiece) using a set of 169 NOE and 17 “hydrogen bond” distance constraints. Eight of ten structures generated by the distance geometry algorithm were refined within 10 ps MD simulation time to structures with low internal energies that satisfied the distance constraints.Although the combination of DG and MD was designed to combine the good sampling properties of the DG algorithm with an efficient method of lowering the internal energy of the molecule, we found that the MD algorithm contributes significantly to the sampling as well.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030402
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  • 3
    Electronic Resource
    Electronic Resource
    Vibrational spectroscopy of bacteriorhodopsin mutants: I. Tyrosine-185 protonates and deprotonantes during the photocycle (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 219-229 
    Details
    ISSN: 0887-3585
    Keywords: proton transport ; energy transduction ; purple membrane ; proton wire ; Schiff base counter-ion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The techniques of FTIR difference spectroscopy and site-directed mutagenesis have been combined to investigate the role of individual tyrosine side chains in the proton-pumping mechanism of bacteriorhodopsin (bR). For each of the 11 possible bR mutants containing a single Tyr→Phe substitution, difference spectra have been obtained for the bR→K and bR→M photoreactions. Only the Tyr-185→Phe mutation results in the disappearance of a set of bands that were previously shown to be due to protonation of a tryosinate during the br→K photoreaction [Rothschild et al.: Proceedings of the National Academy of Sciences of the United states of America 83:347, (1986)]. The Tyr-185→Phe mutation also eliminates a set of bands in the bR→M difference spectrum associated with deprotonation of a Tyr; most of these bands (e.g., positive 1272-cm-1 peak) are completely unaffected by the other ten Tyr→Phe mutations. Thus, tyrosinate-185 gains a proton during the bR→K reaction and loses it again when M is formed. Our FTIR spectra also provide evidence that Tyr-185 interacts with the protonated Schiff base linkage of the retinal chromophore, since the negative C=NH+ stretch band shifts from 1640 cm-1 in the wild type to 1636 cm-1 in the Tyr-185→Phe mutant. A model that is consistent with these results is that Tyr-185 is normally ionized and serves as a counter-ion to the protonated Schiff base. The primary photoisomerization of the chromophore translocates the Schiff base away from Tyr-185, which raises the pKa of the latter group and results in its protonation.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030403
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  • 4
    Electronic Resource
    Electronic Resource
    Structural comparison of the prokaryotic ribosomal proteins L7/L12 and L30 (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 243-251 
    Details
    ISSN: 0887-3585
    Keywords: protein evolution ; structural homology ; ribosome structure ; x-ray crystallography ; common motif ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of two prokaryotic ribosomal proteins, the carboxyterminal half of L7/L12 from Escherichia coli (L12CTF) and 1.30 from Bacilus Stearothermophilus display a remarkably similar fold in which alpaha-helices pack onto one side of an antiparallel, three-stranded, beta-pleated sheet. A detailed comparison of the structures by least-squares methods reveals that more than two-thirds of the alpha carbons can be superimposed with a root mean square distance of 2.33 Å. The principal difference is an extra alpha-helix in L12 CTF. The sequences of the proteins display a distinct conservation in regions which are crucial to the common fold, in particular the hydrophobic core. It is proposed that the similarity is a result of divergent evolution.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030405
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  • 5
    Electronic Resource
    Electronic Resource
    The aggregation state of spin-labeled melittin in solution and bound to phospholipid membranes: Evidence that membrane-bound melittin is monomeric (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 230-242 
    Details
    ISSN: 0887-3585
    Keywords: melittin ; spin-labelling ; EPR spectroscopy ; membrane-protein interaction ; protein-protein interaction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Spin-labeled derivatives of the bee venom protein, melittin, were obtained by reacting on the average one of the four amino groups of the protein with succinimidyl-2,2,5,5-tetramethyl-3-pyrroline-1-oxyl-3-carboxylate All 16 statistically possible reaction products with 0, 1, 2, 3 or 4 spin labels per protein were then separated in a single pass with reversed phase high performance liquid chromatography. With the help of trypsin digestion and diode array detection it was possible to assign the primary structure of all 16 eluting fractions. All fractions with only one spin label per protein were purified for electron paramagnetic resonance measurement. The labeling sites cover different regions of the protein: one is at the N-terminus, one at lysine-7, and two are near the C-terminus at lysine-21 and lysine-23, respectively. This set of specifically labeled melittins was used to study the structure and dynamics of melittin in aqueous solutions and when bound to neutral or negatively charged membranes. In aqueous solution a reduction in rotational correlation time and appearance of spin-spin interaction was observed during salt-induced transition from a random coil monomer to a mostly α-helical retramer. Membrane binding to phospholipid bilayers in low or high ionic strength was reflected only in a further decrease in mobility. The absence of any spin interaction in the membrane-bound state suggests that melittin is monomeric under these conditions. All derivatives were able to detect these structural changes, but melittin labeled at the N-terminal amino group was especially valuable. Because of postulated intramolecular hydrogen bonding, this label reflects directly the motion of the entire protein or tetramer. Broadening experiments with chromium oxalate show that all labeled sites are at least partially exposed to the aqueous phase when melittin is bound to membranes. This suggests that an α-helical melittin monomer binds to membranes with its axis parallel to the membrane surface.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030404
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  • 6
    Electronic Resource
    Electronic Resource
    Preliminary X-ray diffraction studies and biochemical characterization of the antitumor protein mitomalcin indicate close similarity to neocarzinostatin (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 252-255 
    Details
    ISSN: 0887-3585
    Keywords: streptomyces malayensis ; antitumor antibiotic ; holoprotein antibiotic ; crystallization of mitomalcin ; amino acid composition ; partial amino acid sequence ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The antitumor antibiotic protein mitomalcin, from the microorganism Streptomyces malayensis, has been purified to apparent homogenity and crystallized. The crystals belong to space group P212121 and have the following cell parameters : a=27.2 Å, b=34.1 Å, c=101.7 Å, and alpha;=β=γ=90°. These crystal properties are extremely similar to crystals of the antitumor protein neocarzinostatin (11.7 kilodaltons [kDa]) from Streptomyces carzinostaticus in spite of differing pH conditions for crystallizing the two proteins and an apparent difference in molecular weight is similar to that of neocarzinostatin. An amino acid composition analysis of mitomalcin indicates that some differences may exist between the two molecules, but a preliminary amino acid sequence analysis of the first 37 residues found no difference in the N-terminal region of the molecule.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030406
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  • 7
    Electronic Resource
    Electronic Resource
    Unusual zymogen-processing properties of a mutated form of prochymosin (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 256-261 
    Details
    ISSN: 0887-3585
    Keywords: zymogen activation ; protein engineering ; autoproteolytic processing ; protein structure/function ; renaturation ; rDNA expression ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Site-specific mutagenesis of the gene encoding bovine prochymosin was used to produce a mutated zymogen in which seven contiguous amino acids of the N-terminal propeptide had been deleted and an eighth residue had been substituted. This altered region spans the normal site of autocatalytic proteolysis that occurs at the same time as (enzymatic) activation of prochymosin at acidic pH. Activation of the mutated zymogen at pH 4.5 was extremely slow, and cleavage occurred at an unusual Ser-Lys bond in the prochymosin incubated at pH 2 generated the usual pseudochymosin by cleavage of the normal Phe-Leu bond, but at a rate severalfold slower than the authentic zymogen. These results indicate that even after deletion of seven of 42 amino acids of the propeptide the mutant protein could still assume a prochymosin (zymogen) structure, although these changes did result in striking differences in acid-catalyzed activation and processing reactions at one but not the other of the two processing sites of prochymosin.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030407
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  • 8
    Electronic Resource
    Electronic Resource
    Test of circular dichroism (CD) methods for crambin and CD-assisted secondary structure prediction of its homologous toxins (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 262-273 
    Details
    ISSN: 0887-3585
    Keywords: hierarchical assignment ; cereal grain ; mistletoe ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Methods that analyze protein circular dichroism (CD) spectra for fractions of secondary structure are evaluated for the plant protein crambin, which has a known high-resolution crystal structure. In addition, a two-step secondary structure prediction scheme is presented and used for the toxins homologous to crambin, shown by others to have secondary structures similar to crambin.The test of CD spectral analysis methods with the protein crambin employed two computer programs and several CD basis sets. Crambin's crystal structure, known to 0.945 Å resolution (Hendrickson, W.A., Teeter, M.M. Nature 290:107-113, 1981), allows accurate evaluation of results. Analysis with the protein spectra basis sets (Provencher, S. W., Glöckner, J. Biochemistry 20:33-37, 1981) as modified (Manavalan, P., Johnson, W. C., Jr. Anal. Biochem. 167:76-85, 1987) agreed most closely with crambin's crystal structure. This method was then applied to the CD spectra of the membrane-active toxins homologous to crambin (α1- and β-purothionin, phoratoxin A and B, an viscotoxin A3 and B).The new program SEQ (pronounced “seek”) was developed to assign the secondary structure along the protein chain in a hierarchical fashion and applied to the plant toxins. The method constrained the secondary structure fractions to those from CD analysis and combined standard statistical methods with amphipathic helix location.Both CD-arrived secondary structure percentages and sequence assignment indicate that the viscotoxins are structurally most similar to crambin. Purothionin's secondary structure was predicted to be fundamentally similar to crambin's with a difference at the start of the first helix. This assignment agreed with Raman and NMR analyses of Purothionin and lends validity to the method presented here. Differences from the NMR in the CD secondary structure fraction analysis for phoratoxin suggest interference in the CD from tryptophan residues.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040405
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  • 9
    Electronic Resource
    Electronic Resource
    Refined structure of human carbonic anhydrase II at 2.0 Å resolution (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 274-282 
    Details
    ISSN: 0887-3585
    Keywords: crystallography ; refinement ; structure ; carbonic anhydrase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of human erythrocytic carbonic anhydrase II has been refined by constrained and restrained structure-factor least-squares refinement at 2.0 Å resolution. The conventional crystallographic R value is 17.3%. Of 167 solvent molecules associated with the protein, four are buried and stabilize secondary structure elements. The zinc ion is ligated to three histidyl residues and one water molecule in a nearly tetrahedral geometry. In addition to the zinc-bound water, seven more water molecules are identified in the active site. Assuming that Glu-106 is deprotonated at pH 8.5, some of the hydrogen bond donor-acceptor relations in the active site can be assigned and are described here in detail. The Oγ1 atom of Thr-199 donates its proton to the Oε1 atom of Glu-106 and can function as a hydrogen bond acceptor only in additional hydrogen bonds.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040406
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  • 10
    Electronic Resource
    Electronic Resource
    Stereochemistry of salt-bridge formation in α-helices and β-strands (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 294-295 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040408
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  • 11
    Electronic Resource
    Electronic Resource
    Site-directed mutations altering methyl-accepting residues of a sensory transducer protein (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 102-112 
    Details
    ISSN: 0887-3585
    Keywords: bacterial chemotaxis ; sensory adaptation ; protein modification ; membrane protein ; receptor protein ; transmembrane signalling ; Escherichia coli ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Trg protein is one of a family of transducer proteins that mediate chemotactic response in Escherichia coli. Transducers are methylaccepting proteins that gain or lose methyl esters on specific glutamyl residues during sensory adaptation. In this study, the significance of multiple sites of methylation on transducer proteins was addressed by using oligonucleotide-directed, site-specific mutagenesis to substitute an alanyl residue at each of the five methyl-accepting sites in Trg. The resulting collection of five mutations, each inactivating a single site, was analyzed for effects on covalent modification at the remaining sites on Trg and for the ability of the altered proteins to mediate sensory adaptation. Most of the alanyl substitutions had substantial biochemical effects, enhancing or reducing methyl-accepting activity of other sites, including one case of activation of a site not methylated in wild-type protein. Analysis of the altered proteins provided explanations for many features of the complex pattern of electrophoretic forms exhibited by Trg. The mutant proteins were less efficient than normal Trg in mediating adaptation. Correlation of biochemical and behavioral data indicated that reduction in the number of methyl-accepting sites on the transducer lengthened the time required to reach an adapted state.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030205
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  • 12
    Electronic Resource
    Electronic Resource
    Comparison of the dynamics of the membrane-bound form of fd coat protein in micelles and in bilayers by solution and solid-state nitrogen-15 nuclear magnetic resonance spectroscopy (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 123-130 
    Details
    ISSN: 0887-3585
    Keywords: NMR spectroscopy ; protein dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Solid-state and solution 15N nuclear magnetic resonance experiments on uniformly and specifically 15N labeled coat protein in phospholipid bilayers and in detergent micelles are used to describe the dynamics of the membrane-bound form of the protein. The residues in the N- and C-terminal portions of the coat protein in both phospholipid bilayers and in detergent micelles are mobile, while those in the hydrophobic midsection are immobile. There is evidence for a gradient of mobility in the C-terminal region of the coat protein in micelles; at 25°C only the last two residues are mobile on the 109-Hz timescale, while the last six to eight residues appear to be mobile on slower timescales and highly mobile at higher temperatures. Since all of the C-terminal residues are immobile in the virus particles, the mobility of these residues in the membrane-bound form of the protein may be important for the formation of protein-DNA interactions in the assembly process.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040205
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  • 13
    Electronic Resource
    Electronic Resource
    Internal motion of a tryptophan residue in Streptomyces subtilisin inhibitor: Deuterium nuclear magnetic resonance in solution (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 131-136 
    Details
    ISSN: 0887-3585
    Keywords: 2H NMR ; selective deuteration ; tryptophan internal motion ; SSI-subtilisin complex ; protein conformational equilibrium ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Deuterium NMR spectroscopy was used to study internal motions of a deuterium-labeled single tryptophan (Trp) residue (per subunit) of Streptomyces subtilisin inhibitor (SSI) in solution. The free inhibitor with the five ring protons of the Trp replaced with deuterons showed a narrow resonance component (56 Hz) of about one-quarter of the total intensity, in addition to the broad resonance component (about 600 Hz) at 25°C, showing that it exits in an equilibrium mixture of two conformers, in one of which the typtophan side chain is highly mobile. In analogy to the two structures of SSI found in the crystal, these two conformers were attributed to the one in which the contact between the α-lobe and the beta;-lobe of the subunit is tight and the other in which the same contact is loose. When SSI forms a complex with subtilisin BPN′, the broad component becomes invisibly broad, but the narrow component increases with even further narrowing, suggesting that the binding to the enzyme favors the “loose” conformer over the “tight” conformer.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040206
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  • 14
    Electronic Resource
    Electronic Resource
    Surface interactions of γ-crystallins in the crystal medium in relation to their association in the eye lens (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 137-147 
    Details
    ISSN: 0887-3585
    Keywords: eye lens proteins ; protein association ; crystal packing ; surface area ; homologous proteins ; point mutations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A comparative study of intermolecular interactions in crystals of two homologous low molecular weight proteins, γ-II and γ-IIIb crystallins, from calf eye lens was carried out. Crystal packings for these proteins are very different: intermolecular contact areas compose about 33% of the total accessible surface area of γ-II as compared with 13% in γ-III. Two key residues seem to be mainly responsible for the differences in protein association in the crystal medium. These are Ser 103 and Leu 155 in γ-II, which are replaced by Met 103 and His 155 in γ-IIIb. A similar substitution of these residues is observed in different gene products of γ-crystallins from a number of vertebrates. This is consistent with the existence of a genetically controlled mechanism for determining intermolecular association of γ-crystallins in the native medium of the lens.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040207
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  • 15
    Electronic Resource
    Electronic Resource
    Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 148-156 
    Details
    ISSN: 0887-3585
    Keywords: Protein structure ; empirical energy ; energy minimization ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method for the prediction of hydrogen positions in proteins is presented. The method is based on the knowledge of the heavy atom positions obtained, for instance, from X-ray crystallography. It employs an energy minimization limited to the environment of the hydrogen atoms bound to a common heavy atom or to a single water molecule. The method is not restricted to proteins and can be applied without modification to nonpolar hydrogens and to nucleic acids. The method has been applied to the neutron diffraction structures of trypsin ribonuclease A, and bovine pancreatic trypsin inhibitor. A comparison of the constructed and the observed hydrogen positions shows few deviations except in situations in which several energetically similar conformations are possible. Analysis of the potential energy of rotation of Lys amino and Ser, Thr, Tyr hydroxyl groups reveals that the conformations of lowest intrinsic torsion energies are statistically favored in both the crystal and the constructed structures.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040208
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  • 16
    Electronic Resource
    Electronic Resource
    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040301
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  • 17
    Electronic Resource
    Electronic Resource
    X-ray and model-building studies on the specificity of the active site of proteinase K (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 157-164 
    Details
    ISSN: 0887-3585
    Keywords: synthetic inhibitors ; serine proteinase crystallography ; active site geometry ; computer graphics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Proteinase K, the extracellular serine endopeptidase (E.C. 3.4.21.14) from the fungus Tritirachium album limber, is homologous to the bacterial subtilisin proteases. The binding geometry of the synthetic inhibitor carbobenzoxy-Ala-Phechloromethyl Ketone to the active site of proteinase K was the first determined from a Fourier synthesis based on synchrotron X-ray diffraction data between 1.8 Å and 5.0 Å resolution. The protein inhibitor complexes was refined by restrained least-squares minimization with the data between 10.0 and 1.8 Å. The final R factor was 19.1% and the model contained 2,018 protein atoms, 28 inhibitors atoms, 125 water molecules, and two Ca2+ ions. The peptides portion of the inhibitor is bound to the active center of proteinase K by means of a three-stranded antiparallel pleated sheet, with the side chain of the phenylalanine located in the P1 site. Model building studies, with lysine replacing phenylalanine in the inhibitor, explain the relatively unspecific catalytic activity of the enzyme.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040302
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  • 18
    Electronic Resource
    Electronic Resource
    Crystallographic studies of inhibitor binding sites in human carbonic anhydrase II: A pentacoordinated binding of the SCN- ion to the zinc at high pH (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 283-293 
    Details
    ISSN: 0887-3585
    Keywords: crystallography ; structure ; refinement ; sulfonamide ; thiocyanate ; mercury ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The binding of four inhibitors - mercuric ion, 3-acetoxymercuri-4-aminobenzenesulfonamide (AMS), acetazolamide (Diamox), and thiocyanate ion - to human carbonic anhydrase II (HCA II) has been studied with X-ray crystallography.The binding of mercury to HCA II at pH 7.0 has been investigated at 3.1 Å resolution. Mercuric ions are observed at both nitrogens in the His-64 ring. One of these sites is pointing toward the zinc ion. The only other binding site for mercury is at Cys-206.The binding of the two sulfonamide inhibitors AMS and Diamox, has been reinvestigated at 2.0 and 3.0 Å, respectively. Only the nitrogen of the sulfonamide group binds to the zinc ion replacing the hydroxyl ion. The sulfonamide oxygen closet to the zinc ion is 3.1 Å away. Thus the tetrahedral geometry of the zinc is retained, refuting earlier models of a pentacoordinated zinc.The structure of the thiocyanate complex has been investigated at pH 8.5 and the structure has been refined at 1.9 Å resolution using the least-squares refinement program PROLSQ. The crystallographic R factor is 17.6%. The zinc ion is pentacoordinated with the anion as well as a water molecule bound in addition to the three histidine residues. The nitrogen atom of the SCN- ion is 1.9 Å from the zinc ion but shifted 1.3 Å with respect to the hydroxyl ion in the native structure and at van der Waals' distance from the Oγl atom of Thr-199. This is due to the inability of the Oγl atom of Thr-199 to serve as a hydrogen bond donor, thus repelling the nonprotonated nitrogen. The SCN- molecule reaches into the deep end of the active site cavity where the sulfur atom has displaced the so-called “deep” water molecule of the native enzyme. The zinc-bound water molecule is 2.2 Å from the zinc ion and 2.4 Å from the SCN- nitrogen. In addition, this water is hydrogen bonded to the Oγl atom of Thr-199 and to another water molecule.We have observed that solvent and inhibitor molecules have three possible binding sites on the zinc ion and their significance for the catalysis and inhibition of HCA II will be discussed. All available crystallographic data are consistent with a proposed catalytic mechanism in which both the OH moiety and one oxygen of the substrate HCO3- ion are ligated to the zinc ion.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040407
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    Electronic Resource
    Further experimental studies of the disulfide folding transition of ribonuclease A (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 251-261 
    Details
    ISSN: 0887-3585
    Keywords: protein folding kinetics ; disulfide bonds ; thiol-disulfide exchange ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two very different mechanisms of folding have been proposed from experimental studies of disulfide formation in reduced ribonuclease A. (1) A pathway in which the rate-limiting step separates fully folded protein from all other disulfide intermediates and occurs solely in three-disulfide intermediates. (2) A multiple pathway mechanism with different rate-limiting steps for each pathway. The various rate-limiting steps involve disulfide breakage, formation, and rearrangement in intermediates with one, two, three, and four protein disulfides. To distinguish between these two mechanisms, we have carried out further studies of both unfolding and refolding.Refolding of reduced ribonuclease A requires three-disulfide intermediates to accumulate; negligible refolding occurs when only the nearly random one- and two-disulfide intermediate species are populated. Therefore, no rate-limiting steps of the type postulated in mechanism (2) occur in intermediates with one and two protein disulfides. Unfolding and disulfide reduction is an all-or-none process; no disulfide intermediates accumulate to detectable to detectable levels or precede the rate-limiting step. Mechanism (2) requires that such intermediates precede the rate-limiting step and accumulate to substantial levels.The different proposal were shown not to result from the use of different solution conditions or disulfide reagents; the two sets of data are not inconsistent. Instead, the inappropriate mechanism (2) resulted from an incorrect kinetic analysis and misinterpretation of the kinetics of disulfide formation are breakage.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040404
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    Electronic Resource
    Electronic Resource
    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030101
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  • 21
    Electronic Resource
    Electronic Resource
    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030201
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  • 22
    Electronic Resource
    Electronic Resource
    Conformational characteristics of the complete cequence of group A streptococcal M6 protein (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 60-69 
    Details
    ISSN: 0887-3585
    Keywords: coiled-coli ; alpha-helix ; antiphagocytic ; heptad ; antigenic variation ; sequence repeats ; cell wall protein ; intermediate filaments ; myosin ; tropomyosin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: M protein is considered a virulence determinant on the streptococcal cell wall by virtue of its ability to allow the organism to resist attack by human neutrophils. The complete DNA sequence of the M6 gene from streptococcal strain D471 has allowed, for the first time, the study of the structural characteristics of the amino acid sequence of an entire M protein molecule. Predictive secondary structural analysis revealed that the majority of this fibrillar molecule exhibits strong alpha-helical potential and that, except for the ends, nonpolar residues in the central region of the molecule exhibit the 7-residue periodicity typical for coiled-coil proteins. Differences in this heptad pattern of nonpolar residues allow this central rod region to be divided into three subdomains which correlate essentially with the repeat regions A, B, and C/D in the M6 protein sequence. Alignment of the N-terminal half of the M6 sequence with PepM5, the N-terminal half of the M5 protein, revealed that 42% of the amino acids were identical. The majority of the identities were “core” nonpolar residues of the heptad periodicity which are necessary for the maintenance of the coiled coil. Thus, conservation of structure in a sequence-variable region of these molecules may be biologically significant. Results suggest that serologically different M proteins may be built according to a basic scheme: an extended central coiled-coil rod domain (which may vary in size among strains) flanked by functional end domains.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030106
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  • 23
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    Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure*A FORTRAN version of the program DEFINE_STRUCTURE, which defines the secondary structure and characterizes the first level of supersecondary structure, is available from the authors (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 71-84 
    Details
    ISSN: 0887-3585
    Keywords: Cα coordinates ; distance matrix ; difference distance matrix ; helix axes, strand axes ; interaxial angles ; turns ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A computer program is described that produces a description of the secondary structure and supersecondary structure of a polypeptide chain using the list of alpha carbon coordinates as input. Restricting the term “secondary structure” to the conformation of contiguous segments of the chain, the program determines the initial and final residues in helices, extended strands, sharp turns, and omega loops. This is accomplished through the use of difference distance matrices. The distances in idealized models of the segments are compared with the actual structure, and the differences are evaluated for agreement within preset limits. The program assigns 90-95% of the residues in most proteins to at least one type of secondary elementIn a second step the now-defined helices and strands are idealized as straight line segments, and the axial directions and locations are compiled from the input Cα coordinate list. These data are used to check for moderate curvature in strands and helices, and the secondary structure list is corrected where necessary. The geometric relations between these line segments are then calculated and output as the first level of supersecondary structure. A maximum of six parameters are required for a complete description of the relations between each pair. Frequently a less complete description will suffice, for example just the interaxial separation and angle. Both the secondary structure and one aspect of the supersecondary structure can be displayed in a character matrix analogous to the distance matrix format. This allows a quite accurate two-dimensional display of the three-dimensional structure, and several examples are presentedA procedure for searching for arbitrary substructures in proteins using distance matrices is also described. A search for the DNA binding helix-turnhelix motif in the Protein Data Bank serves as an exampleA further abstraction of the above data can be made in the form of a metamatrix where each diagonal element represents an entire secondary segment rather than a single atom, and the off-diagonal elements contain all the parameters describing their interrelations. Such matrices can be used in a straightforward search for higher levels of supersecondary structure or used in toto as a representation of the entire tertiary structure of the polypeptide chain.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030202
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  • 24
    Electronic Resource
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    Human myeloperoxidase and thyroid peroxidase, two enzymes with separate and distinct physiological functions, are evolutionarily related members of the same gene family (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 113-120 
    Details
    ISSN: 0887-3585
    Keywords: evolution ; proximal histidine ; distal histidine ; heme enzyme ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Human myeloperoxidase and human thyroid peroxidase nucleotide and amino acid sequences were compared. The global similarities of the nucleotide and amino acid sequences are 46% and 44%, respectively. These similarities are most evident within the coding sequence, especially that encoding the myeloperoxidase functional subunits. These results clearly indicate that myeloperoxidase and thyroid peroxidase are members of the same gene family and diverged from a common ancestral gene. The residues at 416 in myeloperoxidase and 407 in thyroid peroxidase were estimated as possible candidates for the proximal histidine residues that link to the iron centers of the enzymes. The primary structures around these histidine residues were compared with those of other known peroxidases. The similarity in this region between the two animal peroxidases (amino acid 396-418 in thyroid peroxidase and 405-427 in myeloperoxidase) is 74%; however, those between the animal peroxidases and other yeast and plant peroxidases are not significantly high, although several conserved features have been observed. The possible location of the distal histidine residues in myeloperoxidase and thyroid peroxidase amino acid sequences are also discussed.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030206
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  • 25
    Electronic Resource
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    Peptide synthesis catalyzed by polyethylene glycol-modified chymotrypsin in organic solvents (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 130-137 
    Details
    ISSN: 0887-3585
    Keywords: peptide synthesis ; chymotrypsin specificity ; polyethylene glycol ; nonaqueous solvents ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Chymotrypsin modified with polyethylene glycol was successfully used for peptide synthesis in organic solvents. The benzene-soluble modified enzyme readily catalyzed both aminolysis of N-benzoyl-L-tyrosine p-nitroanilide and synthesis of N-benzoyl-L-tyrosine butylamide in the presence of trace amounts of water. A quantitative reaction was obtained when either hydrophobic or bulky amides of L- as well as D-amino acids were used as acceptor nucleophiles, while almost no reaction occurred with free amino acids or ester derivativesThe acceptor nucleophile specificity of modified chymotrypsin as a catalyst in the formation of both amide and peptide bonds in organic solvents was quite comparable to that in aqueous solution as well as to that of the leaving group in hydrolysis reactions. By contrast, the substrate specificity of modified chymotrypsin in organic solvents was different from that in water since arginine and lysine esters were found to be as effective as aromatic amino acids to form the acyl-enzyme with subsequent synthesis of a peptide bond.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030208
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  • 26
    Electronic Resource
    Electronic Resource
    Crystallization of purified recombinant human interleukin-1β (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 121-129 
    Details
    ISSN: 0887-3585
    Keywords: bioactivity ; SK-hep-1 hepatoma ; interleukin-1 ; recombinant protein ; crystals ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The gene for human interleukin-1β was cloned from SK-hep-1 hepatoma cellular RNA and expressed at high levels in Escherichia coli both as the naturally processed form (rIL-1β) and as a variant with an additional sequence of three amino acids on the N-terminus (rIL-1β+). Expressed protein was purified to homogeneity by a sequence of steps, which included low pH incubation, adsorption and desorption from Procion Red Sepharose, sizing on a Superose 12 fast-performance liquid chromatography (FPLC) column, and anion exchange chromatography on QAE Sepharose. The final step provided a biologically active protein that migrates on twodimensional (2-D) gels as a single spot with a pI of 6.7 ± 0.2 and a molecular mass of 17,500 daltons. Concentrated solutions of rIL-1β have produced crystals by ammonium sulfate precipitation. The crystals are tetragonal, show the symmetry of space group P41 or its enantiomer, have lattice constants of a = 58.46 (1) and c = 77.02 (3) A, and scatter to at least 2 Å resolution. A structure determination based on these crystals is under way.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030207
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  • 27
    Electronic Resource
    Electronic Resource
    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030301
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  • 28
    Electronic Resource
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    Comparison of model and nuclear magnetic resonance structures for the human inflammatory protein C5a (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 139-145 
    Details
    ISSN: 0887-3585
    Keywords: Protein structure ; complement ; anaphylatoxins ; two-dimensional NMR ; computer modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The model structure previously proposed for human C5a, based upon the crystal structure of the homologous protein human C3a, is compared to the solution structure of human C5a recently determined by nuclear magnetic resonance (NMR) methods in our laboratory. The general folding and helix topography of the C5a protein were modeled very well. The N-terminus, which is disordered in teh C3a crystal, was correctly predicted in the C5a model both as to its being a helix and as to its docking site on the rest of the molecule. On the other hand, the NMR data show that the biologically important C-terminal residues are disordered in solution, unlike the model and the C3a crystal structure where this region was helical.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030302
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  • 29
    Electronic Resource
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    Mapping the enzymatic active site of Pseudomonas aeruginosa exotoxin A (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 146-154 
    Details
    ISSN: 0887-3585
    Keywords: Pseudomonas toxin ; x-ray crystallography ; ADP-ribosyl transferase ; sequence homology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Pseudomonas aeruginosa exotoxin A is representative of a class of enzymes, the monoADP-ribosyl, which catalyze the covalent transfer of an ADP-ribose moiety of NAD+ to a target substrate. Availability of the three-dimensional structure of exotoxin A provides the opportunity for mapping substrate binding sites and suggesting which amino acid residues may be involved in catalysis. Data from several sources have been combined to develop a proposal for the NAD+ binding site of exotoxin A: the binding of NAD+ fragments adenosine, AMP, and ADP have been delineated crystallographically to 6.0, 6.0, and 2.7 Å, respectively; significant sequence homology spanning 60 residues has been found between exotoxin A and diphtheria toxin, which has the identical enzymatic activity; iodination of exotoxin A, under conditions in which only tyrosine 481 is iodinated in the enzymatic domain, abolishes ADP-ribosyl transferase activity.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030303
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  • 30
    Electronic Resource
    Electronic Resource
    Differences in crystal properties and ligand affinities of an antifluorescyl fab (4-4-20) in two solvent systems (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 155-160 
    Details
    ISSN: 0887-3585
    Keywords: monoclonal antibodies ; high-affinity combining sites ; MPD ; Effects of fluorescein binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An antigen-binding fragment (Fab) from a murine monoclonal antibody (4-4-20) with high affinity for fluorescein was cocrystallized with ligand in polyethylene glycol (PEG) and 2-methl-2,4-pentanediol (MPD) in forms suitable for X-ray analyses. In MPD the affinity of the intact antibody for fluorescein was 300 times lower than the value (3.4 × 1010 M-1) obtained in aqueous buffers. This decreased affinity was manifested by the partial release of bound fluorescein when MPD was added to solutions of liganded Feb during crystallization trials, In PEG, the ligand remained firmly bound to the protein. The liganded Feb crystallized in the monoclinic space group P21 in PEG, with a = 58.6, b = 97.2, c = 44.5 Å and β = 95.2°. In MPD the space group was triclinic P1, with a = 58.3, b = 43.4, c = 42.3 Å, α = 83.9°, β = 87.6°, and γ = 84.5°. X-ray diffraction data were collected for both forms to 2.5-Å resolution. Surprisingly, the triclinic form of the liganed antifluorescyl Feb had the same space group, closely similar cell dimensions, and practically the same orientation in the unit cell as an unliganded Fab (BV04-01) with activity against single-stranded DNA.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030304
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  • 31
    Electronic Resource
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    Intermolecular localization of epitopes within an oligomeric protein by immunoelectron microscopy and image processing (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 161-183 
    Details
    ISSN: 0887-3585
    Keywords: hemocyanin ; correspondence analysis ; monoclonal antibodies ; electron microscopy ; images analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Three epitopes have been localized by immunoelectron microscopy on subunits Aa6 of the 4 × 6-meric hemocyanin of the scorpion Androctonus australis. Soluble immunocomplexes composed of monoclonal antibodies and of native hemocyanin were purified, negatively stained with uranyle acetate by the single-layer technique, and examined under the electron microscope (EM). The molecule images were digitized, aligned, and submitted to correspondence analysis according to the method of Van Heel and Frank (Ultramicroscopy 6: 187-194, 1981). A high-precision localization of the attachment point of the Fab arm to the antigen was achieved through a careful analysis of the average images. This method easily allowed the discrimination of epitopes located in different domains (Mr 20 kDa) of the same subunit. Nonoverlapping epitopes located in the same structural domain of subunit Aa6 could be distinguished by the stain exclusion patterns of their Fab arms. The method is general and may be used for epitope mapping in any antigen producing definite EM views.
    Additional Material: 12 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030305
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  • 32
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    Crystallization and preliminary X-ray diffraction study of a protein with a high potential rubredoxin center and a hemerythrin-type Fe center (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 184-186 
    Details
    ISSN: 0887-3585
    Keywords: new Fe-protein ; rubredoxin ; hemerythrin ; crystals ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A newly discovered iron-containing protein, isolated from the bacterium Desulfovibrio vulgaris (Hildenborough, NCIB 8303), has been crystallized. The molecule appears to be a dimer of mass 44kDa. This protein has iron centers with spectroscopic similarities to those in rubredoxins and in hemerythrins.The X-ray diffraction shows symmetry consistent with space group I222 or I212121. Cell parameters are a = 49.2 Å, b = 81.3 Å, c= 100.1 Å, and α, β, γ = 90°. X-ray diffraction data have been collected to 3.0 Å, and a search for useful heavy atom derivatives is in progress for the analysis of the crystal structure of this Fe-protein.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030306
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  • 33
    Electronic Resource
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    Lecithin: Cholesterol acyltransferase activation by synthetic amphipathic peptides (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 187-198 
    Details
    ISSN: 0887-3585
    Keywords: amphipathic peptide ; liposomes ; peptide ; serum apolipoproteins ; synthetic ; LCAT ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The amphipathic helical theory of Segrest and colleagues (FEBS Lett.: 38: 247-253, 1974) proposes that the lipid-binding segments of serum apolipoproteins are in an alpha helical conformation. Furthermore the helices have a hydrophobic face and a hydrophilic face with a specific distribution of positively and negatively charged residues. The importance of the pattern of the charged residues in the lipid binding and lecithin:cholesterol acyltransferase (LCAT) activation by the segments is still debated. We designed a 30-residue peptide, GALA, which in the alpha helical conformation hs a hydrophilic face composed of glutamic acid residues (Sabbarao et al.: Biochemistry 26: 2964-2972, 1987). GALA behaves like the serum apolipoproteins in its interaction with dimyristoylphospatidylcholine (DMPC) at neutral pH; the amino terminal tryptophan of GALA undergoes a blue shift in its fluorescence emission spectrum, and the circular dichroism (CD) spectrum indicates that GALA acquires alpha helical structure in the presence of DMPC. A DMPC-GALA:19/1 (molar ratio) complex can be isolated by gel-permeation chromatography. This complex has a discoidal structure with the approximate dimensions of 44-Å diameter. GALA edge thickness and a 170- to 350-Å diameter. GALA activates LCAT with DMPC but not with unsaturated phospholipids as the substrate. The apparent partition coefficient of GALA into DMPC vesicles is 100-fold larger than into egg phosphatidlylcholine vesicles. The interaction of GALA with unsaturated lipids at neutral pH is so weak that no detectable change in the spectroscopic properties of GALA or the structure of the liposomes can be detected under the conditions used here. The sequence of GALA differs from previously studied model Apo A1 peptides by the absence of positively charged residues on the hydrophilic face. This indicates that positive charges in Apo A1-like peptides are not required in order to form discoidal structures with saturated phospholipids or to activate LCAT with such lipid substrates.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030307
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    Electronic Resource
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    Mechanism of protein folding: I. General considerations and refolding of myoglobin (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 199-207 
    Details
    ISSN: 0887-3585
    Keywords: folding pathway ; hydrophobic interaction ; long-range and long-distance interactions ; secondary structure ; tertiary structure ; module structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To explain the rapidity of the process of protein folding, we cite two aspects of hydrophobic interaction: its long-range nature and the specificity of pairing after the formation of secondary structures. These two factors, when incorporated with the growth-type mechanism, can determine the folding pathway of proteins. This mechanism is applied to myoglobin. Appropriate introduction of side chins of amino acid residues and the heme group attached to His 93 yield a refolded tertiary structure that is in good agreement with the native structure.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030308
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  • 35
    Electronic Resource
    Electronic Resource
    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340030401
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  • 36
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    Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequences (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 99-122 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; protein coding regions ; sequence homology ; reading frame ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have examined oligopeptides with lengths ranging from 2 to 11 residues in protein sequences that show no obvious evolutionary relationship. All sequences in the Protein Identification Resource database were carefully classified by sensitive homology searches into superfamilies to obtain unbiased oligopeptide counts. The results, contrary to previous studies, show clear prejudices in protein sequences. The oligopeptide preferences were used to help decide the significance of sequence homologies and to improve the more general methods for detecting protein coding regions within nucleotide sequences.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040204
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  • 37
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    Flexibility of the DNA-binding domains of trp repressor (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 18-31 
    Details
    ISSN: 0887-3585
    Keywords: flexibility ; trp repressor ; DNA-binding domains ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An orthorhombic crystal form of trp repressor (aporepressor plus L-tryptophan ligand) was solved by molecular replacement, refined to 1.65 Å resolution, and compared to the structure of the repressor in trigonal crystals. Even though these two crystal forms of repressor were grown under identical conditions, the refined structures have distinctly different conformations of the DNA-binding domains. Unlike the repressor/aporepressor structural transition, the conformational shift is not caused by the binding or loss of the L-tryptophan ligand. We conclude that while L-tryptophan binding is essential for forming a specific complex with trp operator DNA, the corepressor ligand does not lock the repressor into a single conformation that is complementary to the operator. This flexibility may be required by the various binding modes proposed for trp repressor in its search for and adherence to its three different operator sites.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030103
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    Ribosome-inhibiting proteins, retroviral reverse transcriptases, and RNase H share common structural elements (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 53-59 
    Details
    ISSN: 0887-3585
    Keywords: ricin ; retroviral integrase ; conserved residues ; homologous sequences ; active site ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Plant ribosome-inhibiting proteins are shown to be homologous at the domain level to RNase H form Escherichia coli and to two regions of the pol gene product of retroviral reverse transcriptases. One of these regions carries the viral integrase or int function, while the other has previously been suggested to contain the viral RNase H exo activity. Several residues conserved among the ribosome inhibitors, E. coli RNase H, and the integrase proteins are seen to occupy a prominent cleft in the tertiary structure of the ribosome inhibitor ricin, suggesting roles in binding or catalysis. It is likely that these homologous sequences represent modern derivatives of an ancient protein-folding unit capable of nucleic acid binding and modification which has been incorporated into a variety of enzyme functions.
    Additional Material: 5 Ill.
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    Energetics of charge-charge interactions in proteins (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 32-52 
    Details
    ISSN: 0887-3585
    Keywords: alpha-helix ; distance-dependent ; finite-difference method ; Poisson-Boltzmann equation ; protein electrostatics ; rhodanese ; solvent effects ; subtilisin ; Tanford-Kirkwood theory ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Electrostatic interactions between pairs of atoms in proteins are calculated with a model based on the linearized Poisson-Boltzmann equation. The equation is solved accurately by a method that takes into account the detailed shape of the protein. This paper presents applications to several systems. Experimental data for the interaction of ionized residues with an active site histidine in subtilisin BPN' allow the model to be tested, using various assumptions for the electrical properties of the protein and solvent. The electrostatic stabilization of the active site thiolate or rhodanese is analyzed, with attention to the influence of α-helices. Finally, relationships between electrostatic potential and charge-charge distance are reported for large and small globular proteins. The above results are compared with those of simpler electrostatic models, including Coulomb's law with both a distance-dependent dielectric constant (∊ = R) and a fixed dielectric constant (∊ = 2), and Tanford-Kirkwood theory. The primary conclusions are as follows: (1) The Poisson-Boltzmann model agrees with the subtilisin data over a range of ionic strengths; (2) two α-helices generate a large potential in the active site of rhodanese; (3) ∊ = R overestimates weak electrostatic interactions but yields relatively good results for strong ones; (4) Tanford-Kirkwood theory is a useful approximation to detailed solutions of the linearized Poisson-Boltzmann equation in globular proteins; and (5) the modified Tanford-Kirkwood theory overscreens the measured electrostatic interactions in subtilisin.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030104
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    Electronic Resource
    Pattern descriptors and the unidentified reading frame 6 human mtDNA dinucleotide-binding site (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 97-101 
    Details
    ISSN: 0887-3585
    Keywords: URF ; nucleotide-binding sites ; pattern descriptor ; computer search ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In an effort to identify the structural elements essential to a given protein function a new pattern-directed inference system has been developed. It has been employed to identify a potential dinucleotide-binding domain within the human mitochondrial unidentified reading frame 6 product, thereby supporting an earlier study that this gene may encode a NADH dehydrogenase subunit.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030204
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    Lysine/fibrin binding sites of kringles modeled after the structure of kringle 1 of prothrombin (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 85-96 
    Details
    ISSN: 0887-3585
    Keywords: molecular modeling ; energy minimization ; lysine/fibrin binding ; kringle structures ; plasminogen ; tissue plasminogen activator ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Lys binding site of kringle 1 and 4 (K1 and K4) of plasminogen (PG) has been modeled on the basis of the three-dimensional structure of kringle 1 of prothrombin and 300- and 600-MHz proton nuclear magnetic resonance observations. These structures were then compared to the corresponding regions of modeled kringle 1 and 2 of tissue plasminogen activator (PA). The coordinates of the modeled structures have been refined by energy minimization in the presence and absence of ∊-aminocaproic acid ligand in order basically to remove unacceptable van der Waals contacts. The binding site is characterized by an apparent dipolar surface, the polar parts of which are separated by a hydrophobic region of highly conserved aromatic residues. Zwitterionic ligands such as Lys and ∊-aminocaproic acid form ion pair interactions with Asp55 and Asp57 located on the dipolar surface; the latter are also conserved in all the Lys binding kringles. The cationic center of the dipolar surface is Arg71, in the case of PGK4, and is composed of Arg34 and Arg71 in PGK1. The doubly charged anionic/cationic interaction centers of the latter might account for the larger binding constants of PGK1 for like-ligands but the modeling suggests that PGK4 might be kinetically faster in binding bulkier ligands. The binding site region of PAK2, which also binds Lys, resembles those of PGK1 and PGK4. Since PAK2 lacks both cationic center Arg residues, ligand carboxylate binding appears to be accomplished though an imidazolium ion of His64, which is located just below the outer surface of the kringle.
    Additional Material: 6 Ill.
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    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040101
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    Microfolding: Conformational probability map for the alanine dipeptide in water from molecular dynamics simulations (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 3 (1988), S. 262-265 
    Details
    ISSN: 0887-3585
    Keywords: protein conformation ; conformational equilibria ; free energy stimulation ; protein folding ; thermodynamic perturbation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A direct attack on the protein-folding problem has been initiated with the free energy perturbation methods of molecular dynamics. The complete conformational probability map for the alanine dipeptide is presented. This work uses the SPC model for the explicit hydration of the dipeptide. Free energy differences for the four observed minima (β, αR, αL, C7ax) are given, and the free energy barriers between minima are outlined.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340030408
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    In memorium: Emil Thomas Kaiser, 1938-1988 (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040102
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  • 45
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    Photochemical crosslinking of bacteriophage T4 single-stranded DNA-binding protein (gp32) to oligo-p(dT)8: Identification of phenylalanine-183 as the site of crosslinking (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 1-6 
    Details
    ISSN: 0887-3585
    Keywords: single-standard DNA-binding protein ; protein-nucleic acid interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using ultraviolet light, both the 33,000-dalton single-standard DNA-binding protein from T4 bacteriophage (gp32)as well as a 25,000-dalton limited trypsin cleavage product of gp32 (core gp32*) that retains high affinity for single-stranded DNA can be crosslinked to an oligodeoxynucleotide, p(dT)8. After photolysis, a single tryptic peptide crosslinked to p(dT)8 was isolated by anion-exchange high-performance liquid chromatography. Gas-phase sequencing of this modified peptide gave the following sequence: Gln-Val-Ser-Gly-(X)-Ser-Asn-Tyr-Asp-Glu-Ser-Lys, which corresponds to residues 179-190 in gp32. Based on the absence of the expected phenylthiohydantoin derivative of phenylalanine 183 at cycle 5 (X) we infer that crosslinking has occurred at this position and that phenylalanine 183 is at the interface of the gp32:P(dT)8 complex in an orientation that allows covalent bond formation with the thymine radical produced by ultraviolet irradiation.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040103
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    Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 7-18 
    Details
    ISSN: 0887-3585
    Keywords: protein electrostatics ; conformational energy ; solvation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this report we describe an accurate numerical method for calculating the total electrostatic energy of molecules of arbitrary shape and charge distribution, accounting for both Coulombic and solvent polarization terms. In addition to the solvation energies of individual molecules, the method can be used to calculate the electrostatic energy associated with conformational changes in proteins as well as changes in solvation energy that accompany the binding of charged substrates. The validity of the method is examined by calculating the hydration energies of acetate, methyl ammonium, ammonium, and methanol. The method is then used to study the relationship between the depth of a charge within a protein and its interaction with the solvent. Calculations of the relative electrostatic energies of crystal and misfolded conformations of Themiste dyscritum hemerythrin and the VL domain of an antibody are also presented. The results indicate that electrostatic charge-solvent interactions strongly favor the crystal structures. More generally, it is found that charge-solvent interactions, which are frequently neglected in protein structure analysis, can make large contributions to the total energy of a macromolecular system.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040104
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    Criteria that discriminate between native proteins and incorrectly folded models (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 19-30 
    Details
    ISSN: 0887-3585
    Keywords: Conformation search ; CONGEN ; misfolded structures ; solvent-modified potentials ; protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Various theoretical concepts, such as free energy potentials, electrostatic interaction potentials, atomic packing, solvent-exposed surface, and surface charge distribution between native proteins and misfolded protein models. Misfolded models were constructed by introducing incorrect side chains onto polypeptide backbones: side chains of the α-helical hemerythrin were modeled on the β-sheeted backbone of immunoglobulin VL domain, whereas those of the VL domain were similarly modeled on he hemerythrin backbone. CONGEN, a conformational space sampling program, was used to construct the side chains, in contrast to the previous work,1 where incorrect side chains were modeled in all trans conformations. Capability of the conformational search procedure to reproduce native conformations was gauged first by rebuilding (the correct) side chains in hemerythrin and the VL domain: constructs with r.m.s differences from the x-ray side chains 2.2-2.4 Å were produced, and many calculated conformations matched the native ones quite well. Incorrectly folded models were then constructed by the same conformational protocol applied to incorrect amino acid sequences. All CONGEN constructs, both correctly and incorrectly folded, were characterized by exceptionally small molecular surfaces and low potential energies. Surface charge density, atomic packing, and Coulomb formula-based electrostatic interactions of the misfolded structures and the correctly folded proteins were similar, and therefore of little criteria clearly favored the native structures over the misfolded ones: (1) solvent-exposed side-chain nonpolar surface, (2) number of buried ionizable groups, and (3) empirical free energy functions that incorporate solvent effects.
    Additional Material: 4 Ill.
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    Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 31-47 
    Details
    ISSN: 0887-3585
    Keywords: protein simulation ; dihydrofolate reductase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A study of the binding of the antibacterial agent trimethoprim to Escherichia coli dihydrofolate reductase was carried out using energy minimization techniques with both a full, all-atom valence force field and a united atom force field. Convergence criteria ensured that no significant structural or energetic changes would occur with further minimization. Root-mean-square (RMS) deviations of both minimized structures with the experimental structure with the experimental structure were calculated for selected regions of the protein. In the active site, the all-atom minimized structure fit the experimental structure much better than did the united atom structure. To ascertain what constitutes a good fit, the RMS deviations between crystal structures of the same enzyme either from different species or in different crystal environments were compared. The differences between the active site of all-atom minimized structure and the experimental structure are similar to differences observed between crystal structures of the same protein.Finally, the energetics of ligand binding were analyzed for the all-atom minimized coordinates. Strain energy induced in the ligand, the corresponding entropy loss due to shifts in harmonic frequencies, and the role of specific residues in ligand binding were examined. Water molecules, even those not in direct contact with the ligand, were found to have significant interaction energies with the ligand. Thus, the inclusion of at least one shell of waters may be vital for accurate simulations of enzyme complexes.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040106
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    Preferred conformational state of the N-terminus section of a bovine growth hormone fragment (residues 96-133) in water is an omega loop (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 48-55 
    Details
    ISSN: 0887-3585
    Keywords: nuclear magnetic resonance ; computer modeling ; linear peptides ; omega loop ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The solution structure of a 38-amino-acid-residue, biologically active fragment of bovine growth hormone (bGH96-133) was investigated with a combined nuclear magnetic resonance (NMR) and computer modeling approach. With the distance geometry program DISGEO and distance constraints derived from the nuclear Overhauser enhancement (NOE) experiments, it was found that residues Ser-100 to Tyr-110 circumscribe an Ω-loop, a recently categorized feature of nonregular secondary protein structure.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040107
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  • 50
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    Structure-function relationships in 3-phosphoglycerate kinase: Role of the carboxy-terminal peptide (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 56-62 
    Details
    ISSN: 0887-3585
    Keywords: Protein engineering ; mutagenesis ; enzyme catalysis ; conformational changes ; domain movement ; hinge bending ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Yeast 3-phosphoglycerate kinase (PGK) is a monomeric enzyme (Mr ∼ 45,000) composed of two globular domains. Each domain corresponds approximately to the amino- and carboxyterminal halves of the polypeptide chain. The carboxy-terminal end extends over the interdomain “hinge” region and packs against the amino-terminal domain. It has been proposed that domain movement, resulting in closure of the active site left, is essential for the catalytic of PGK. Large-scale conformational changes have also been postulated to explain activation of the enzyme by sulfate ions. Using site-specific mutagenesis, we have removed a 15-amino-acid carboxy-terminal fragment, in order to probe its role in the substrate- and sulfate-induced conformational changes. The truncated enzyme exhibited approximately 1% of the activity of native PGK and lost the ability to undergo sulfateinduced activation. The Km for ATP was essentially unchanged (Km = 0.23mM), whereas the Km value for 3-phosphoglycerate was increased about eightfold (Km = 3.85 mM and 0.50 mM, respectively). These results suggest that the carboxy-terminal segment is important for the mechanism of substrate- and specific-induced conformational transitions. CD spectra and sedimentation velocity measurements indicate that the carboxy-terminal peptide is essential for structural integrity of PGK. The increased susceptibility of the truncated enzyme to thermal inactivation implies that the carboxy-terminal peptide also contributes to the stability of PGK.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040108
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    Model of a complex between the tetrahemic cytochrome c3 and the ferredoxin I from Desulfovibrio desulfuricans (Norway strain) (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 63-70 
    Details
    ISSN: 0887-3585
    Keywords: molecular graphics ; protein complex ; electron transfer ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A three-dimensional model of an electron-transfer complex between the tetrahemic cytochrome c3 and the ferredoxin I from the sulfatereducing bacterium Desulfovibrio desulfuricans (Norway strain) has been generated through computer graphics methods. The model is based on the known X-ray structure of the cytochrome and on a model of the ferredoxin that has been derived through computer graphics modeling and energy minimization methods, from the X-ray structure of the homologous ferredoxin from Peptococcus aerogenes. Four possible models of interaction between the two molecules were examined by bringing in close proximity each of the four hemes and the redox center (4Fe-4S) of the ferredoxin and by optimizing the ion pairs interactions. One of these models shows by far the “best” structure in terms of charges, interactions, and complementary f the topology of the contact surfaces. In this complex, the distance between the iron atoms of the ferredoxin redox center and the hemic iron atom is 11.8 Å, which compares well with those found between redox centers in other complexes. The contact surface area between the two molecules is 170 Å2.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040109
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    Electronic Resource
    Electronic Resource
    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040201
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    Crystallization and preliminary investigation of single crystals of deoxyuidine triphosphate nucleotidohydrolase from Escherichia coli (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 71-75 
    Details
    ISSN: 0887-3585
    Keywords: dUTPase ; nucleotide binding enzyme ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Deoxyuridine triphosphate nucleotidohydrolase (dUTPase), an enzyme in the nucleotide metabolism that is a pyrophosphatase hydrolyzing dUTP, has been crystallized. The crystals belong to the trigonal space group R3 and diffract beyond 2 Å. The native dUTPase crystals and a mercury derivative are stable in the X-ray beam and are suitable for a high resolution X-ray structure analysis.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040110
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    Crystallographic structure analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 77-88 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; diffraction ; anomalous scattering ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The molecular structure of lamprey hemoglobin was previously determined and refined by conventional crystallographic analysis. In this study, the structural analysis has been repeated in the course of developing the method of multiwavelength anomalous diffraction (MAD) for phase determination. New experimental and analytical procedures that were devised to perform this determination should have general applicability. These include an experimental design to optimize signal strength and reduce systematic errors, experimental evaluation of anomalous scattering factors, and a least-squares procedure for analyzing the MAD data. MAD phases for the structure at 3Å resolution are as accurate overall as the multiple isomorphous replacement (MIR) phases determined previously.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040202
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    Conformation of alamethicin in phospholipid vesicles: Implications for insertion models (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 89-98 
    Details
    ISSN: 0887-3585
    Keywords: membrane proteins ; channels ; circular dichroism spectroscopy ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The secondary structure of alamethicin, a membrane channel-forming polypeptide, has been examined by circular dichroism spectroscopy to determine the relationship of its conformation in organic solution to its conformation in a membrane-bound state. The spectrum of alamethicin in small unilamellar dimyristoyl phosphatidylcholine vesicles is significantly different from its spectrum in 10% methanol/acetonitrile, the solvent from which it was crystallized (Fox and Richards: Nature 300:325-330, 1982), as well as its spectrum in methanol, the solvent in which NMR studies have been done (Banerjee and Chan: Biochemistry 22:3709-3713, 1983). This suggests that structural models based on studies of the molecule in organic solvents may not be entirely appropriate for the membrane-bound state. To distinguish between different models for channel formation and insertion, two different methods were used to associate the alamethicin with vesicles; in addition, the effect of oligomerization on the conformation of the membrane-bound state was investigated. These studies are consistent with a modified insertion model in which alamethicin monomers, dimers, or trimers associate with the bilayer and then spontaneously oligomerize to form a prechannel with a higher helix content. This aggregate could then “open” upon application of an appropriate gating transmembrane potential.
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    Structural analysis of the 2.8 Å model of xylose isomerase from Actinoplanes missouriensis (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 165-172 
    Details
    ISSN: 0887-3585
    Keywords: α/β barrels ; crystal structure ; glucose isomerase ; xylose isomerase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of Xylose isomerase (X.I.) from Actinoplanes missouriensis has been solved to 2.8 Angstroms resolution. Phases were determined from a single Eu3+ derivative and from the noncrystallographic 22 symmetry of the tetrameric molecule. An atomic model was built and subjected to restrained crystallographic refinement. The resulting model is shown to be closely similar to the recently reported X.I.'s structures from three other bacterial sources. Each monomer is found to be composed of an eight-stranded α/β “T.I.M.” barrel forming an N-terminal domain of 328 residues followed by a large loop of 66 residues embracing an adjacent subunit. Analysis of intersubunit packing shows that the X.I. tetramer is an assembly of two tight dimers. The β barrel fits a simple hyperboloid model as other T.I.M. barrels do. The active site, identified as the binding site for the inhibitor xylitol, is located at the carboxyl end of the beta strands in the barrel next to a pair binding site for Eu3+ ions, which are assumed to the sites for the divalent ions involved in catalysis. Active sites in the tetramer are oriented towards the interface between dimmers. It is suggested that subunit interfaces might stabilize the active site region and this might explain the oligomeric nature of the other α/β barrel enzymes.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040303
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  • 57
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    Formation of heterodimers between wild type and mutant trp aporepressor polypeptides of Escherichia coli (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 173-181 
    Details
    ISSN: 0887-3585
    Keywords: DNA binding protein ; ligand binding ; equilibrium dialysis ; dimer ; stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Availability of the three-dimensional structure of the trp repressor of Escherichia coli and a large group of repressor mutants has permitted the identification and analysis of mutants with substitutions of the amino acid residues that from the tryptophan binding pocket. Mutant aporepressors selected for study were overproduced using a multicopy expression plasmid. Equilibrium dialysis with 14C-tryptophan and purified mutant and wild type aporepressors was employed to determine tryptophan binding constants. The results obtained indicate that replacement of theronine 44 by methionine (TM44) or arginine 84 by histidine (RH84) lowers the affinity for tryptophan approximately two-and four-fold, respectively. Replacement of ariginine 54 by histidine (RH84) or glycine 85 by ariginine (GR85) results in complete loss of tryptophan binding activity. Purified mutant and wild type aporepressors were used in vitro heterodimer studies. The trp repressor of E. coli functions as a stable dimer. A large number of trp repressor mutants prduces defective repressors that are transdominant to the wild type repressor in vivo. The transdominance presumably results from the formation of inactive or slightly active heterodimers between the mutant and wild type polypeptide subunits. An in vitro assay was developed to detect and measure heterodimer formation. Heterodimer formation was thermally induced, and heterodimers were separated on nondenaturing polyacrylamide gels. Aporepressors readily formed heterodimer formation upon treatment at 65°C for 3 minutes. Heterodimer formation was significantly retarded by the presence of the corepressor, L-tryptophan. Indole-3-propionic acid, 5-methyl tryptophan, and other analogs of tryptophan, as well as indole, also inhibited heterodimer formation. These results indicate that the presence of the indole moiety in the corepressor binding pocket increases the stability of the dimer.
    Additional Material: 5 Ill.
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    Homology of lysosomal enzymes and related proteins: Prediction of posttranslational modification sites including phosphorylation of mannose and potential epitopic and substrate binding sites in the α- and β-subunits of hexosaminidases, α-glucosidase, and rabbit and human isomaltase (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 182-189 
    Details
    ISSN: 0887-3585
    Keywords: consensus sequences ; secondary structure ; mannose 6-phosphate ; substrate specificity ; proteolytic processing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recently developed computer programs, including secondary structure and epitopic site predictions, have been used to align lysosomal proteins for maximum homology, based on conservative interchanges, and the aligned sequences have been searched for potential sites for posttranslational modification, glycosyaltion, and binding and catalysis of substrate. The homology and prediction of the posttranslational modification of the α- and β-subunits of hexosaminidase is in good agreement with previous observations, and an explanation of the differing substrate specificities of the two subunits is advanced. We shows that the striking homology between α-glucosidase and isomaltase is reflected in that apparent conversation of the active site in both enzymes. Nonhomologous regions have been examined in detail in a search for binding sited for glycogen and maltose, and two such sites have been tentatively identified. A highly redundant consensus sequence for the Phosphorylation of mannose in lysosomal proteins, YXX(Y, W, or F), is suggested.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040305
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    Comparative molecular model building of two serine proteinases from cytotoxic T lymphocytes (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 190-204 
    Details
    ISSN: 0887-3585
    Keywords: computer graphics ; energy minimization ; proteolytic enzymes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two genes that are expressed when precursor cytotoxic T lymphocytes are transformed to T killer cells have been cloned and sequenced. The derived amino acid sequences, coding for the cytotoxic cell protease 1 (CCP1) and Hannuka factor (HF) are highly homologous to members of the serine proteinase family. Comparative molecular model building using the known three-dimensional structures and the derived amino acid sequences of the lymphocyte enzymes has been provided useful information, especially in predicting the conformations of the substrate binding sites. In applying this modelling procedure, we used the X-ray structures of four serine proteinase to provide a structurally based sequences alignment: α-chymotrypsin (CHT), bovine trypsin (BT), Streptomyces griseus trypsin (SGT), and rat must cell protease 2 (RMCP2). The root mean square differences in α-carbon atom positions among these four structures when compared in a pairwise fashions range form 0.79 to 0.97 Å for structurally equivalent residues. Te sequences of the two lymphocyte enzymes were then aligned to these proteinase using chemical criteria and the superimposed X-ray structures as guides. The alignment showed that the sequence of CCP1 was most similar to RMCP2, whereas HF has regions of homology with both RMCP2 and BT. RmCP2 and BT as templates for HF, the molecular models were constructed. Intermolecular steric clashes that resulted from replacement of amino acid chains of the templates by the aligned residues of CCP1 and HF were relieved by adjustment of the side chain conformational angels in an interactive computer graphics device. This process was followed by energy minimization of the enzyme model to optimize the stereochemical geometry and to relieve any remaining unacceptably close nonbonded contacts. The resulting model of CCP1 has an arginie residue at position 226 in the specificity pocket, thereby predicting a substrate preference for P1 aspartate or glutamate residues. The model also predicts favorable binding for a small hydrophobic residue at the P2 position of the substrate. The primary specificity pocket of HF resembles that of BT and therefore predicts a lysine or arginine preference for the P1 residue. The arginine at position 99 in the model of HF suggests a preference for aspartate or glutamate side chains in the P2 positions of the substrate. Both CCP1 and HF have a free cysteine in the segment of the polypeptide 88 to 93. Models of the dimeric form of these enzymes can be constructed by forming disulfide bridges between the suitably oriented monomers, ie., Cys88-Cys88′ for CCP1 and Cys93-Cys93′ for HF.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040306
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    Interaction of peptide boronic acids with elastase: Circular dichroism studies (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 205-210 
    Details
    ISSN: 0887-3585
    Keywords: slow-binding inhibition ; transition-state analog ; conformational change ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Boronic acid derivatives of good peptide substrate of the serine proteases cause slow-binding inhibition, manifested as biphasic binding (Kettner and Shenvi: J. Biol. Chem. 259:15106-15114, 1984). These inhibitors are thought to act as reaction-intermediate analogs. Three peptides Boronic acids - Ac-Pro-boro-Val-OH, DNS-Ala-Pro-boro-Val-OH, and Ac-Ala-Ala-Pro-boro-Val-OH - were chosen for farultraviolet circular dichroism (CD) studies in order to determine whether the second phase involves a conformational change of pancreatic elastase. The dipeptide is a simple competitive inhibitors (Ki = 0.27 μM) and the latter are slow-binding inhibitors (Ki = 16.4 and 0.25 nM, respectively). Spectral deconvolution and correction for the formation of antiparallel β-sheet by the peptide inhibitors itself indicate that there is no significant change in the secondary structure of the enzyme in the either the initial or final inhibitors complex. A kinetic experiment confirmed that the slow-binding step was not associated with a CD spectral change, and that therefore a protein conformational change was not responsible for the sow binding.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040307
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    Masthead (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340040401
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  • 62
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    Helix lap-joints as ion-binding sites: DNA-binding motifs and Ca-binding “EF hands” are related by charge and sequence reversal (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 229-239 
    Details
    ISSN: 0887-3585
    Keywords: repressor proteins ; helix dipole ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The DNA-binding helix pairs in gene repressor and activator were compared with other approximately perpendicular pairs of adjacent helices in the known protein structures. Two other examples of closely matching conformations were found in cytochrome c peroxidase (residues 153-174) and in ribosomal L7/L12 protein (residues 68-89). Another group of such offset “lap-joints” are the Ca-binding “EF hand” structures, which bind a positive rather than a negative ligand. The EF hands turn out to match the DNA-binding motifs quite well (outside of the loop) if their sequence direction is reversed. This conformation is thus not as unusual as had been thought, but may have a more generalized role in ion binding and occasionally occur in a purely structural role.
    Additional Material: 12 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040402
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    Structural alignment and analysis of two distantly related proteins: Aplysia limacina myoglobin and sea lamprey globin (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 240-250 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; X-Ray crystal structure ; homology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two new globin structures have recently been determined at high resolution: the globin from the mollusc Aplysia limacina at 1.6 A resolution and a new refinement of the structure from sea lamprey. Two amino acid sequences of these homologous molecules have only 30% residue identity in an optimal alignment. We discuss some of the problems arising in the alignment of Aplysia globin with other globins of known structure, a challenging problem because of the distant relationship. Four independent approaches were applied to the alignment of the Aplysia and lamprey globins, including those based on individual sequence comparisons, structural analysis, and the relatively new method of templates or fingerprints derived for an entire family of proteins. We also compare these two new structures with what is already known about the globin family. A detailed description of the two structures shows that the two molecules contain the main structural features common to all the globins so far studied with several minor but interesting hitherto unobserved variations.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040403
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    Diffusion-collision model for the folding kinetics of myoglobin (1988)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 4 (1988), S. 211-227 
    Details
    ISSN: 0887-3585
    Keywords: protein-folding ; multiple pathways ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The diffusion-collision model has been used to analyze the folding kinetics of myoglobins. The microdomains, which are the basic units that coalesce during the folding, are identified with the helices and the stabilizing contacts between helices are determined form the native structure. Both association and disassociation reactions are included and a range of stabilization parameters is investigated to determine the variations in overall rate and the relative contributions made by the different intermediates during the folding process. In a comparison of folding to the native state and to the midpoint of the folding transitions. (i.e., 50% native protein at the completion of the reaction) significant differences in the contributing intermediates are found.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340040308
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    Tutorials in molecular and cell biology: Protein engineering. Alan R. Liss., New York. 1987. 365pp. $36.00 (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. i 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jmr.300010209
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    Molecular recognition: Model studies with convergent functional groups (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 1-8 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Model studies of molecular recognition are reviewed with emphasis on contributions from macrocyclic chemistry. Recent developments concerning new molecular shapes are discussed. The advantages of a molecular cleft are presented. In these structures functional groups converge to create a microenvironment complementary to substrates. Specifically, di-, tri- and tetracarboxylic acids of varying sizes are shown to recognize smaller molecules of complementary shape. The new receptors function by a combination of hydrogen bonding and aryl stacking interactions. Substrates include amines, acids, amino acids, metal ions and nucleotide components. The relationship between functional group orientation and catalysis is explored and two systems capable of concerted acid/base catalysis are introduced.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jmr.300010103
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    Monosized, magnetic polymer particles: Their use in separation of cells and subcellular components, and in the study of lymphocyte function in vitro (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 9-18 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: By employing the principles of “activated swelling”, monosized, superparamagnetic polymer particles have been prepared ranging in size from 1-100 μm. Both during and after the swelling process, the particles can be modified to meet a series of specific demands making them potentially very interesting for many separation and assay purposes.Using monoclonal antibodies to direct the magnetic beads to their targets, immunomagnetic separation has turned out to be one of the most specific, reliable and, above all, the fastest technique available today to isolate particulate material for further studies. So far, most efforts have been concentrated on methodology for fractionation of cells in suspension, such as removal of tumour cells from bone marrow or isolation of lymphoid cells from peripheral blood. These studies have both established the parameters necessary for optimal performance and at the same time laid the groundwork for future developments making immunomagnetic separation an exciting new tool in many research areas.High speed and specificity are the most conspicuous features of immunomagnetic cell separation. These properties have been exploited in the successful development of a new technique for tissue typing of cells directly from peripheral blood specimens. Both higher sensitivity and specificity have been obtained. The same principles can be used for fast and safe quantification of cell populations and subpopulations in blood and cell suspensions.The functions of, and interactions between, peripheral blood cell populations or subpopulations in the immune response have also been studied with high precision. The significance of direct cell contact on the one hand, and soluble factors on the other, can now be established in detail. Immunomagnetic beads have also been used to study the interaction between various T lymphocyte membrane molecules in the early phases of the activation process.Finally, the usefulness of specially developed particles for the fractionation of subcellular components is described.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010104
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    Cognitive features of continuous antigenic determinants (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 32-41 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We sought to identify the features controlling the specificity of antibody recognition and thus gain insights into molecular recognition between proteins in general. A total of 103 epitopes with in 63 well-defined antigenic peptides homologous with the relevant antigen sequence were identified. The contribution of each amino acid residue to the antibody binding activity of each apitope was investigated by ELISA testing of complete sets of peptide analogs containing single amino acid replacements. The data are summarized in a replaceability matrix. Some of the high frequency replaceabilities were expected, such as aspartate for glutamate, serine for threonine, etc., but unexpected relationships were also found, such as a high degree of acceptability of methionine as a replacement. Replaceability with a residue of opposite charge was rare. Glycine and tyrosine were frequently of low acceptability, except for glycine as a replacement for alanine. It was found that on average only about four to five amino acid residues in epitopes were required to determine specificity and provide binding energy. Specificity and binding energy were attributed to amino acid side chains rather than main chain atoms. Propensity factors for occurrence of amino acids in antigenic determinants were calculated. The prominence of certain hydrophobic residues as residues critical to recognition by antibody suggests that the molecular surface of an antigen in its combined from with antibody is altered from that occurring in the absence of antibody. Thus, antigenicity is not a static surface phenomenon but depends on the ability of the antigen to undergo rearrangement, supporting the induced fit concept.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010107
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    Chemical probes reveal no evidence of Hoogsteen base pairing in complexes formed between echinomycin and DNA in solution (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 138-151 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Five different DNA fragments have been treated with a range of conformationally sensitive reagents in an effort to probe structural chages in DNA associated with binding of the bis-intercalating antibiotic echinomycin. For each probe, the intensity and pattern of its reactivity with DNA have been analyzed in order to elucidate the effect of antibiotic binding on the accessibility of a specific site of sites to chemical attack. It was found that in one of the DNA fragments, pTyr2DNA, several purine residues exhibit enhanced reactivity to diethyl pyrocarbonate (DEPC) in the absence of bound antibiotic, and that this strongly sequence specific reaction is enhanced in the presence of quite low echinomycin concentrations. The echinomycin-dependent reactivities towards DEPC of three homologous DNA fragments, chosen for their subtly different antibiotic binding characteristics, were also investigated. It was found that small changes in base sequence generate striking changes in susceptibility to modification by DEPC. The abolition of one antibiotic binding site leads to the creation of an new, intense DEPC-reactive site. In the presence of moderate concentrations of echinomycin, specific thymidine residues exhibit enhanced reactivity towards osmium tetroxide. No differences in the reactivities of the DNA fragments towards bromoacetaldehyde, S1 nuclease, dimethyl sulphate of potassium tetrachloropalladinate were observed in the presence of the antibiotic. DEPC reactions were performed on tubercidin (7-deaza-adenosine) to determine the DEPC reactive positions in situations where N-7 is inaccessible. Tubercidin was found to be generally resistant to attack by DEPC followed by treatment with base. We conclude that the bulk of structural changes induced by the binding of echinomycin to DNA do not involve Hoogsteen base pairing, but rather are due to sequence-specific unwinding of the helix in a manner which is strongly dependent on the nature of surrounding nucleotide sequences.
    Additional Material: 13 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010307
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    Molecular foundations of drug-receptor interaction. Cambridge University Press, Cambridge, London, New York, New Rochelle, Melbourne, Sydney 1987. 381 pp. (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. ii 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jmr.300010308
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    Truncation of the ectodomain of the human insulin receptor results in secretion of a soluble insulin binding protein from transfected CHO cells (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 25-31 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Insulin receptor is an integral transmembrane glycoprotein comprised of two α-(∼ 135kDa) and two β-(∼ 95kDa) subunits, which is synthesized as a single polypeptide chain precursor (αβ). The primary sequence of the human insulin receptor (hIR) protein, deduced from the nucleotide sequence of cloned human placental mRNAs, predicts two large domains (929 and 403 residues) on either side of a single membrane spanning domain (23 residues); each of these major domains has a distinct function (insulin binding and protein/tyrosine kinase activity, respectively). To experimentally test this deduced topology, and to explore the potential for independent domain function by the hIR extracellular domain, we have constructed an expression plasmid encoding an hIR deletion mutant which is truncated 8 residues from the beginning of the predicted transmembrane domain (i.e., 921 residues). This domain of the hIR is in fact processed into α-and truncated β-subunits and secreted with high efficiency from transfected CHO cell lines which express this mutant hIR, and the protein accumulates as an (αβ)2 dimer in the medium. This molecule is recognized by a battery of 13 monoclonal antibodies to epitopes on the IR extracellular domain, four of which block insulin binding and two of which require the native conformation of the IR for recognition. Further, this domain, binds insulin with an apparent dissociation constant comparable to that of the wild-type hIR. However, the secreted dimmer displays a linear Scatchard plot, while that of the wild-type membrane-associated hIR curvilinear. These results, together with previous results with a soluble derivative of the hIR cytoplasmic protein/tyrosine kinase domain, are consistent with the deduced topology. The IR is indeed comprised of two large soluble domains connected by a single membrane spanning domain, which on the one hand act concert upon ligand binding (insulin-dependent activation of the protein/tyrosine kinase) to initiate the insulin response in cells, but on the other hand are each capable of autonomous function (ligand binding and protein/tyrosine kinase activity, respectively).
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010106
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    Conformational and receptor binding properties of human EGF and TGF-α second loop fragments (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 116-123 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The solution conformation of the second loop fragment of human EGF, [Ala20]EGF(14-31), was determined using two-dimensional NMR homonuclear Hartmann-Hahn and rotating frame nuclear Overhauser enhancement spectroscopy. The results are compared with the conformation of the second loop fragment of human TGF-α, [Ala21] TGF-α(16-32), and with that of the second loop of intact EGF. Comparison of the two experimentally determined structures of the second loop fragments shows significant differences in the turn regions of each peptide. For the EGF fragment, hydrophobic side chain groups protrude away from the ring, whereas for the TGF-α fragment hydrophilic groups are directed away from the ring. Although these turn regions represent the putative receptor binding sites, neither second loop fragment binds to the EGF receptor. The biological activity is discussed in terms of the conformational differences found for the two second loop fragments.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010304
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    Anhydroelastase: Enhanced affinity toward product-type ligands revealed by affinity chromatography (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 93-98 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Anhydroelastase was effectively isolated by a single operation of affinity chromatography from a complex mixture produced by phenylmethylsulfonylation and alkaline treatment of porcine pancreatic elastase. The adsorbent used for the chromatography was 6-aminohexanoyl-trialanine, which corresponds to a product of elastase action, immobilized on Sepharose 4B. Successful resolution by the operation indicated that this immobilized ligand possesses the highest affinity for anhydroelastase among various proteins including regenerated elastase in the mixture. Comparative affinity chromatography on immobilized anhydroelastase and on immobilized native elastase further confirmed the stronger interaction of anhydroelastase with the product-type peptides. Immobilized anhydroelastase was also found to be useful in the purification and search for naturally occurring proteinase inhibitors.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010207
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    Masthead (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988) 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jmr.300010301
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    Contribution of antigen processing to the recognition of a synthetic peptide antigen by specific T cell hybridomas (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 99-106 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Most antigens recognized by T cells require unfolding or partial degradation (processing) followed by association with Major Histocompatibility Complex (MHC) molecules. We examined the processing requirements for the presentation of antigen to two T cell hybridomas which recognize the α-helical synthetic polypeptide antigen Poly 18, Poly [EYK(EYA)5], in association with I-Ad. Hybridoma A.1.1 responds to EYK(EYA)4 as the minimum antigenic sequence while hybridoma B.1.1 recognizes (EYA)5 sequence. It was found that these hybridomas responded to Poly 18 and to minimum peptide sequences presented by glutaraldehyde and chloroquine treated antigen presenting cells (APC), suggesting that antigen processing is not a requirement for the activation of these cells. The reactivity pattern of hybridoma B.1.1 in the presence of glutaraldehyde fixed APC revealed that antigens containing lysine were presented with much less efficiency than antigens without lysine, suggesting an interaction of these residues with the antigen presenting cell surface. We discuss the possibility that alanine residues in the α-helical Poly 18 form a hydrophobic ridge which may be required for appropriate interaction between antigen, the T cell receptor, and MHC molecules.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010208
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    Estrogen receptor interaction with immobilized metals: Differential molecular recognition of Zn2+, Cu2+ and Ni2+ and separation of receptor isoformsSupported in part by the US Department of Agriculture, Agricultural Research Service Agreement No. 58-7MNI-6-100. The contents of this Publication do not necessarily reflect the views or policies of the US Department of Agriculture nor does mention of tread names, commercial products, or organizations imply endorsement by the US Government. (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 80-92 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have utilized iminodiacetate (IDA) gels with immobilized Zn2+, Cu2+ and Ni2+ ions to evaluate the metal binding properties of uterine estrogen receptor proteins. Soluble (cytosol) receptors labeled with [3H]estradiol were analyzed by immobilized metal affinity chromatography (IMAC) before as well as after (1) 3 M urea-induced transformation to the DNA-binding form, and (2) limited trypsin digestion to separate the steroid- and DNA-binding domains. Imidazole (2-200 mM) affinity elution and pH-dependent (pH 7-3.6) elution techniques were both evaluated and found to resolve several receptor isoforms differentially in both the presence and absence of 3 M urea. Individual receptor forms exhibited various affinities for immobilized Zn2+, Cu2+ and Ni2+ ions, but all intact receptor forms were strongly adsorbed to each of the immobilized metals (Ni2+ 〉 Cu2+ » Zn2+) at neutral pH. Generally, similar results were obtained with IDA-Cu2+ and IDA-Ni2+ in the absence of urea. Receptors were tightly bound and not eluted before 100 mM imidazole or pH 3.6. Different results were obtained using IDA-Zn2+; at least four receptor isoforms were resolved on IDA-Zn2+. Receptor-metal interaction heterogeneity and affinity for IDA-Zn2+ and IDA-Cu2+, but not IDA-Ni2+, were substantially decreased in the presence of 3 M urea. The receptor isoforms identified and separated by IDA-Zn2+ chromatography were not separable using high-performance size-exclusion chromatography, density gradient centrifugation, chromatofocusing or DNA-affinity chromatography. The affinity of trypsin-generated (mero) receptor forms for each of the immobilized metals was decreased relative to that of intact receptor. High-affinity metal-binding sites were mapped to the DNA-binding domain, but at least one of the metal-binding sites is located on the steroidbinding domain. Recovery of all receptor forms from the immobilized metal ion columns was routinely above 90%. These results demonstrate the differential utility of various immobilized metals to characterize and separate individual receptor isoforms and domain structures. Receptor-metal interactions warrant further investigation to establish their effects on receptor structure/function relationships. In addition to the biological implications, recognition of estrogen receptor proteins as metal-binding proteins suggests new and potentially powerful receptor immobilization and purification regimes previously unexplored by those in this field.
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010206
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    Transition of environmental polarity of tyrosine-76 of Trimeresurus flavoviridis phospholipase A2 upon active site ligand binding (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 124-129 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Modification of Trmeresurus flavoviridis phospholipase A2 with a 5-fold molar excess of tetranitromethane produced 40% active mononitrotyrosyl phospholipase A2 in which Try-76 was specifically nitrated. This is in contrast to the case of mammalian pancreatic phospholipases A2 where Tyr-70 but not Tyr-76 was nitrated. When Ca2+ was bound to T. flavoviridis mononitrotyrosyl phospholipase A2, nitrated tyrosine (Tyr)NO2-76 moved from a less polar site to a polar site with the decrease of the pKa value of its hydroxyl group. Nitration of Tyr-76 did not influence the binding affinity to Ca2+. Addition of laurylphosphorylcholine to mononitrotyrosyl phospholipase A2 in the presence of Ca2+ caused the movement of Try(NO2)-76 from a polar environment to a less polar environment with the rise in the pKa value. Tyrosine-76 is located in the site whose environmental polarity is affected by the binding of the ligands to the active site. As Tyr-76 is located in the site not proximal to the active site, it could be assumed that the conformational change induced by the binding of the ligands extends to the region remote from the active site in T. flavoviridis phospholipase A2. This might provide evidence of long-range diffusional coupling between remote sites in the noncooperative globular protein.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010305
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    Reconstitutions of transporters, receptors, and pathological states. Academic Press, Orlando, FL. 1985. 27lpp. £22.50 (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 58-58 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jmr.300010110
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  • 79
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    Substance P synthesis by enzymatic fragment condensation using product-directed antibodies as molecular traps (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 59-62 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: This paper describes the enzyme catalyzed synthesis of the undecapeptide substance P from its non-associated fragments (1-7) and (8-11) or (1-8) and (9-11). The fragment condensation was mediated by the use of product specific antibodies as molecular traps. As catalyst a previously purified endopeptidase was used which specifically hydrolyzes substance P at the Phe7-Phe8 and Phe8-Gly9 bonds. The synthesis was performed in analytical scale and product formation was guided by reversed phase HPLC combined with radioimmunoassay. It appeared that the substance P fragments (1-8) and (9-11) were condensed to a larger extent than (1-7) and (8-11). This observation may well result from the higher affinity of the antibodies observed for substance P (8-11) as compared to that found for the other fragments. Increased concentration of the antibodies also seemed to result in enhanced resynthesis of substance P.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010202
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    T4 Phage deoxyribonucleoside triphosphate synthetase: Purification of an enzyme complex and identification of gene products required for integrityFinancial support for the this work came from National Institutes of Health Research Grant No. AI-15145. (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 48-57 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have isolated a highly enriched preparation of the multienzyme complex which synthesize Deocyribonuleoside triphosphates (dNTPs) from bacteriophage T4-infected bacteria. By a combination of SDS polyacrylamide gel electrophoresis and assays for specific enzyme activities, we have been able to identify in our final preparation ten different gene products which were previously identified as constituents of this complex, based upon studies with crude preparation. The complex dissociates at high concentrations of NaCl and MgCl2 but is stable under ionic conditions thought to exits in vivo. The purified complex catalyzes the efficient five-step conversion of dCTP to dTTP. Experiments with several T4 mutants have demonstrated that gene product encoded by cd, regA, nrdA, and nrdB are necessary to retain physical integrity of the complex throughout the preparative procedure, while gp44, gp55, and gppseT are not required. We conclude from this evidence that the T4 early gene products which function in dNTP biosynthesis are, in fact, physically linked as a multienzyme complex, and that regA contributes to the integrity of this complex. However, the dNTP-synthesizing complex as we isolate it contains no detectable DNA polymerase, nor have other known replication proteins been detected.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010109
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  • 81
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    Conformational homologies among cytokines: Interleukins and colony stimulating factors (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 107-110 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Some 30 cytokine amino acid sequences (mainly interleukins, colony stimulating factors and tumor necrosis factors) have been examined for evidence of secondary structure as well as longer-range interactions of a type likely to lead to stable α-helical bundles. Most, though not all, of the cytokines examined have a high predicted α-helical content (40-60%) and quasi-repeating heptads containing i/i+3 apolar periodicities. This major subset of the cytokines is predicted to be characterized by molecules in which 4-α-helical bundles with an average length of 25Å are the most marked conformational features. Based on these conclusions, we suggest structures for huG-CSF, huGM-CSF and muIL-5 in which defined loop segments at the ends of helical bundles are the most likely sites for binding and recognition by specific cell receptors. As such, they provide a means for testing or refining the three working models we have defined, using currently available methods of site-directed substitution and deletion mutagenesis, as well as synthetic peptides corresponding to the proposed loop sequences and the use of monoclonal antibodies of defined epitopic specificity. The structure arrived at for huGM-CSF is consistent with the limited data currently available concerning the residues which are important for binding and activity.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010302
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  • 82
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    Glycolipid-directed FH6 monoclonal antibody recognizes high molecular weight glycprotein antigen carrying sialyl LeX-i determinant in the culture supernatant of PC-9 cellsFor the nomenclature for the antigen, Lex, refer to the footnote in the Kannagi et al. (1986) (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 111-115 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The properties of the antigen recognized by monoclonal antibody FH6 have been analyzed. FH6 was originally generated against a glycolipid, i.e. a difucoganglioside isolated from human colonic adenocarcinoma, and specifically reacts with sialyl Lex-i detreminant. Several culture supernatants of human carcinoma cell line cells were found to have high levels of FH6-reactive antigen, and PC-9, a human lung carcinoma cell line was used for the analysis. A solid-phase sandwich radioimmunoassay was performed to detect the antigen. The antigenic activity was extractable in 0.6 M PCA or 7% TCA, and was sensitive to mild alkaline treatment and to Pronase digestion. Most of the antigen was eluted in the void volume of a Sepharose CL-2B column, which indicates that its molecular weights is greater than several million. It was eluted from a DEAE-cellulose column at a NaCl concentration in the range of 0.2-0.25 M. The immunoaffinity-purified antigen has a high carbohydrate content of more than 80%. These data indicate that the antigen recognized by FH6 in the culture supernatant of PC-9 is not a glycolipid, but a high molecular weight glycoprotein which could be referred to as a mucin, or a proteoglycan, which contains keratan-sulfate like glycosaminoglycan chains, as judged from the results of the glycosidase treatments.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010303
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  • 83
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    Zymogen activation: Effect of peptides sequentially related to the bovine β-trypsin N-terminus on kazal inhibitor and benzamidine binding to bovine trypsinogen (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 130-137 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The activating effect of peptides sequentially related to the Ile 16-Vall7-Gly 18 N-terminus of bovine β-trypsin (nemely Ile-Val-Gly, Ile-Val, Ile-Leu Ile-Ala, Val-Val, Leu-Val, and Val-Leu) on the thermodynamic parameters for the binding of the porcine pancreatic secretory trypsin inhibitor (Kazal inhibtor) and benzamidine to bovine trypsinogen was investigated at pH 5.5 (Bis tris-HCI buffer, I=0.1 M) and T=21 ± 0.5°C. Thermodynamic parameters for Kazal inhibitor and benzamidine association to the binary peptide/zymogen adducts are more favorable than those observed for ligand binding to the proenzyme alone, although never as much as those reported for the formation of bovine β-trypsin/Kazal inhibitor and bovine β-trypsin/benzamidine adducts. Analogously, the affinity of activating peptides for the binary proenzume/Kazal inhibitor and binary proenzyme/benzamidine complexes is higher than that observed for peptide binding to free bovine trysinogen. Differences in affinity for ligand binding to free bovine trypsinogen. Differences in affinity for ligand binding to free bovine trypsinogen, to its binary adducts and to bovine β-trypsin suggest the presence of different activation levels of the proenzyme, none of which structurally coincide with that achieved in bovine β-trypsin. The existence of different discrete states suggests that the zymogen-to-active enzyme transition should not be considered as a two-state process but as a multistep event.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010306
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    Editorial (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. i 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jmr.300010102
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    Studies on a possible molecular basis for the structure of mitochondrial cristae (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 19-24 
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    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have investigated a possible molecular basis for mitochondrial cristae formation. Proteoliposomes containing electron transport proteins, cytochrome oxidase, or complex III in their proper orientation bind to pig heart mitoplasts but not pig heart mitochondria. Using Leydig tumor cells, we have confirmed earlier reports that chloramphenicol causes a diminution in cristae content and a change in its characteristic lamellar form. We show that the proteoliposomes containing cytochrome oxidase or complex III in the proper orientation bind to mitoplasts from Leydig tumor cells but do not bind as well to mitoplasts from chloramphenicol-treated Leydig tumor cells. These experiments provide a possible mechanism to explain cristae formation.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010105
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    A design approach to the structural analysis of interleukin-2 (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 42-47 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A semi-synthetic protein design approach has been employed for the structural investigation of a putative helical region at the C-terminus of Interleukin-2. With crystallographic or NMR derived conformational data as yet unavailable, we have relied only on primary sequence information and computer-assisted modelling to direct the analysis. By employing both chemical peptide synthesis and recombinant DNA methods, the C-terminus of IL-2 was modified according to a strategy designed to stabilize helical secondary structure. A semi-synthetic protein incorporating 12 simultaneous amino acid replacements was constructed, which possessed potentiated biological activity and displayed a far UV circular dichroism spectrum comparable to a hybrid protein with the authentic sequence. By comparison, another hybrid protein containing a C-terminal region designed to contain helix breaking residues was totally devoid of bioactivity. These findings provide evidence that the modelling method correctly identified a helix necessary for the formation of a bioactive tertiary fold. Moreover, by employing semi-synthesis it was possible to circumvent the difficulties associated with the preparation, purification and analysis of multiple recombinant proteins, and also to avoid the unreliability of total chemical synthesis for proteins greater than 100 residues.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010108
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  • 87
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    Masthead (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988) 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jmr.300010201
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  • 88
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    Theoretical analysis of compartmented coupling in linear enzyme systems (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 63-68 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Exact equations which describe the kinetic patterns of enzyme/enzyme complexes, when compartmented coupling occurs between them, are presented. Compartmented coupling refers to the creation of a local environment in which the concentration of an intermediate, shared by two enzymes, is higher than its solution concentration. This result in a higher coupling enzyme activity, a condition reflected in a shorter transition time for the system. In this paper, equations are presented which allow experimenters to quantitate the effect of compartmented coupling in terms of changes in the apparent Km and Vmax values. The equations presented in this paper are more exact than those previously derived since they do not incorporate first order assumptions before derivation.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010203
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  • 89
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    Analysis and use of the serum albumin binding domains of streptococcal protein G (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 69-74 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Streptococcal protein G is an IgG-binding receptor with a molecular weight of 63 kDa as predicted from the sequence of the corresponding gene. Here we show that a truncated recombinant protein of 23 kDa still has IgG-binding capacity and also interacts specifically with human serum albumin (HSA). This demonstrates that protein G is a bifunctional receptor. To investigate the structures needed for IgG- and albumin-binding, different parts of the receptor molecule were produced in E. coli using a coupled expression/secretion system. Affinity Chromatography, using IgG or HSA immobilized on Sepharose, Showed that the two binding activities are structurally separated. From these experiments, it was concluded that a region of 64 amino acid residues is sufficient for albumin-binding. The structure of this part of the proteins suggests either a divalent or a trivalent binding capacity. The specific interaction to albumin was used to purify a heterologous protein by affinity chromatography to yield a pure fusion protein in a one-step procedure. The implication of this novel affinity system as a tool to facilitate protein immobilization and purification is discussed.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010204
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  • 90
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    The design and synthesis of mimetics of peptide β-turns (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988), S. 75-79 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The synthesis of an 11 membered ring bis-lactam, a system which is designed as a conformationally restricted mimetic of type I and II β-turns is described. Computer assisted molecular modeling was used to compare the predicted low energy conformers of the turn mimetic with idealized type I and type II turn structures. Initial computation analysis indicates that the basic ring structure will provide an excellent foundation for the development of variety of β-turn mimetics.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300010205
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  • 91
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    Masthead (1988)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 1 (1988) 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jmr.300010101
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    The effects of cation competition on metal adsorption by Rhizopus arrhizus biomass (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 31 (1988), S. 282-286 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260310315
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  • 93
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    Selection of thermotolerant yeast strains for simultaneous saccharification and fermentation of cellulose (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 31 (1988), S. 300-303 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A total of 58 yeast strains from 12 genera were assayed for their ability to grow and ferment carbohydrates in standard Durham tube test at 40, 43, and 46°C. Based on the kinetic parameters for glucose fermentation in shaken flask cultures, the strain Fabospora fragilis CCY51-1-1 was chosen for further studies. It reached about 56.0 and 35.0 g ethanol/L from ∼140 g glucose/L at 43 and 46°C in less than 48 h, respectively. Trichoderma reesei cellulase preparation (400 FPU/L) had not distinct effect on the ethanol yield and biomass production by the selected strain in the first 12 h fermentation at 46°C. Later a negligible decrease in both yields was observed. It was found that Fabospora fragilis did not grow or produce ethanol at 46°C as tho initial ethanol concentration overcame 40 g/L.
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    URL: http://dx.doi.org/10.1002/bit.260310404
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  • 94
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    Chemical stabilization of glucoamylase from Aspergillus niger against thermal inactivation (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 31 (1988), S. 267-277 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The applicability of crosslinking an enzyme to an oxidized polysaccharide by reductive alkylation to enhance thermostability has been investigated for glucoamylase from Aspergillus niger. Direct covalent coupling of the enzyme to periodate-oxidized dextran in the presence of NaBH3CN results in a conjugate which has thermal properties similar to those of the native enzyme. Our working hypothesis postulates that enhancement of thermostability will result from rigidification of the protein's conformation subsequent to the formation of multiple covalent bonds between the protein and the support. On the basis of the known characteristics of glucoamylase from Aspergillus niger, it would seem necessary to introduce additional amino groups in the polypeptide chain of the protein. The incorporation of new amino groups was performed in two phases. First, the glycosidic part of glucoamylase was oxidized by periodate and the resulting aldehyde groups were reductively aminated by a diaminoalkane and NaBH3CIM. Secondly, additional amino groups were introduced on carboxyl functions into the previously aminated glucoamylase by a diaminoalkane and a water-soluble carbodiimide in the presence of maltose to protect the active site. The final derivative was then coupled to periodate-oxidized dextran T-70 in the presence of NaBH3CN. Starting with native glucoamylase, three successive operations give rise to a conjugate which retained 27% of the initial activity when measured with soluble starch and 39% when measured with maltopentaose. Using substrates of various sizes, it was observed that steric hindrance at the active site may result from covalent coupling to dextran T-70. It was demonstrated in heat inactivation experiments that the thermostability of the conjugate was in all cases superior to that of the native enzymes. Finally, it was observed that the operational stability of the conjugate was at least twice that of native glucoamylase at 70°C on 18% maltodextrin. Additional experiments rule out the possibility that thermosta-bilization of the complex is due to other reasons than the increase in the amino content of the protein prior to crosslinking. Neither chemical modification, reticulation nor change in the net charge of the protein resulted in a derivative of glucoamylase which presented enhanced thermostability after conjugation. We conclude that for enzymes which have a low content of available amino groups, the thermostabilization method proposed previously by the present authors may still be applicable if additional amino groups are introduced into the protein prior to its crosslinking to an oxidized polysaccharide. This new example reinforces the generality of this method of stabilization.
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    URL: http://dx.doi.org/10.1002/bit.260310313
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    Production of optically active 2,3-butanediol by Bacillus polymyxa (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 31 (1988), S. 366-377 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Bacillus polymyxa produces (R, R)-2,3-butanediol from a variety of carbohydrates. Other metabolites are also produced including acetoin, acetate, lactate, and ethanol. The excretion of each metabolite was found to depend on the relative availability of oxygen to the culture. When the relative oxygen uptake rate was high, enhanced yields of acetate and acetoin were noted. At an intermediate oxygen availability, the butanediol yield was maximal. When the availability of oxygen was more restricted, higher yields of lactate and ethanol occurred. The cells appeared to regulate themselves such that energy generation is optimal subject to the constraint that the cells do not produce more reducing equivalents than can be oxidized by the electron transport system. The dependence of each product yield on the relative oxygen availability was determined, and this knowledge was used to carry out a fed-batch fermentation that attained a final butanediol concentration of over 40 g/L in 50 h.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/bit.260310413
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    Antifoam effects on ultrafiltration (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 31 (1988), S. 385-389 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260310416
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  • 97
    Electronic Resource
    Electronic Resource
    Fed-batch fermentation for the production of α-amylase by Bacillus amyloliquefaciens (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 31 (1988), S. 426-432 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Fed-batch cultures were performed to maximize the α-amylase activity in a bioreactor. Kinetic equations containing a catabolite repression effect were used to model the enzyme formation from Bacillus amyloliquefaciens. Fed-batch culture experiments were performed using maltose to implement the optimal feeding strategy. Optimal fed-batch culture based on sequential parameter estimation was performed successfully using off-line analysis while the fermentation was in progress. The enzyme activity from the fed-batch culture employing maltose was higher than that of the batch culture by 60%. Enzyme production using starch showed similar trends to those obtained using maltose.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260310506
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  • 98
    Electronic Resource
    Electronic Resource
    Effect of cycling on the stability of plasmid-bearing microorganisms in continuous culture (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 31 (1988), S. 464-469 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The implication of the possible existence of differences in the times required for plasmid-bearing and non-plasmid-bearing microorganisms to adjust their metabolic activities to step changes in their environment is examined. This adaptability difference suggests the possibility of maintaining an engineered strain in continuous culture by transient operation. It is shown for the case where adaptability is neglected that no cycling strategy will prevent the washout of the engineered strain, but the addition to the model of a time delay in substrate utilization can result in coexistence upon cycling. Numerical simulations of cycling in feed substrate concentration are carried out to illustrate the concept Operating diagrams are also constructed to indicate the conditions under which washout of the plasmid bearing strain can be prevented.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260310511
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  • 99
    Electronic Resource
    Electronic Resource
    A new pilot reactor for solid-state fermentation: Application to the protein enrichment of sugar beet pulp (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 31 (1988), S. 476-486 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A new pilot reactor for solid-state fermentation has been used for single-cell protein production on raw sugar beet pulp with a mutant, Trichoderma viride T.S. This pilot plant, having a maximum working capacity of one ton (ca. 200 kg dry matter) can be scaled up to the production plant level. During the process, the protein content increases from 9 to 20-21% (on the basis of dry matter) in 48 h. A material and heat balance is presented in relation with temperature and moisture level regulation during the process.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260310513
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  • 100
    Electronic Resource
    Electronic Resource
    Development of ultraporous fired bricks as support for yeast cell immobilization (1988)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 31 (1988), S. 470-475 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Ultraporous fired bricks (porosities from 56 to 72%) were developed from materials locally available in Nigeria. The grog particle size was used to modulate the porosity of the bricks. The porous bricks produced were then employed as supports for the immobilization of a yeast strain isolated from a local alcoholic beverage, palm wine. The influence of a brick's porosity and particle size on the cell-loading capacity and cell growth inside the fired brick support were studied. The study revealed that a brick's porosity varied linearly with the mean particle size of the grog, increasing from a porosity of 56% at a particle size of 0.805 mm to 72% at a particle size of 0.075 mm. Cell saturation of the surface area available within the support matrix was completed within four hours of contact between the cell and the adsorbing surface especially for the most porous samples. Cell growth was therefore not observed in such cases; however, the less porous samples supported some cell growth upon incubation. Cell holdup was also observed to increase exponentially when either the porosity was increased or the particle size was decreased. The influence of particle size, however, became insignificant at very high porosities.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260310512
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