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  • Electronic Resource  (994)
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  • 1990-1994  (994)
  • 1990  (994)
  • Biochemistry and Biotechnology  (725)
  • Atomic, Molecular and Optical Physics  (269)
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  • Electronic Resource  (994)
  • Loose Leaf
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  • 1990-1994  (994)
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  • 1
    Electronic Resource
    Electronic Resource
    A genetic screen to identify variants of bovine pancreatic trypsin inhibitor with altered folding energetics (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 16-31 
    Details
    ISSN: 0887-3585
    Keywords: BPTI ; dithiothreitol ; DTT-sensitive mutants ; protein folding ; random mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A genetic screening procedure has been developed to identify mutant forms of bovine pancreatic trypsin inhibitor (BPTI) that can fold to an active conformation but are inactivated more rapidly than the wild type protein. Small cultures of Escherichia coli containing plasmids with mutagenized BPTI genes were grown in microtiter plates, lysed, and treated with dithiothreitol (DTT). Under these conditions, unfolding and inactivation of wild-type protein has a half-time of about 10 hours. Variants of BPTI that are inactivated within 1 hour were identified by adding trypsin and a chromogenic substrate. Approximately 11,000 mutagenized clones were screened in this way and 75 clones that produce proteins that can fold but are inactivated by DTT were isolated. The genes coding for 68 “DTT-sensitive” mutant proteins were sequenced, and 25 different single amino acid substitutions at 15 of the 58 residues of the protein were identified. Most of the altered residues are largely buried in the core of the naive wild-type structure and are highly conserved among proteins homologous to BPTI. These results indicate that a large fraction of the sequence of the protein contributes to the kinetic stability of the active conformation, but it also appears that substitutions can be tolerated a most sites without completely preventing folding Because this genetics, further studies of the isolated mutants are expected to provide information about the roles of the altered residues in folding and unfolding.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070103
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  • 2
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990) 
    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.340070201
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  • 3
    Electronic Resource
    Electronic Resource
    Erratum (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 296-297 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070311
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  • 4
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990) 
    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.340070401
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  • 5
    Electronic Resource
    Electronic Resource
    Role of phosphorylation in conformational adaptability of bovine myelin basic protein (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 32-40 
    Details
    ISSN: 0887-3585
    Keywords: myelin basic protein ; phosphorylation ; protein conformation ; β-structure ; thrombin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Controlled thrombic digestion of a preparation of components 2 + 3 isolated from the 18.5 kDa bovine myelin basic protein (MBP) yielded a polypeptide that was monophosphorylated on threonine 97 (component 3pT97). This is the first posttranslationally phosphorylated MBP isolated in pure form. We studied the effect of this single phosphate on the conformational adaptability of 18.5 kDa bovine MBP by comparing the circular dichroism (CD) spectrum of component 3pT97 with the spectra of highly purified nonphosphorylated components 1 and 2. The CD spectra of nonphosphorylated component 1 and component 2 [monodeamidated forms(s) of component1] were indistinguishable, while component 3pt97 exhibited a different spectrum. The singly phophorylated MBP component exhibited 13% more ordered conformations than that adopted by nonphosphorylated MBP in dilute aqueous solutions. This was estimated from the CD spectra, and apparently involved about 17 additional amino acid residues in β-structure(s).
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070104
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  • 6
    Electronic Resource
    Electronic Resource
    Crystallographic refinement of human serum retinol binding protein at 2Å resolution (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 44-61 
    Details
    ISSN: 0887-3585
    Keywords: RBP ; RBP family ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Human serum retinol binding protein (RBP) in complex with retinol has been crystallographically refined to an R-factor of 18.1% with 2Å resolution data. The protein topology results in an anti-parallel β-barrel that encapsulates the retinol ligand. A detailed description of the protein and the binding site is provided. Our structural work has helped to define a family of proteins, many of which are carrier proteins for smaller ligand molecules. We describe the structural basis for the conservation of sequence within the family.
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080108
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  • 7
    Electronic Resource
    Electronic Resource
    The three-dimensional structure of recombinant bovine chymosin at 2.3 Å resolution (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 82-101 
    Details
    ISSN: 0887-3585
    Keywords: chymosin ; acid proteinase ; rennin ; X-ray structure ; structure comparison ; catalytic site ; crystal packing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of recombinant bovine chymosin (EC 3.4.23.4; renin), which was cloned and expressed in Escherichia coli, has been determined using X-ray data extending to 2.3 Å resolution. The crystals of the enzyme used in this study belong to the space group I222 with unit cell dimensions a = 72.7 Å, b = 80.3 Å, and c = 114.8 Å. The structure was solved by the molecular replacement method and was refined by a restrained least-squares procedure. The crystallographic R factor is 0.165 and the deviation of bond distances from ideality is 0.020 Å. The resulting model includes all 323 amino acid residues, as well as 297 water molecules. The enzyme has an irregular shape with approximate maximum dimensions of 40 × 50 × 65 Å. The secondary structure consists primarily of parallel and antiparallel β-strands with a few short α-helices. The enzyme can be subdivided into N- and C- terminal domains which are separated by a deep cleft containing the active aspartate residues Asp-34 and Asp-216. The amino acid residues and waters at the active site form an extensive hydrogen-bonded network which maintains the pseudo 2-fold symmetry of the entire structure. A comparison of recombinant chymosin with other acid proteinases reveals the high degree of structural similarity with other members of this family of proteins as well as the subtle differences which make chymosin unique. In particular, Tyr-77 of the flap region of chymosin does not hydrogen bond to Trp-42 but protrudes out in the P1 pocket forming hydrophobic interactions with Phe-119 and Leu-32. This may have important implications concerning the mechanism of substrate binding and substrate specificity.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080110
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  • 8
    Electronic Resource
    Electronic Resource
    Conformational flexibility of a scorpion toxin active on mammals and insects: A circular dichroism study (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 164-172 
    Details
    ISSN: 0887-3585
    Keywords: protein secondary structure ; sodium channel ; CD spectra analysis program ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Three scorpion toxins have been analyzed by circular dichroism in water and in 2,2,2-trifluoroethanol (TFE) solutions. These toxins were chosen because they are representative of three kinds of pharmacological activities: (1) toxin AaH IT2, an antiinsect toxin purified from the venom of Androctonus australis Hector, which is able to bind to insect nervous system preparation, (2) toxin Css II, from the venom of Centruroides suffusus suffusus, which is a β-type antimammal toxin capable of binding to mammal nervous system preparation, and (3) the toxin Ts VII from the venom of Tityus serrulatus, which is able to bind to both types of nervous systems. In order to minimize bias, CD data were analyzed by a predictive algorithm to assess secondary structure content. Among the three molecules, Ts VII presented the most unordered secondary structure in water, but it gained in ordered forms when solubilized in TFE. These results indicated that the Ts VII backbone is the most flexible, which might result in a more pronounced tendency for this toxin molecule to undergo conformational changes. This is consistent with the fact that it competes with both antiinsect and β-type antimammal toxins for the binding to the sodium channel.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080206
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  • 9
    Electronic Resource
    Electronic Resource
    HERA - A program to draw schematic diagrams of protein secondary structures (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 203-212 
    Details
    ISSN: 0887-3585
    Keywords: hydrogen bonding diagram ; motifs ; helical wheel ; helical net ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A program is described which generates hydrogen bonding diagrams of protein structures and optionally helical wheels and helical nets. The program can also be used simply to calculate the connectivities of β-strands and to automatically extract simple structural motifs such as hairpins or Greek keys. The program greatly reduces the effort required to produce these diagrams and offers considerable flexibility in the information which can be represented. The usefulness of the program is illustrated by several examples including comparing homologous families, correlating protein structure with attributes of individual residues, and extracting all examples of the ψ-loop motif from the Brookhaven Data Bank.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080303
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  • 10
    Electronic Resource
    Electronic Resource
    Structural homology among the peroxidase enzyme family revealed by hydrophobic cluster analysis (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 251-257 
    Details
    ISSN: 0887-3585
    Keywords: peroxidase ; active site ; structure conservation ; hydrophobic cluster analysis ; sequence comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A number of peroxidase amino acid sequences show limited homology to short regions comprising the known active site cleft of yeast cytochrome c peroxidase. Otherwise no clear homology is visible in linear alignments between this enzyme and other peroxidases. We have subjected eight peroxidase sequences to hydrophobic cluster analysis. Our results suggest that these peroxidases are evolutionary related and that they share many folding characteristics.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080307
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  • 11
    Electronic Resource
    Electronic Resource
    Generation of potential structures for the G-domain of chloroplast EF-Tu using comparative molecular modeling (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 237-250 
    Details
    ISSN: 0887-3585
    Keywords: elongation factor ; energy minimization ; G-protein ; Guanine nucleotide binding ; protein structure ; protein synthesis ; structural homology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Comparative molecular modeling has been used to generate several possible structures for the G-domain of chloroplast elongation factor Tu (EF-Tuchl) based on the crystallographic data of the homologous E. coli protein. EF-Tuchl contains a 10 amino acid insertion not present in the E. coli protein and this region has been modeled based on its predicted secondary structure. The insertion appears to lie on the surface of the protein. Its orientation could not be determined unequivocally but several likely structures for the nucleotide binding domain of EF-Tuchl have been developed. The effects of the presence of water in the Mg2+ coordination sphere and of the protonation sate of the GDP ligand on the conformation of the guanine nucleotide binding site have been examined. Relative binding constants of several guanine nucleotide analogs for EF-Tuchl have been obtained. The interactions between EF-Tuchl and GDP predicted to be important by the models that have been developed are discussed in relation to the nucleotide binding properties of this factor and to the interactions proposed to be important in the binding of guanine nucleotides to related proteins.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080306
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  • 12
    Electronic Resource
    Electronic Resource
    In memoriam (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), 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.340080402
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  • 13
    Electronic Resource
    Electronic Resource
    Hormone phage: An enrichment method for variant proteins with altered binding properties (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 309-314 
    Details
    ISSN: 0887-3585
    Keywords: hormone-receptor interactions ; epitope libraries ; binding selection ; fusion phage ; human growth hormone ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Human growth hormone (hGH), a 191 residue protein containing two disulfide bonds, was fused to the carboxyl-terminal domain of the gene III protein, a minor coat protein exposed at one end of the filamentous phage M13. The gene fusion was cloned into a plasmid containing origins of replication for Escherichia coli and filamentous phage and was packaged into phagemid particles upon infection by an M13KO7 helper phage. Transcription of the hGH-gene III fusion was controlled so that usually no more than one copy of the fusion protein was displayed along with the four copies of the wild-type gene III protein. The hGH-gene III fusion protein was properly folded, as judged by reactivity with six hGH monoclonal antibodies whose epitopes are sensitive to the folded conformation of hGH. Moreover, the hGH-gene III phagemid particles were enriched over 5000-fold from non-hGH phage, and 8-fold from a mutant hGH phagemid following a single hGH-specific elution step from hGH receptor-coated beads. The hGH phagemid should be useful for isolating new receptor binding mutants of hGH. More generally, this expression system may allow other large proteins with discontinuous binding epitopes to be displayed, and binding selections applied to their mutated gene III fusions on filamentous phage.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080405
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  • 14
    Electronic Resource
    Electronic Resource
    Distinct character in hydrophobicity of amino acid compositions of mitochondrial proteins (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 173-178 
    Details
    ISSN: 0887-3585
    Keywords: mitochondria ; amino acid composition ; hydrophobicity ; composition space ; membrane protein ; transmembrane region ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A compact mitochondrial gene contains all essential information about the synthesis of mitochondrial proteins which play their roles in a small compartment of the mitochondrium. Almost no noncoding regions have been found through the gene, but a necessary set of tRNAs for the 20 amino acids is provided for biosynthesis, some of them coding different amino acids from those in a usual cell. Since the gene is so compact that the produced proteins would have some characteristic aspects for the mitrochondrium, amino acid compositions of mitochondrial proteins (mt-proteins) were examined in the 20-dimensional composition space. The results show that compositions of proteins translated from the mitochondrial genes have a distinct character having more hydrophobic content than others, which is illustrated by a clustered distribution in the multidimensional composition space. The cluster is located at the tail edge of the global distribution pattern of a Gaussian shape for other various kinds of proteins in the space. The mt-proteins are rich in hydrophobic amino acids as is a membrane protein, but are different from other membrane proteins in a lesser content of Val. A good correlation found between the base and amino acid compositions for the mitochondria was examined in comparison to those of organisms such as thermophilic bacterium having an extreme G-C-rich base composition.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080207
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  • 15
    Electronic Resource
    Electronic Resource
    Models of δ-hemolysin membrane channels and crystal structures (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 213-225 
    Details
    ISSN: 0887-3585
    Keywords: molecular modeling ; energy calculations ; δ-hemolysin ; melittin ; crystal packing ; raft ; bilayer ; membrane insertion ; channel formation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular modeling and energy calculations have been used to study how δ-hemolysin and melittin helices may aggregate on membrane surfaces and insert through membranes to form channels. In these models adjacent antiparallel amphipathic helices form planar “raft” structures, in which one surface is hydrophobic and the other hydrophilic. Models of δ-hemolysin crystal structure were developed using these “rafts.” These models are based on the unit cell constants and the crystal symmetry obtained from the preliminary crystal data. Energy calculations favor channel models of δ-hemolysin with six or eight monomers per channel.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080304
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  • 16
    Electronic Resource
    Electronic Resource
    Changes in secondary structure follow the dissociation of human insulin hexamers: A circular dichroism study (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 280-286 
    Details
    ISSN: 0887-3585
    Keywords: circular dichroism ; secondary structure ; insulin ; insulin analogs ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Vacuum UV circular dichroism spectra measured down to 178 nm for hexameric 2-zinc human insulin, zinc-free human insulin, and the two engineered and biologically active monomeric mutants, [B/S9D] and [BS9D, T27E] human insulin, show significant differences. The secondary structure analysis of the 2-zinc human insulin (T6) in neutral solution was determined: 57% helix, 1% β-strand, 18% turn, and 24% random coil. This is very close to the corresponding crystal structure showing that the solution and solid structures are similar. The secondary structure of the monomer shows a 10-15% increase in antiparallel β-structure and a corresponding reduction in random coil structure. These structural changes are consistent with an independent analysis of the corresponding difference spectra. The advantage of secondary structure analyses of difference spectra is that the contribution of odd spectral features stemming mainly from side chain chromophores is minimized and the sensitivity of the analyses improved. Analysis of the CD spectra of T6 2-zinc, zinc-free human insulin and monomeric mutant insulin by singular value decomposition indicates that the secondary structure changes following the dissociation of hexamers into dimers and monomers are two-state processes.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080309
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  • 17
    Electronic Resource
    Electronic Resource
    Design of biologically active, conformationally constrained GnRH antagonists (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 295-304 
    Details
    ISSN: 0887-3585
    Keywords: gonadotropin-releasing hormone ; molecular dynamics ; nuclear magnetic resonance ; antagonist design ; conformation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The introduction of conformational constraints into a flexible peptide hormone can be exploited to develop models for the conformation required for receptor binding and activity. In this review, we illustrate this approach to analog design using our work on antagonists of gonadotropin-releasing hormone (GnRH). Design of a conformationally constrained, competitive antagonist of GnRH, cyclo[Δ3,4 Pro-D4ClPhe-DTrp-Ser-Tyr-DTrp-NMeLeu-Arg-Pro-βAla], led to the prediction of its bioactive conformation. Template forcing experiments show that this conformation is accessible to other active GnRH analogs. Two-dimensional NMR studies verified the predicted conformation in solution. The predicted binding conformation has recently been used to design two new analogs incorporating side chain-side chain linkages suggested by the conformational model: These analogs were synthesized and the one predicted to be most similar to the parent conformation had equivalent potency while the second, designed to refine the conformational hypothesis, was found to exhibit enhanced potency, thus confirming the original binding conformation hypothesis. These compounds and their derivatives now provide a new class of GnRH antagonists possessing both high biological potency and limited conformational flexibility, thus making them ideal for both biophysical and structure-activity studies.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080403
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  • 18
    Electronic Resource
    Electronic Resource
    A helix-turn-strand structural motif common in α-β proteins (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 334-340 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; structural comparison ; α-β barrels ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: By exhaustive structural comparisons, we have found that about one-third of the α-helix-turn-β-strand polypeptides in α-β barrel domains share a common structural motif. The chief characteristics of this motif are that first, the geometry of the turn between the α-helix and the β-strand is somewhat constrained, and second, the β-strand contains a hydrophobic patch that fits into a hydrophobic pocket on the α-helix. The geometry of the turn does not seem to be a major determinant of the α-β unit, because the turns vary in length from four to six residues. However, the motif does not occur when there are few constraints on the geometry of the turn-for instance, when the turns between the α-helix and the β-strands are very long. It also occurs much less frequently in flat-sheet α-β proteins, where the topology is much less regular and the amount of twist on the sheet varies considerably more than in the barrel proteins. The motif may be one of the basic building blocks from which α-β barrels are constructed.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080407
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  • 19
    Electronic Resource
    Electronic Resource
    Fragment peptide library for classification and functional prediction of proteins (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 341-351 
    Details
    ISSN: 0887-3585
    Keywords: conserved sequence ; diagnostic peptide ; superfamily classificaiton ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: From protein sequence comparison data found in the literature, a library was organized using peptide fragment sequences which are common to related proteins. Each of the fragments was then examined for its occurrence in all the protein superfamilies defined by the NBRF-PIR data base. We have selected those fragment peptides that appear exclusively in one or a few superfamilies, and thus made a library of fragment peptides that characterize specific superfamilies. Such characteristic peptides are, in general, five to seven residues long and contain unusually high proportions of glycine and cysteine. This collection is a useful resource for the classification and functional prediction of protein molecules.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080408
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  • 20
    Electronic Resource
    Electronic Resource
    The structure of rubredoxin from Desulfovibrio desulfuricans strain 27774 at 1.5 Å resolution (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 352-364 
    Details
    ISSN: 0887-3585
    Keywords: crystallography ; refinement ; structure comparison ; molecular replacement ; precision ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of a small rubredoxin from the bacterium Desulfovibrio desulfuricans has been determined and refined at 1.5 Å resolution. The hairpin loop containing seven residues in other rubredoxins is missing in this 45 residue molecule, and once that fact was determined by amino acid sequencing studies, refinement progressed smoothly to an R value of 0.093 for all reflections from 5 to 1.5 Å resolution. Nearly all of the water molecules in the well-ordered triclinic unit cell have been added to the crystallographic model. As in the other refined rubredoxin models, the Fe-S4 complex is slightly distorted from ideal tetrahedral coordination.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080409
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  • 21
    Electronic Resource
    Electronic Resource
    Refinement of the NMR structures for acyl carrier protein with scalar coupling data (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 377-385 
    Details
    ISSN: 0887-3585
    Keywords: structure deteremination ; two-dimensional NMR ; molecular mechanics ; molecular dynamics ; conformational equilibrium ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observation, not just distance constraints. Here, coupling constant constraints have been added to molecular mechanics and molecular dynamics protocols for structure determination in the form of a psuedoenergy function that is minimized in a search for an optimum molecular conformation. Application is made to refinement of a structure for a 77 amino acid protein involved in fatty acid synthesis, Escherichia coli acyl carrier protein (ACP). 54 3JHNα coupling constants, 12 coupling constants for stereospecifically assigned side chain protons, and 450 NOE distance contraints were used to calculate the 3-D structure of ACP. A three-step protocol for a molecular dynamics calculation is described, in analogy to the protocol previously used in molecular mechanics calculations. The structures calculated with the molecular mechanics approach and the molecular dynamics apporach using a rigid model for the protein show similar molecular energies and similar agreement with experimental distance and coupling constant constraints. The molecular dynamics approach shows some advantage in overcoming local minimum problems, but only when a two-state averaging model for the protein was used, did molecular energies drop significantly.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080411
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  • 22
    Electronic Resource
    Electronic Resource
    α-Helical coiled coils and bundles: How to design an α-helical protein (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 1-15 
    Details
    ISSN: 0887-3585
    Keywords: α-fibrous proteins ; 4-α-helix bundle ; membrane-spanning proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070102
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  • 23
    Electronic Resource
    Electronic Resource
    Molecular dynamics study of secondary structure motion in proteins: Application to myohemerythrin (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 265-279 
    Details
    ISSN: 0887-3585
    Keywords: potential of means force ; motions of helices ; correlated fluctuations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The concept of secondary structure motions is examined in a molecular dynamics simulation of the protein myohemerythrin. We extracted from the simulation a corresponding trajectory of helices and demonstrated that the fluctuations of the protein are dominated by a rigid shift of these secondary structure elements. The relative motions of the helices are regular, with no clear periodicity. They are bounded by ∼2 for the center of mass motions and by 20° for the relative orientations. The potential of mean force for the interactions of the helices was calculated, and the correlations between the different extended motions were investigated. It shown that the one-dimensional mean force potentials are close to quadratic for most of the helices coordinates. The anharmonicity is reflected by changes in the direction of the normal modes as a function of the energy and by the existence of multiple free energy minima for the helices packing. The multiple conformations are associated with a single type of secondary structure coordinate: the angle that describes the relative orientation of the helices in a plane perpendicular to the line connecting their center of mass.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070308
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  • 24
    Electronic Resource
    Electronic Resource
    An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 41-51 
    Details
    ISSN: 0887-3585
    Keywords: DNA binding proteins ; maximum likelihood ; CRP ; finite mixtures ; transcription regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Statistical methodology for the identification and characterization of protein binding sites in a set of unaligned DNA fragments is presented. Each sequence must contain at least one common site. No alignment of the sites is required. Instead, the uncertainty in the location of the sites is handled by employing the missing information principle to develop an “expectation maximization” (EM) algorithm. This approach allows for the simultaneous identification of the sites and characterization of the binding motifs. The reliability of the algorithm increases with the number of fragments, but the computations increase only linearly. The method is illustrated with an example, using known cyclic adenosine monophophate receptor protein (CRP) binding sites. The final motif is utilized in a search for undiscovered CRP binding sites.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070105
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    Electronic Resource
    Electronic Resource
    Understanding structural relationships proteins of unsolved three-dimensional structure (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 99-111 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070202
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  • 26
    Electronic Resource
    Electronic Resource
    Protein secondary structure and circular dichroism: A practical guide (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 205-214 
    Details
    ISSN: 0887-3585
    Keywords: protein secondary structures ; circular dichroism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070302
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  • 27
    Electronic Resource
    Electronic Resource
    Modelling of the human intercellular adhesion molecule-1, the human rhinovirus major group receptor (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 227-233 
    Details
    ISSN: 0887-3585
    Keywords: rhinovirus receptor ; ICAM-1 ; structure prediction ; immunoglobulin superfamily ; docking receptor to virus ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model has been built of the amino-terminal domain of the intercellular adhesion molecule-1 (ICAM-1), the receptor for most human rhinovirus serotypes. The model was based on sequence and presumed structural homology to immunoglobulin constant domains. It fits well into the putative receptors attachment site, the canyon, on the human rhinovirus-14 (HRV14) surface in a manner consistent with most of the mutational data for ICMA-1 (Staunton, D. E., Dustin, M. L., Erickson, H. P., Springer, T. A. Cell, in press, 1989) and HRV14 (Colonno, R. J., Condra, J. H., Mizutani, S., Callahan, P. L., Davies, M. E., Murcko, M. A. Proc. Natl. Acad. Sci. U.S.A. 85: 5449-5453, 1988).
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070304
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  • 28
    Electronic Resource
    Electronic Resource
    Structure determination and refinment of Bacillus stearothermophilus lactate dehydrogenase (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 74-92 
    Details
    ISSN: 0887-3585
    Keywords: thermostability ; bacterial lactate dehydrogenase ; allosteric regulations ; crystallography ; molecular replacement ; coenzyme binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structures have been determined of Bacillus stearothermophilus “apo” and holo lactate dehydrogenase. The holo-enzyme had been co-crystallized with the activator fructose 1,6-biosphosphate. The “apo” lactate dehydrogenase structure was solved by use of the known apo-M4 dogfish lactate dehydrogenase molecule as a starting model. Phases were refined and extended from 4 Å resolution by means of the noncrystallographic molecular 222 symmetry. The R-factor was reduced to 28.7%, using 2.8 Å resolution data, in a restrained least-squares refnement in which the molecula rsymmetry was imposed as a constraint. A low occupancy of coenzyme was found in each of the four subunits of the “apo” enzyme.Further refinement proceeded with the isomorphous holo-enzyume from Bacillus Stearothermophilus. After removing the noncrystallographic constraints, the R-factor dropped from 30.3% to a final value of 26.0% with a 0.019 Å and 1.7° r.m.s. deviation from idealized bond length and angles, respectively.Two sulfate ions per subunit were included in the final model of the “apo” -from-one at the substrate binding site and one close to the molecular P -axis near the location of the fructose 1,6-bisphosphate activator. The final model of the holo-enzyme incorporated two sulfate ions per subunit, one at the substrate binding site and another close to the R-axis. One nicotinamide adenine dinucleotide coenzyme molecule per subunit and two fructose 1,6-bisphosphate molecules per tetramer were also included. The phosphate positions of fructose 1,6-bisphosphate are close to the sulfate ion near the P-axis in the “apo” model.This structure represents the first reported refined model of an allosteric activated lactate dehydrogenase. The structure of the activated holo-enzyme showed far greater similarity to the ternary complex of dogfish M4 lactate dehydrogenase with incotinamide adenine dinucleotide and oxamate than to apo-M4 dogfish lactate dehydrogenase. The conformations of nicotinamide adenine dinucleotide and fructose, 1,6-bisphosphate were also analyzed.
    Additional Material: 15 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070108
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    Electronic Resource
    Electronic Resource
    Substrate recognition by the EcoRI endonuclease (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 185-197 
    Details
    ISSN: 0887-3585
    Keywords: restriction enzyme ; DNA-protein interactions ; DNA recognition ; enzyme-substrate interaction ; active site ; site-directed mutagenesis ; protein structure-function ; DNA double-strand breaks ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The EcoRI restriction endonuclease is one of the most widely used tools for recombinant DNA manipulations. Because the EcoRI enzyme has been extremely well characterized biochemically and its structure is known at 3 Å resolution as an enzyme-DNA complex, EcoRI also serves as an important model of DNA-protein interactions. To facilitate a genetic analysis of the EcoRI enzyme, we devised an in vivo DNA scission assay based on our finding that DNA double-strand breaks induce the Escherichia coli SOS response and thereby increase β-galactosidase expression from SOS::lacZ gene fusions. By site-directed mutagenesis, 50 of 60 possible point mutations were generated at three amino acids (E144, R145, and R200) implicated in substrate recognition by the crystal structure. Although several of these mutant enzymes retain partial endonuclease activity, none are altered in substrate specificity in vivo or in vitro. These findings argue that, in addition to the hydrogen bond interactions revealed by the crystal structure, the EcoRI enzyme must make additional contacts to recognize its substrate.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070207
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  • 30
    Electronic Resource
    Electronic Resource
    Model for the interaction of amphiphilic helices with troponin C and calmodulin (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 234-248 
    Details
    ISSN: 0887-3585
    Keywords: computer modelling ; Ca2+-binding proteins ; hydrophobic binding interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of troponin are stabilized by an intermolecular interaction that involves the packing of helix A from the N-terminal domain of one molecule onto the exposed hydrophobic cleft of the C-terminal domain of a symmetry related molecules. Analysis of this molecular recognition interaction in troponin C suggests a possible mode for the binding of amphiphilic helical molecules to troponin C and to calmodulin. From the template provided by this troponin C packing, it has been possible to build a model of the contact region of mastoporan as it might be bound to the two Ca2+ binding proteins. A possible binding mode of melittin to calmodulin is also proposed. Although some of the characteristics of binding are similar for the two amphiphilic peptides, the increased length of melittin requires a significant bend in the calmodulin central helix similar to that suggested recently for the myosin light chain kinase calmodulin binding peptide (Persechini and Kretsinger: Journal of Cardiovascular Pharmacology 12:501-512, 1988). Not only are the hydrophobic interactions important in this model, but there are several favorable electrostatic interactions that are predicted as a result of the molecular modeling. The regions of troponin-C and calmodulin to which amphiphilic helices bind are similar to the regions to which the neuroleptic drugs such as trifluoperazine have been predicted to bind (Strynadka and James: Proteins 3:1-17, 1988).
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070305
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  • 31
    Electronic Resource
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    The design of idealized α/β-barrels: Analysis of β-sheet closure requirements (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 249-256 
    Details
    ISSN: 0887-3585
    Keywords: β-barrels ; β-strand ; scaffold design ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The 8-old parallel α/β-barrel topology is encountered in proteins that display an impressive variety of functions, suggesting that this topology may be a rather nonspecific and stable folding motif. Consequently, this motif can be considered as an interesting framework to design novel proteins. It has been shown that the shape of the β-sheet portion of the barrel can be approximated by a hyperboloid. This geometric object may therefore be used as a scaffold to construct an idealized eight-standard β-barrel. To facilitate the de novo design of such structures, a collection of modelling tools has been developed allowing secondary structure elements to be mapped onto the scaffold surface and rotation and translation operations to be performed about user defined axes while evaluating their contribution to the conformational energy of the system. These tools have been applied in a systematic study assessing the φ, ψ requirements to design symmetric eight standard β barrels with optimal hydrogen bonding between adjacent β-strands. It is observed that: (a) the β-sheet structure can be closed without introducing irregular stagger between β-strands and (b) the region of φ, ψ dihedral angle space compatible with the formation of regular symmetric eight standard β-barrels coincides with the φ, ψ region corresponding to average β-strands in known protein structures, suggesting that barrel closure does not impose gross constraints on β-strand geometry.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070306
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  • 32
    Electronic Resource
    Electronic Resource
    The characterization of recombinant mouse glandular kallikreins from E. coli (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 280-290 
    Details
    ISSN: 0887-3585
    Keywords: proteases ; protein turnover ; post-translational processing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A system has been developed or the expression in E. coli of 12 of the 14 expressed mouse submandibular gland kallikreins as cassettes subcloned directly from cDNA. Using the epidermal growth factor binding protein (mGK-9) and the γ-subunit of nerve growth factor (nGK)-3, as test cases, mature processed forms, obtained as functionally active proteins, as well as various precursor forms, were isolated. The expression system described allows rapid isolation of kallikrein protein from corresponding cDNA with yields of approximately 1.0 mg of purified protein from 10 g of initial cell paste. This expression system will facilitate structure/function studies of the mouse glandular kallikrein gene family and help elucidate the regions of the mature proteins responsible for the diverse catalytic behavior and growth factors interactions observed in this family of proteins.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070309
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  • 33
    Electronic Resource
    Electronic Resource
    Functionally acceptable substitutions in two α-helical regions of λ repressor (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 306-316 
    Details
    ISSN: 0887-3585
    Keywords: neutral mutations ; random mutagenesis ; protein structure ; protein folding ; protein families ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method of targeted random mutagenesis has been used in investigate the informational content of 25 residue positions in two α-helical regions of the N-terminal domain of λ repressor. Examination of the functionally allowed sequences indicates that there is a wide range in tolerance to amino acid substitution at these position. At position that are buried in the structure, there are severe limitations on the number and type of residues allowed. At most surface positions, many different residues and residue types are tolerated. However, at several surface positions there is a string preference for hydrophilic amino acids, and at one surface position proline is absolutely conserved. The results reveal the high level of degeneracy in the information that specifies a particular protein fold.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070403
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    Electronic Resource
    Crystal structure of subtilisin BPN′ variants containing disulfide bonds and cavities: Concerted structural rearrangements induced by mutagenesis (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 343-357 
    Details
    ISSN: 0887-3585
    Keywords: engineered disulfide groups ; X-ray structure ; hydrophobic cavities ; water structure, altered ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The X-ray structure of four genetically engineered disulfide variants of subtilisin have been analyzed to determine the energetic and structural constraints involved in inserting disulfide bonds into proteins. Each of the engineered disulfides exhibited atypical sets of dihedral angles compared with known structures of natural disulfide bridges in proteins and affected its local structural environment to a different extent. The disulfides located in buried regions, Cys26-Cys232 and Cys29-Cys87 and Cys22-Cys87, which are located on the surface of the molecule. An analysis of the concerted changes in secondary structure units such as α-helices and β-sheets indicated systematic long-range effects. The observed changes in the mutants were largely distributed asymmetrically around the inserted disulfides, reflecting different degrees of inherent flexibility of neighboring secondary structure types. The disulfide substitution in each variant molecule created some invaginations or cavities, causing a reorganization of the surrounding water structure. These changes are described, as well as the changes in side chain positions of groups that border the cavities.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070406
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  • 35
    Electronic Resource
    Electronic Resource
    The building of protein structures form α-carbon coordinates (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 366-377 
    Details
    ISSN: 0887-3585
    Keywords: computer modeling ; protein ; structure ; α-carbons ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A procedure for the construction of complete protein structures from only αcarbon coordinates is described. This involves building the backbone by sequential addition of Pro, Gly, or Ala residues. This main chain structure is then refined using molecular dynamics. Side chains are constructed by sequential addition of atoms with intermediate molecular dynamics refinement. For α lytic protease (a structure that is mostly β sheet) a backbone root mean square deviation (RMSD) of 0.19 Å and an overall RMSD of 1.24 Å from the crystallographic coordinates are attained. For troponin C (67% β-helix), where the coordinates are available only for the α-carbons, a backbone RMSD of 0.41 Å and an overall RMSD of 1.68 Å are attained (fits kindly provided by Dr. Michael James and Natalie Strynadka). For flavodoxin a backbone RMSD of 0.49 Å and an overall RMSD of 1.64 Å were attained.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070408
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  • 36
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    Quantitative organization of the known protein x-ray structures. I. Methods and short-length-scale results (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 378-402 
    Details
    ISSN: 0887-3585
    Keywords: conformational distance ; conformational comparison ; generalized bond matrix representation ; structure space ; evolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We address herein the problem of delineating the relationships between the known protein structures. In order to study this problem, methods have been developed to represent arbitrarily sized fragments of biopolymer backbone, and to compare distributions of such fragments. These methods are applied to a classification of 123 structures representing the entire set of known x-ray structures. The resulting data are analyzed (on the four-Cα length scale) to determine both the large-scale organization of the set of known structures (i.e., the relationships between large groups of structures, each comprised of proteins that are structurally related) and its local structure (i.e., the quantitative degree of similarity between any two specific structures). It is shown that the set of structures from a continuum of structural types, ranging from allhelical to all-sheet/barrel proteins. It is further demonstrated that the density of protein structures is not uniform across this continuum, but rather that structures cluster in certain regions, separated by regions of lower population. The properties of the various regions of the structural space are determined. The existence is demonstrated of strong quantitative correlations between the contents of different types of four-Cα fragments within protein structures, which imply significant constraints on the types of architecture that can occur in proteins. Analysis of the distribution of structures demonstrates some hitherto unsuspected similarities and suggests that, in some circumstances, neither structural similarity no sequence homology may be necessary conditions for evolutionary relationship between proteins. It is also suggested that these unsuspected similarities may imply similar folding mechanisms for structures of apparently different global architecture. Cases are also noted in which apparently similar structures may fold by different mechanisms. The connection between structure and dynamic properties is discussed, and a possible role of dynamics in the evolution of protein structures is suggested. The sensitivity of the methods presented herein to anomalies of structure refinement is demonstrated. It is suggested that present results provide a frame-work for analyzing experimental results on structural similarity obtained using vibrational circular dichroism spectra, which are sensitive to local backbone structure.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070409
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  • 37
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    Prediction of homologous protein structures based on conformational searches and energetics (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 30-43 
    Details
    ISSN: 0887-3585
    Keywords: molecular mechanics ; solvation energy ; trypsin ; energy minimization ; side chains ; protein crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A “knowledge-based” method of predicting the unknown structure of a protein from a homologous known structure using energetics to determine a sidechain conformation is proposed. The method consists of exchangin the residues in the known structure for the sequence of the unknown protein. Then a conformational search with molecular mechanics energy minimization is done on the exchanged residues. The lowest energy conformer is the one picked to be the predicted structure. In the structure of bovine trypsin, the importance of including a solvation energy term in the search is demonstrated for solvent accessible residues, while molecular mechanics alone is enough to correctly predict the conformation of internal residues. The correctness of the model is assessed by a volume error overlap of the predicted structure compared to the crystal structure. Finally, the structure of rat trypsin is predicted from the crystal structure of bovine trypsin. The sequences of these two proteins are 74% identical and all of the significant changes between them are on external residues. Thus, the inclusion of solvation energy in the conformational search is necessary to accurately predict the structure of the exchanged residues.
    Additional Material: 13 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080107
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  • 38
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    Revised 2.3 Å structure of porcine pepsin: Evidence for a flexible subdomain (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 62-81 
    Details
    ISSN: 0887-3585
    Keywords: pepsin ; aspartic proteinases ; subdomains ; structure comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A revised three-dimensional crystal structure of ethanol-inhibited porcine pepsin refined to an R-factor of 0.171 at 2.3 Å resolution is presented and compared to the refined structures of the fungal aspartic proteinases: penicillopepsin, rhizopuspepsin, and endothiapepsin. Pepsin is composed of two nearly equal N and C domains related by an intra dyad. The overall polypeptide fold and active site structures are homologous for pepsin and the fungal enzymes. The weak inhibition of pepsin by ethanol can be explained by the presence of one or more ethanol molecules, in the vicinity of the active site carboxylates, which slightly alter the hydrogen-bonding network and which may compete with substrate binding in the active site. Structural superposition analysis showed that the N domains aligned better than the C-domains for pepsin and the fungal aspartic proteinases: 107-140 Cα pairs aligned to 0.72-0.85 Å rms for the N domains; 64-95 Cα pairs aligned to 0.78-1.03 Å rms for the C domains. The major structural difference between pepsin and the fungal enzymes concerns a newly described subdomain whose conformation varies markedly among these enzyme structures. The subdomain in pepsin comprises nearly 100 residues and is composed of two contiguous segments within the C domain (residues 192-212 and 223-299). The subdomain is connected, or “hinged,” to a mixed β-sheet that forms one of the structurally invariant, active site ψ-loops. Relative subdomain displacements as large as a 21.0° rotation and a 5.9 Å translation were observed among the different enzymes. There is some suggestion in pepsin that the subdomain may be flexible and perhaps plays a structural role in mediating substrate binding, determining the substrate specificity, or in the activation of the zymogen.
    Additional Material: 12 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080109
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    Acid helix-turn activator motif (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 156-163 
    Details
    ISSN: 0887-3585
    Keywords: transcription activation ; secondary structure ; machine learning ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A common sequence/structural motif pattern has been identified within the steroid/thyroid hormone receptors and other transcriptional activators using a new massively parallel symbolic learning assistant computer system. The pattern appears nearly diagnostic of transcription activation, including relative activation strength, among nuclear and DNA-binding prokaryotic proteins. In cases where mutation/deletion/chimeric studies have identified the activation domain, the pattern matches within that domain. These facts and the nature of the pattern itself strongly support the idea that the patterned domain is directly involved in a protein-protein transcription activation interaction.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080205
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  • 40
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    Automated docking of substrates to proteins by simulated annealing (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 195-202 
    Details
    ISSN: 0887-3585
    Keywords: simulated annealing ; computer-aided drug design ; substrate docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Metropolis technique of conformation searching is combined with rapid energy evaluation using molecular affinity potentials to give an efficient procedure for docking substrates to macromolecules of known structure. The procedure works well on a number of crystallographic test systems, functionally reproducing the observed binding modes of several substrates.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080302
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  • 41
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    Bundles of amphipathic transmembrane α-helices as a structural motif for ion-conducting channel proteins: Studies on sodium channels and acetylcholine receptors (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 226-236 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; ionic pores ; neural membranes ; protein design ; energy minimization ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Channel proteins are transmembrane symmetric (or pseudosymmetric) oligomers organized around a central ionic pore. We present here a molecular model of the pore forming structures of two channel proteins with different primary structures and oligomeric size: the voltage-sensitive sodium channel and the nicotinic cholinergic receptor. We report low-energy arrangements of α-helical bundles calculated by semiempiricial potential energy functions and optimization routines and further refined using molecular dynamics. The ion-conducting pore is considered to be a symmetric or pseudosymmetric homooligomer of 3-5 amphipathic α-helices arranged such that the polar residues line a central hydrophilic pathway and the apolar residues face the hydrophobic bilayer interior. The channel lining exposes either charged (Asp, Glu, Arg, Lys) or polar-neutral (Ser, Thr) residues. A bundle of four parallel helices constrained to C4 symmetry, the helix axis aligned with the symmetry axis, and the helices constrained to idealized dihedral angles, produces a structure with a pore of the size inferred for the sodium channel protein (area ∼ 16 Å2). Similarly, a pentameric array optimized with constraints to maintain C5 symmetry and backbone torsions characteristic of α-helices adopts a structure that appears well suited to form the lining of the nicotinic cholinergic receptor (pore area ∼ 46 Å2). Thus, bundles of amphipathic α-helices satisfy the structural, energetic, and dynamic requirements to be the molecular structural motif underlying the function of ionic channels.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080305
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    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990) 
    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.340080401
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    Preliminary crystallographic analysis of class 3 rat liver aldehyde dehydrogenase (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 305-308 
    Details
    ISSN: 0887-3585
    Keywords: aldehyde dehydrogenase ; crystals ; X-ray analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: NAD-linked aldehyde dehydrogenases (A1DH) (EC 1.2.1.3) catalyze the irreversible oxidation of a wide variety of aldehydes to their respective carboxylic acids. Crystals of a class 3 A1DH (from an Escherichia coli expression system) suitable for X-ray analysis have been obtained. These crystals, which can be grown to a size of 0.8 × 0.3 × 0.2 mm, diffract to 2.5 Å resolution. Analysis of the diffraction pattern indicates that the crystals belong to the monoclinic space group P21, with cell parameters a = 65.11 Å, b = 170.67 Å, c = 47.15 Å, and β = 110.5°. Assuming one dimer per asymmetric unit, the value Vm is calculated to be 2.45 and the solvent content of the crystal is estimated to be 50%. A self-rotation function study produced significant rotation peaks (58% of the origin) on the K = 180 section at ψ = 90° and φ = 71° and 341°, indicating that the pseudo-dimer axis is (or is very nearly) perpendicular to the b-axis.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080404
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    Plastic adaptation toward mutations in proteins: Structural comparison of thymidylate synthases (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 315-333 
    Details
    ISSN: 0887-3585
    Keywords: thymidylate synthase ; plasticity ; crystal structure ; B factor ; mutation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of thymidylate synthase (TS) from Escherichia coli was solved from cubic crystals with a = 133 Å grown under reducing conditions at pH 7.0, and refined to R = 22% at 2.1 Å resolution. The structure is compared with that from Lactobacillus casei solved to R = 21% at 2.3 Å resolution. The structures are compared using a difference distance matrix, which identifies a common core of residues that retains the same relationship to one another in both species. After subtraction of the effects of a 50 amino acid insert present in Lactobacillus casei, differences in position of atoms correlate with temperature factors and with distance from the nearest substituted residue. The dependence of structural difference on thermal factor is parameterized and reflects both errors in coordinates that correlate with thermal factor, and the increased width of the energy well in which atoms of high thermal factor lie. The dependence of structural difference on distance from the nearest substitution also depends on thermal factors and shows an exponential dependence with half maximal effect at 3.0 Å from the substitution. This represents the plastic accommodation of the protein which is parameterized in terms of thermal B factor and distance from a mutational change.
    Additional Material: 16 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080406
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    Announcement (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), 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.340080102
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    Energetics of the structure and chain tilting of antiparallel β-barrels in proteins (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 14-22 
    Details
    ISSN: 0887-3585
    Keywords: computation ; conformational energy ; interactions in proteins ; protein folding ; twisted β-sheets ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The preferred structural pattern of antiparallel β-barrels in proteins, described as the right-handed tilting of the peptide strands with respect to the axis of the barrel, is accounted for in terms of intra- and interchain interaction energies. It is related to the preference of β-sheets for right-handed twisting. Conformational energy computations have been carried out on three eight-stranded antiparallel β-barrels composed of six-residue strands, in which L-Val and Gly alternate, and having a right-handed, a left-handed, or no tilt. After energy minimization, the relative energies of these structures were 0.0, 8.6, and 46.1 kcal/mol, respectively; i.e., the right-tilted β-barrel is favored energetically, in agreement with anti-parallel β-barrels observed in proteins. Tilting of the barrel is favored, relative to the nontilted structure, by both intra- and interstrand interactions, because tilting allows better packing of the bulky side chains. On the other hand, the energy difference between the left- and right-tilted barrels arises essentially from intrachain interactions. This is a consequence of the preference of β-sheets for a right-handed twist. Space limitations inside the barrel are satisfied if there is an alternation of bulky residues and residues with small or no side chain (preferably Gly) in neighboring positions on adjacent strands. Such a pattern is seen frequently in antiparallel β-barrels of globular proteins. The computations indicate that a structure with Val…Gly pairs can be accommodated in a β-barrel with no distortion.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080105
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    Conformational and helicoidal analysis of the molecular dynamics of proteins: “Curves,” dials and windows for a 50 psec dynamic trajectory of BPTIEditors note: The authors submitted an entire data set, and agreed to publish in this article only the first panel in each of Figures 9 through 12. The entire data set in these figures is available from David Beveridge or Richard Lavery upon request. (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 179-193 
    Details
    ISSN: 0887-3585
    Keywords: protein conformation ; helicoidal parameters ; molecular dynamics ; bovine pancreatic trypsin inhibitor ; simulation ; protein-protein interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new procedure for the graphic analysis of molecular dynamics (MD) simulations on proteins is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the conformational and helicoidal parameters for each structure entering the analysis via the method “Curves,” developed for proteins by Sklenar, Etchebest, and Lavery (Proteins: Structure, Function Genet. 6:46-60, 1989) followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels (“dials”) for each torsional parameter and “windows” on the range values assumed by the linear and angular helicoidal parameters, and is present in a form isomorphous with the primary structure per se. The complete time evolution of dynamic structure can then be depicted in a set of four composite figures. Dynamic aspects of secondary and tertiary structure are also provided. The procedure is illustrated with an analysis of a 50 psec in vacuo simulation on the 58 residue protein, bovine pancreatic trypsin inhibitor (BPTI), in the vicinity of the local minimum on the energy surface corresponding to a high resolution crystal structure. The time evolution of 272 conformational and 788 helicoidal parameters for BPTI is analyzed. A number of interesting features can be discerned in the analysis, including the dynamic range of conformational and helicoidal motions, the dynamic extent of 2° structure motifs, and the calculated fluctuations in the helix axis. This approach is expected to be useful for a critical analysis of the effects of various assumptions about force field parameters, truncation of potentials, solvation, and electrostatic effects, and can thus contribute to the development of more reliable simulation protocols for proteins. Extensions of the analysis to present differential changes in conformational and helicoidal parameters is expected to be valuable in MD studies of protein complexes with substrates, inhibitors, and effectors and in determining the nature of structural changes in protein-protein interactions.
    Additional Material: 15 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080208
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    Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 258-279 
    Details
    ISSN: 0887-3585
    Keywords: topology of atom packing ; hinge bending motion ; accessible surface area ; elastic deformation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A normal mode analysis of human lysozyme has been carried out at room temperature. Human lysozyme is an enzyme constituted of two domains separated by an active site cleft, the motion of which is thought to be relevant for biological function. This motion has been described as a hinge bending motion. McCammon et al.1 have determined the characteristics of the hinge bending motion but they assumed a prior knowledge of the hinge axis. In this work we propose a method which is free from this assumption and determines the hinge axis and root mean square (rms) rotation angle which give the best agreement with the pattern of changes in all the distances between nonhydrogen atoms in the two domains, obtained by the normal mode analysis. The hinge axis we found is notably different from the one previously determined and goes, roughly, through the Cα 55 and Cα 76, i.e., it is located at the base of the β-sheet of the second domain. The rms value for the rotation angle is also twice as large as the previous one: 3.37°. It is shown that this hinge bending motion provides a fairly good approximation of the dynamics of human lysozyme and that the normal mode with the lowest frequency has a dominating contribution to this hinge bending motion.A study of the accessible surface area of the residues within the cleft reveals that the motion does not result in a better exposure to the solvent of these residues.A characterization of the thermally excited state (under the hypothesis of the harmonicity of the potential energy surface) has been done using the concept of topology of atom packing. Under this hypothesis the thermal fluctuations result only in a small change of the topology of atom packing, leading therefore to nearly elastic deformations of the protein.
    Additional Material: 12 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080308
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    The effect of solvent viscosity on the rate-determining step of fatty acid synthetase (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 287-293 
    Details
    ISSN: 0887-3585
    Keywords: fatty acid synthetase ; overall activity ; viscogens ; diffusion limited intramolecular motion ; rate-determining step ; microviscosity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The overall activity of animal fatty acid synthetase at the saturation level of substrate concentration decreased when the solvent viscosity, η, of the reaction mixture was increased with viscogens such as glycerol, sucrose, and polyethylene glycol. The activity of the enzyme changed roughly proportional to η-p, where p = 1.0 for glycerol, p = 0.66 for sucrose, and p 〈 0.6 for polyethylene glycol with different molecular sizes. The thioesterase activity, which catalyzes the final partial reaction in the multifunctional enzyme, was not affected by 5-fold increase of solvent viscosity with sucrose. These results suggested that the rate-determining step of the enzyme other than the thioesterase reaction involves a microscopic transport step, the rate of which is influenced by the solvent viscosity. The microscopic transport step may be related to the transfer of the reaction intermediate from one active site to another or to the motion of a larger part of the enzyme requisite for the catalytic reaction. In the solution containing glycerol, the rate-determining motion was primarily diffusion limited since the inverse of the initial rate was proportional to η, i.e., p = 1. Since the substrate concentration was at a saturation level in this experiment, the viscosity-dependent step cannot be the encounter between the enzyme and substrates, but must be intramolecular in origin, most probably the reaction catalyzed by β-ketoacyl synthetase. In solutions containing other viscogens, however, p was less than 1.0, indicating a significant involvement of chemical steps in the rate-determining step as well. Bovine serum albumin, when used as a proteinic viscogen, also decreased the initial rate. In the living cells therefore, the rate-determining intramolecular motion of fatty acid synthetase could be affected by the presence of high concentrations of cytoplasmic proteins.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080310
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    Functional interaction among catalytic residues in subtilisin BPN′ (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 335-342 
    Details
    ISSN: 0887-3585
    Keywords: serine protease ; catalytic triad ; oxyanion binding site ; site-directed mutagenesis ; protease inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Variant of the serine protease, subtilisin BPN′, in which the catalytic triad residues (Ser-221, His-64, and Asp-32) are replaced singly or in combination by alanine retain activities with the substrate N-succinyl-L-Ala-L-Ala-L-Pro-L-Phe-p-nitroanilide (sAAPF-pna) that are at at least 103 to 104 above the non-enzymatic rate [Carter, P., Wells, J.A. Nature (London) 322:564-568, 1988]. A possible source of the residual activity was the hydrogen bond with the Nδ2 of Asn-155 that helps to stabilize the oxyanion generated in the tetrahedral transition state during amide bond hydrolysis by the wild-type enzyme. Replacing Asn-155 by Gly (N155G) lowers the turnover number (kcat) for sAAPF-pna by 150-fold with virtually no change in the Michaelis constant (KM). However, upon combining the N155G and S221A mutations to give N155G:S221A, kcat is actually 5-fold greater than for the S221A enzyme. Thus, the catalytic role of Asn-155 is dependent upon the presence of Ser-221. The residual activity of the N155G:S221A enzyme (∼104-fold above the uncatalyzed rate) is not an artifact because it can be completely inhibited by the third domain of the turkey ovomucoid inhibitor (OMTKY3), which forms a strong 1:1 complex with the active site. the mutations N155G and S221A individually weaken the interaction between subtilisin and OMTKY3 by 1.8 and 2.0 kcal/mol, respectively, and in combination by 2.1 kcal/mol. This is consistent with disruption of stabilizing interactions around the reactive site carbonyl of the OMTKY3 inhibitor. These data suggest that Ser-221 functions together with Asn-155 to accelerate amide bond hydrolysis and that other transition state stabilizing interactions account for the residual rate enhancement of 103- to 104-fold. More generally, these studies illustrate the limitations of using site-directed mutagenesis to probe the energetic importance of a single catalytic group whose function is dependent upon the interaction with others.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070405
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    Electronic Resource
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    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990) 
    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.340070301
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    Solution structure of a zinc finger domain of yeast ADR1 (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 215-226 
    Details
    ISSN: 0887-3585
    Keywords: zinc finger ; DNA-binding motif ; two-dimensional NMR ; synthetic peptides ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The “zinc finger” is a 30-residue repeating motif that has been identified in a variety of eukaryotic transcription factors. Each domain is capable of binding a Zn2+ ion through invariant Cys and His residues. We have determined the three-dimensional structure of a synthetic peptide that corresponds to one of the two zinc finger domains in the yeast transcription factor ADR1, using two-dimensional nuclear magnetic resonance spectroscopy. The Zn2+ -bound structure of the peptide consists of a loop containing the two Cys residues, a “fingertip,” a 12- to 13-residue α-helix containing the two His residues, and a C-terminal tail. A majority of the interrresidue contacts observed invlove the seven conserved residues of the prototypic zinc finger (i.e., four zinc ligands and the three hydrophobic residues), indicating that these residues are largely responsible for the three-dimensional structure of the domain and that all the zinc finger domains of the TFIIIA class will have similar structures, with the highest concentration of such residues on the external face of the α-helix.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070303
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    Identification of protein folds: Matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 257-264 
    Details
    ISSN: 0887-3585
    Keywords: protein families ; structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hydrophobic side chains often are buried in the interior of a protein, and evolutionarily related proteins usually maintain the hydrophobic character of buried position. In this paper we shown that a pattern of hydrophobicity values derived from a set of related protein sequences is well correlated with the linear pattern of side-chain solvent accessibility values, calculated from a known protein structure representative of the sequences. In several cases, information from aligned sequences can be used to select the correct tertiary fold from a large database of protein structures.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070307
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    ALMA, an editor for large sequence alignments (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 291-295 
    Details
    ISSN: 0887-3585
    Keywords: full screen editor ; consensus calculation ; secondary structure ; automatic alignment ; alignment merging ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A dedicated sequence editor ALMA, was developed for aligning many sequences of proteins or RNA molecules or longer DNA fragments. Like previously published editors, ALMA is menu directed, screen oriented, and offers similarity and consensus display. ALMA has the additional features of collective movement of sequences, acceptance of input from many sources including structure files and databases, secondary structure display, and easy merging of alignments. In order to maintain sequence integrity and save disk space, gaps and sequences are stored separately. Automatic recovery of a session is possible. Finally, The program allows interaction between manual and automatic alignment.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070310
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    Comparative modeling methods: Application to the family of the mammalian serine proteases (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 317-334 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; computer modeling ; structure prediction ; sequence homology ; structure homology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Comparative modeling methods are described that can be used to construct a three-dimensional model structure of a new protein from knowledge of its sequence and of the experimental structure and sequences of other members of its homology family. The methods are illustrated with the mammalian serine protease family, for which seven experimental structures have been reported in the literature, and the sequence for over 35 different protein members of the family are available. The strategy for modeling these proteins is presented, and criteria are developed for determining and assigning the reliability of the modeled structure. Criteria are described that are specially designed to help detect cases in which it is likely that the local structure diverges significantly from the usual conformation of the family.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070404
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    Protein-drug interactions: Characterization of inhibitor binding in complexes of DHFR with trimethoprim and related derivatives (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 52-61 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; protein simulations ; dihydrofolate reductase ; trimethoprim ; drug binding ; solvation ; binding free energies ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structural and thermodynamic interactions for the binding of trimethoprim and related congeners to the binary complex of diphydrofolate reductase (from chicken) and NADPH are explored using free energy simulation methods. Good agreement between structures from experimental X-ray refinement and molecular dynamics simulations is found for the complexes. Agreement with thermodyanmic measurements is found as well. Our thermodynamic calculations suggest that entropic contributions and desolvation thermodynamics can play a crucial role in overall bindings, and that extreme care must be taken in the use of simple model building to rationalize or predict protein-drug binding.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070106
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    Computer analysis of mutations that affect antibody specificity (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 93-98 
    Details
    ISSN: 0887-3585
    Keywords: protein conformation ; CONGEN ; immunoglobulin ; hydrogen bond ; digoxin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The mouse hybridoma cell line 40-150 scretes antibodies with high affinity towards the cardiac glycosides digoxin and digitoxin. A spontaneous mutant, 40-150 A2.4, produces and antibody which carries a single residue mutation, Ser → Arg, in its heavy chain (H94) and has an altered specificity. A second order mutant 40-150 A2.4 P.10, produces two antibody molecules, one the same as 40-150 A2.4, the other lacking two residues at the N-terminus of its H chain, and having a specificity profile approaching that of 40-150 antibody. 1 The N-terminus and the position H94 are distant from the antigen-binding site of the antibody; thus, the structural basic of the specificity changes was not immediately clear. Approximate structures of the 40-150 antibody and its mutants were constructed in the computer, based on atomic coordinates of the homologous mouse antibody McPC 603. Using the program OCNGEN, the torsional space of the polypeptide backbone and side chains around position H94 was uniformly sampled, and the lowest energy conformations were analyzed in detail. The results indicate that when Arg-H94 is substituted for Ser. Agr-H94 can hydrogen bond to side chains of Asp-H101, Arg-L46, and Asp-L55. The results in a change in the surface of the combining site which may account for the affinity changes. Deletion of the two N-terminal residues increases solvent accessibility of Arg-H94. The solvation may cause a hydrogen bond between Arg-H94 and Asp-H101 to be lost, restoring the structure to one similar to that of 40-150.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070109
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    Evaluation of homology modeling of HIV Protease (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 172-184 
    Details
    ISSN: 0887-3585
    Keywords: aspartic proteases ; retroviral proteases ; sequence homology ; related structures ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The model of human immuno-deficiency virus (HIV-1) protease which was based on the crystal structure of Rous sarcoma virus (RSV) protease has been compared to the recently determined crystal structure of chemically synthesized HIV-1 protease. The overall difference between the model and crystal structure was 1.4 Å root mean square (rms) deviation for 86 superimposed Cα atoms. The position of the flexible flap differs in the model and six residues at the amino terminus were incorrectly placed. With these exceptions, all atoms of the model and crystal structure agree to 2.11 Å runs deviation. The conformation of some surface bends in the model agrees less well with the crystal structure. Identical amino acids in RSV and HIV proteases were modeled more reliably than different types of amino acids. The amino acids which form the substrate binding site were modeled most accurately to 1.2 Å rms deviation for all atoms compared to the crystal structure. This suggests that functionally significant regions of related proteins can be modeled with high accuracy. The model gave correct predictions for residues making interactions with the substrate, and thereof could be used to design inhibitors, The model based on the RSV protease structure is more similar to the experimental structure than are previous models based on the structures of non-viral aspartic proteases.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070206
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    Polyproline, β-turn helices. Novel secondary structures proposed for the tandem repeats within rhodopsin, synaptophysin, synexin, gliadin, RNA polymerase II, hordein, and gluten (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 125-155 
    Details
    ISSN: 0887-3585
    Keywords: phosphorylation ; tyrosine ; cis-peptide ; exocytosis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Seven proteins each contain 8 to 52 tandem repeats of a unique class of oligopeptide. The consensus peptide for each is rhodopsin Tyr Pro Pro Gln Glysynapto-physin Tyr Gly Pro Gln Glysynexin Tyr Pro Pro Pro Pro Glygliadin Tyr Pro Pro Pro Gln ProRNA polymerase II Tyr Ser Pro Thr Ser Pro Serhordein Phe Pro Gln Gln Pro Gln Gln Progluten Tyr Pro Thr Ser Pro Gln Gn Gly TyrAlthough there is obvious variations of sequence and of length, the penta-to nonapeptides share an initial Tyr(or Phe) and have high Pro contents and abundant Gly, Gln, and Ser. We have evaluated helical models that both recognize the uniqueness of these sequence repeats and accommodate variations on the basic theme.We have developed a group of related heical model for these proteins with about three oligopeptide repeats per turn of 10-20 Å. These models share several common features: Most of the φ dihedral angels are -54°, to accommodate Pro at all positions expect the first (Tyr). Except for the β-turns, most ψ dihedral angles are near +140° as found in polyproline. Each oligopeptide has at least one β-turn; several have two. Some contains a cis-Tyr, Pro peptide bond; a few have a cis-bond plus one β-turn. Tyr side chains vary from totally exposed to buried within the helices and could mode to accommodate either external hydrophobic interactions or phosphorylation. The several related structures seem to be readily interconverted without major change in the overall helical parameters, and therein may lie the key to their functions.
    Additional Material: 10 Ill.
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    β-Lactamase of Bacillus licheniformis 749/C at 2 Å resolution (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 156-171 
    Details
    ISSN: 0887-3585
    Keywords: β-lactamase ; penicillinase ; penicillin-binding protein ; penicillin antibiotics ; X-ray diffraction ; protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two crystal (A and B) of the 29,500 Da Class A β-lactamase (penicillinase) from Bacillus licheniformis 749/C have been examined crystallographically. The structure of B-form crystals has been solved to 2 Å resolution, the starting model for which was a 3.5 Å structure obtained from A-form crystals. The β-lactamase has an α + β structure with 11 helices and 5 β-strands seen also in a peinicilin target DD-peptidase of Streptomyces R61.1 Atomic parameters of the two molecules in the asymmetric unit were refined by simulated annealing at 2.0 Å resolution. The R factor is 0.208 for the 27,330 data greater than 3 (F), with water molecules excluded from the model. The catalytic Ser-70 is at the N-terminus of a helix and is within hydrogen bonding distance of conversed Lys-73. Also interacting with the Lys-73 are Asn-132 and the conserved Glu-166, which is on a potentially flexible helix-containing loop. The structure suggests the binding of β-lactam substrates is facilitated by interactions with Lys-234, Tyhr-235, and Ala-237 in a conserved β-strand peptide, which is antiparallel to the β-lactam's acylamido linkage; an exposed cavity near Asn-170 exits for acylamido Substituent. The reactive double bond of clavulanate-type inhibitors may interact with Arg-244 on the fourth β-strand. A very similar binding site architecture is seen in the DD-peptidase.
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    A mutant T4 lysozyme (Val 131 → Ala) designed to increase thermostability by the reduction of strain within an α-helix (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 198-204 
    Details
    ISSN: 0887-3585
    Keywords: protein stability ; protein design ; strain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An attempt has been made to identify residues in T4 phage lyoszyme that may have strained conformations and, by appropriate site-directed replacements, to reduce this strain and thus increase the thermostability of the protein. Valine 131, within α-helix 126-134, was identified as a potential candidate. Its side-chain rotational as a potential candidate. Its side-chain rotation angle, χ1, differs by approximately 18° from the low-energy trans configuration. In addition, it is largely solvent exposed, yet is held in a rigid conformation. The mutant protein with Val 131 replaced by alanine temperature 0.9°C higher than that of wildtype lyoszyme at pH 2.8. As a control, The mutant Val 131 → Thr was also constructed and its melting temperature was found to be marginally lower than wild type. Higher-resolution crystal structure determination of the mutant lysozymes show that their structure are virtually identical with that of wild-type lyoszyme, except for the Val → Ala or Val → Thr replacement. Analysis of the different structures suggests that the design of the Val→Ala substitution was, in principle, successful, although the apparent gain in stability caused by reduction in strain is modest and is somewhat offset by the loss of hydrophobic interactions and by entrophic effects. The results also help to provide a structural retionalization that alanine has a higher helix propensity than valine or theronine.
    Additional Material: 2 Ill.
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    Accommodation of single amino acid insertions by the native state of staphylococcal nuclease (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 299-305 
    Details
    ISSN: 0887-3585
    Keywords: protein stability ; guanidine hydrochloride denaturation ; conformational changes ; polypeptide backbone ; alanine insertion ; glycine insertion ; circular dichroism spectra ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Single alanine and glycine insertions were introduced at 20 randomly selected positions in staphylococcal nuclease. The resulting changes in catalytic activity and in stability to guanidine hydrochloride denaturation indicate that the native state structure is frequently able to accommodate the extra residue without great difficulty, even insertions within secondary structural elements such as alpha helices and beta sheets. On average, an inserted residue reduces the free energy of denaturation (ΔGH2O) by an amount roughly comparable to an alanine or glycine substitution for one of the residues flanking the site of insertion. Several positions outside of the enzyme active site were found where insertions, but not substitutions, lead to structural changes that modify catalytic activity and the circular dichroism spectrum. Amino acid insertions represent a virtually unexplored class of genetic mutation that may prove complementary to amino acid substitutions for engineering proteins with altered functional and structural properties.
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    Crystal structure of myoglobin form a synthetic gene (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 358-365 
    Details
    ISSN: 0887-3585
    Keywords: synthetic myoglobins ; X-ray crystallography ; protein engineering ; heme proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystal have been grown of myoglobin produced in Escherichia coli from a synthetic gene, and the structure has been solved to 1.9 Å resolution. The space group of the crystals is P6, which is different from previously solved myoglobin crystal forms. The synthetic myoglobin is essentially identical to myoglobin isolated from sperm whale tissue, except for the retention of the initiator methionine at the N-terminus and the substitution of asparagine for aspartic acid at position 122. Superposition of the coordinates of native and synthetic sperm whale myoglobins reveals only minor changes in the positions of main chain atoms and roeientation of some surface side chains. Crystals of variant of the “synthetic” myoglobin have also been grown for structural analysis of the role of key amino acid residues in ligand and specificity.
    Additional Material: 5 Ill.
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    Comparison of the structures of globins and phycocyanins: Evidence for evolutionary relationship (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 133-155 
    Details
    ISSN: 0887-3585
    Keywords: evolution ; alignment ; globins ; phycocyanin ; helix interfaces ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Globins and phycocyanins are two classes of proteins with different function, different ligands, and no substantial sequence similarity, yet the conformations of their polypeptide chains show very similar folding patterns. Does this arise from a genuine, albeit very distant, evolutionary relationship, or does it represent a common solution of a structural problem? We address this question by a very detailed comparison of the structures of the two protein families. An analysis of the helices and their interactions shows many features common to globins and phycocyanins, including some exceptional features of the globins such as a 3-10 C helix and the unusual “crossed-ridge” packing pattern at the B/E helix interfaces. We conclude that the evidence supports the hypothesis of distant evolutionary relationship between globins and phycocyanins.
    Additional Material: 12 Ill.
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    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990) 
    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.340080301
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    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990) 
    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.340070101
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    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990) 
    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.340080101
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    Hydrophobicity of amino acid subgroups in proteins (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 6-13 
    Details
    ISSN: 0887-3585
    Keywords: hydrophobicity ; hydrophobic effect ; protein folding ; solvent accessibility ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Protein folding studies often utilize areas and volumes to assess the hydrophobic contribution to conformational free energy (Richards, F. M. Annu. Rev. Biophys. Bioeng. 6:151-176, 1977). We have calculated the mean area buried upon folding for every chemical group in each residue within a set of X-ray elucidated proteins. These measurements, together with a standard state cavity size for each group, are documented in a table. It is observed that, on average, each type of group buries a constant fraction of its standard state area. The mean area buried by most, though not all, groups can be closely approximated by summing contributions from three characteristic parameters corresponding to three atom types: (1) carbon or sulfur, which turn out to be 86% buried, on average; (2) neutral oxygen or nitrogen, which are 40% buried, on average; and (3) charged oxygen or nitrogen, which are 32% buried, on average.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080104
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    Apolar peptide models for conformational heterogeneity, hydration, and packing of polypeptide helices: Crystal structure of hepta- and octapeptides containing α-aminoisobutyric acid (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 62-73 
    Details
    ISSN: 0887-3585
    Keywords: hydrophobic α-helices ; water insertion into helix ; water in hydrophobic pocket ; helix unfolding ; helix folding ; parallel packing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structures of two helical peptides Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe (VALU-7) and Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe (VALU-8) have been determined to a resolution of 1.0 and 0.9 Å, respectively. Both the seven and eight residue peptides crystallize with two conformers per asymmetric unit. The VALU-8 conformers are completely helical and differ only at the C-terminus by a sign reversal of the φ, ψ angles of the last residue. One of the VALUE-7 conformers occurs as a normal α-helix, whereas in the other, the N(7)=O(3) α-type hydrogen bond is ruptured by the entry of a water molecule (W) into the helix, which in turn makes hydrogen bonds N(7)⃛W = 2.97 Å and ⃛O(3) = 2.77 Å. The other side of the water molecule is surrounded by a hydrophobic pocket. These two conformers give a static representation of a step in a possible helix unwinding or folding process. In the value-8 crystal the helices aggregate in a parallel mode, whereas the aggregation is antiparallel in the VALU-7 crystal. The crystal parameters are VALUE-7 crystal. The crystal parameters are VALUE-7, P21, a = 10.203 (3) Å, b = 19.744 (6) Å, c = 22.561 (6) Å, α = 96.76°, Z = 4, C38, H69N7O10·0.5 H2O, R = 6.65% for 3674 reflections observed 〉3σ(F): and VALU-8, P21, a; = 10.596 (4) Å, b = 27.57 (6) Å, c = 17.745 (5) Å, β = 95.76 (3)°, Z = 4, C42H76N76O11·0.25 CH3OH, R = 6.63% for 4701 reflections observed 〉3σ(F).
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070107
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    On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 112-124 
    Details
    ISSN: 0887-3585
    Keywords: amino acid propensities ; aromatic residues ; conformational entropy ; exposure patterns ; interaction energy ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A detailed analysis of the structural aspects of antibody-antigen interactions has been made possible by the availability of X-ray structures for three complexes of antilysozyme Fabs to lysozyme (reviewed by Davies et al: J. Biol. Chem. 263:10541-10544, 1988.) Examination of the antigen-contacting residues in the three antilysozyme Fabs reveals the occurrence of a large number of aromatics, particularly tyrosines, and the absence of apolar, aliphatic residues. Calculation of the frequency of occurrence of the various amino acids types reveals that tyrosines are three times, and histidines and asparagines eight times, more likely to be found in the complementarity-determinig regions that in the framework of the variability of the residue in FVs (the modules containing variable domains of the light and heavy chains) of known three-dimensional structure indicates that tryosines and tryptophans are more exposed when they occur in the complementarity-determining regions that when in the framework. Furthermore, many more of the asparagines in the complementarity-determining regions than in the framework are buried. These aspararagines appear to have a structural role in that they hydrogen bond through their side chains to other side chains and, Even more so, to the protein backbone. The stabilizing effect of the asparragines, plus the rigidity of the framework, may serve to allow the greater exposure of the aromatic residues to solvent. In view of the greater potential contribution of aromatic side chains to the total binding energy, these results suggest that antibody-combining sites have structural features that make them especially studied for interacting with lagands.
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    Molecular interactions in protein crystals: Solvent accessible surface and stability (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 1-5 
    Details
    ISSN: 0887-3585
    Keywords: accessible area ; crystalline environment ; hydrophobic interaction ; linear correlation ; monomeric proteins ; dimeric proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The accessible surface areas of 58 monomeric and dimeric proteins, when measured in the crystalline environment, are found to be simply related to molecular weight. The loss of accessible surface when the proteins go from a free to their crystalline environment is well defined, implying that the hydrophobic interaction, which has been found to contribute to protein folding and stability in living systems, also contributes to protein crystal stability.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080103
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    Protein stability and electrostatic interactions between solvent exposed charged side chains (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 23-29 
    Details
    ISSN: 0887-3585
    Keywords: urea induced unfolding ; increased stability ; site-directed mutagenesis ; calbindin D9k ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To investigate the contribution to protein stability of electrostatic interactions between charged surface residues, we have studied the effect of substituting three negatively charged solvent exposed residues with their side-chain amide analogs in bovine calbindin D9k - a small (Mr 8,500) globular protein of the calmodulin superfamily. The free energy of urea-induced unfolding for the wildtype and seven mutant proteins has been measured. The mutant proteins have increased stability towards unfolding relative to the wildtype. The experimental results correlate reasonably well with theoretically calculated relative free energies of unfolding and show that electrostatic interactions between charges on the surface of a protein can have significant effects on protein stability.
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    URL: http://dx.doi.org/10.1002/prot.340080106
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    Amphipathic helix motif: Classes and properties (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 103-117 
    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.340080202
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    Crystal structure of a protein-toxin α1-purothionin at 2.5Å and a comparison with predicted models (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 118-132 
    Details
    ISSN: 0887-3585
    Keywords: molecular modeling ; α1-purothionin ; x-ray structure determination ; molecular replacement ; comparison of crystal structure and predicted models ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: α1-Purothionin (α1-P), a wheatgerm protein and lytic toxin, has a secondary and tertiary structure similar to that of crambin as revealed by CD and NMR studies. α1-P crystallizes in the tetragonal space group I422 with unit cell dimensions: a = b = 53.59 and c = 69.79 Å. X-ray diffraction data have been measured to 2.5 Å Bragg spacing. The crystal structure has been determined by molecular replacement methods, using an energy-minimized α1-P model structure derived from crambin (Whitlow and Teeter: Journal of Biomolecular Structure and Dynamics 2:831-848, 1985, Journal of the American Chemical Society 108:7163-7172, 1986). The energy-minimized model gives a slightly cleaner rotation solution and better refinement against the x-ray data than do the crambin or unminimized α1-P structures. The final crystallographic residual with the data in the 10-2.5 Å resolution range is 0.216. The refined α1-P structure has a backbone rms difference of 0.74 Å from crambin and 0.55 Å from the energy-minimized α1-P model. A low resolution NMR model of α1-P calculated from metric matrix distance geometry and restrained molecular dynamics differs from crambin's backbone by 2.3 Å rms deviation (Clore et al.: EMBO Journal 5:2729-2735, 1986). Backbone dihedral angles for our predicted model differ from the refined α1-P structure in only one region (at a turn where there is a deletion relative to crambin). The NMR model had differences in four regions.
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    Erratum (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 398-399 
    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.340080413
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    Three-Dimensionnal structures of complexes of Lathyrus ochrus isolectin I with glucose and mannose: Fine specificity of the monosaccharide-binding site (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 365-376 
    Details
    ISSN: 0887-3585
    Keywords: lectins ; crystal structure ; lectin specificity ; mannose ; glucose ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of the methyl-α-D-mannopyranoside-LOL I complex has been solved by the molecular replacement method using the refined saccharide-free LOL I coordinates as starting model. The methyl-α-D-mannopyranoside-LOL I complex was refined by simulated annealing using the program X-PLOR. The final R-factor value is 0.182 [Fo 〉 1σ(Fo)]. The isostructural methyl-α-D-glucopyranoside-LOL I complex was refined by X-Ray coupled energy minimization using the methyl-α-D-mannopyranoside-LOL I structure as a starting model to an R factor of 0.179 (all data). In both crystal forms, each dimer binds two molecules of sugar in pockets found near the calcium ions. The two saccharide moieties, which are in the C1 chair conformation, establish the same hydrogen bond pattern with the lectin. However, the van der Walls contacts are different between the O2, C2, C6, and O6 atoms of the two molecules and the backbone atoms of residues 208-211. Mannose, due to its axial C2 conformation, encloses the backbone atoms of the protein in a clamplike way. Van der Waals energy calculations suggest that this better complementarity of the mannoside molecule with the lectin could explain its higher affinity for isolectin I.
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    Modeling of agonist binding to the ligand-gated ion channel superfamily of receptors (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 386-397 
    Details
    ISSN: 0887-3585
    Keywords: LGIC superfamily ; proto-binding site ; cys-loop motif ; docking model ; anionic site ; specificity residue ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A generalized model is presented of agonist binding to ligand-gated ion channels (LGICs). Broad similarity in the structure of agonists suggests that the binding sites of LGICs may have evolved from a protobinding site. Aligned sequence data identified as a candidate for such a site a highly conserved 15 residue stretch of primary structure in the N-terminal extracellular region of all known LGIC subunits. We modeled this subregion, termed the cys-loop, as a rigid, amphiphilic β-hairpin and propose that it may form a major determinant of a conserved structural binding cleft.In the model of the binding complex (1) an invariant aspartate residue at position 11 of the cys-loop is the anionic site interacting with the positively charged amine group of agonists, (2) a local dipole within the π-electron system of agonists is favorably oriented in the electrostatic field of the invariant aspartate, (3) the ε ring-proton of a conserved aromatic residue at the turn of the cys-loop interacts orthogonally with the agonist α-electron density at its electronegative center, and (4) selective recognition is partly a result of the type of amino acid residue at position 6 of the cys-loop. Additionally, the formation of a hydrogen bond between the electronegative atom of the π-electron system of agonist and a complementary group in the receptor may be important in the high-affinity binding of agonists.
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    URL: http://dx.doi.org/10.1002/prot.340080412
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    Announcement (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 404-405 
    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.340080414
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    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990) 
    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.340080201
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    Calendar of events (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), 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.300030408
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  • 81
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    The specificity of the binding of platelet activating factor (PAF) to anti-PAF antibodies (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 169-173 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Quantitative hapten inhibition experiments employing sheep anti-PAF antibodies and selected PAF analogues were undertaken with the aim of defining the antigenic determinant structures complementary to the antibody combining sites. The most important fine structural features for inhibition of antibody binding to PAF were shown to be an acetyl group at position 2 of the phospholipid glycerol backbone and an ether group at position 1. Of the naturally occurring compounds, C16- and C18:1-PAF proved to be the most potent inhibitors and more active than C18-PAF while phospholipids with a propionyl, butyryl or hexanoyl group at position 2 showed either weak or no inhibitory activity. The 1-acyl, thioether and deoxy analogues proved inactive. Variations in the polar head group of PAF were found to be less critical with, for example, the dimethyl and ethanolamine derivatives retaining some activity. This antibody recognition pattern is very similar to that of the PAF receptor, although the antibodies appear to have a more specific requirement for an acyl linkage at position 2.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030406
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  • 82
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    Masthead (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990) 
    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.300030501
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  • 83
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    X-ray crystal structure of the bovine α-chymotrypsin/eglin c complex at 2.6 Å resolution (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 163-168 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of the molecular complex formed by bovine α-chymotrypsin and the recombinant serine proteinase inhibitor eglin c from Hirudo medicinalis has been solved using monoclinic crystals of the complex, reported previously. Four circle diffractometer data at 3.0 Å resolution were employed to determine the structure by molecular replacement techniques. Bovine α-chymotrypsin alone was used as the search model; it allowed us to correctly orient and translate the enzyme in the unit cell and to obtain sufficient electron density for positioning the eglin c molecule. After independent rigid body refinement of the two complex components, the molecular model yielded a crystallographic R factor of 0.39. Five iterative cycles of restrained crystallographic refinement and model building were conducted, gradually increasing resolution. The current R factor at 2.6 Å resolution (diffractometer data) is 0.18. The model includes 56 solvent molecules. Eglin c binds to bovine α-chymotrypsin in a manner consistent with other known serine proteinase/inhibitor complex structures. The reactive site loop shows the expected conformation for productive binding and is in tight contact with bovine α-chymotrypsin between subsites P3 and P′2; Leu 45I acts as the P1 residue, located in the primary specificity S1 site of the enzyme. Hydrogen bonds equivalent to those observed in complexes of trypsin(ogen) with the pancreatic basic- and secretory- inhibitors are found around the scissile peptide bond.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030405
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  • 84
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    Ligand-binding properties of estrogen receptor proteins after interaction with surface-immobilized Zn(II) ions: Evidence for localized surface interactions and minimal conformational changesSupported, 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 trade names, commercial products, or organizations imply endorsement by the US Government. (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 174-179 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The site- or domain-specific immobilization of steroid receptor proteins with preserved structure and function would facilitate the identification and purification of receptor-associated regulatory components and nucleic acids. We have demonstrated previously that restricted surface regions of the estrogen receptor protein contain high affinity binding sites for immobilized Zn(II) ions. Possible conformational changes in receptor at the stationary phase immobilized metal ion interface were evaluated by monitoring alterations in the equilibrium dissociation constant (Kd) for [3H]estradiol. Soluble estrogen receptor proteins (unliganded) present in immature calf uterine cytosol were immobilized via surface-exposed Zn(II)-binding sites to beads of agarose derivatized with iminodiacetate (IDA)-Zn(II) ions. The IDA-Zn(II) bound receptor was incubated with increasing concentrations of [3H]estradiol (0.01-20 nM) in the presence and absence of unlabeled competitor (diethylstilbestrol) to determine the level of specific hormone binding. Steroid-binding experiments were performed in parallel with identical aliquots of soluble receptor. Analyses of the equilibrium binding data revealed the presence of a single class of high-affinity (Kd = 2.44 ± 1.5 nM, n = 10) steroid-binding sites which were only marginally affected by receptor immobilization via surface-exposed Zn(II) bindings sites (Kd = 2.58 ± 0.56 nM, n = 4). These data are consistent with the location of surface accessible Zn(II) binding site(s) on the receptor at or near the DNA binding domain which, upon occupancy, do not influence the steroid binding domain. The high affinity of receptor for immobilized metal ions and lack of evident conformational changes in the immobilized receptor suggest that stationary phases of immobilized metal ions loaded with receptor proteins may be useful as affinity tools for the analysis and purification of receptor-associated macromolecules.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030407
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    Molecular recognition between oligopeptides and nucleic acids. DNA sequence specificity and binding properties of an acridine-linked netropsin hybrid ligandThis investigation was supported by grants (to J.-P.H.) from the Institut National de la Santé et de la Recherche Médicale and the Fédération Nationale des Centres de Lutte contre le Cancer France, and by grants (to J.W.L.) from the Medical Research Council of Canada and the Natural Sciences and Engineering Research Council of Canada. (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 26-35 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The binding to DNA of a mixed function ligand (NETGA) is described, in which a potential intercalating group, an acridine moiety, is incorporated at the carboxyl terminus of the minor groove binding oligopeptide netropsin skeleton. Scatchard analysis of absorption data provided evidence of two modes of binding to DNA with K1 = 9.1 × 105 M-1 at low r values (0.003-0.1), and a binding site size n = 10, indicative of binding of both moeities. At high binding ratios (〉0.1), K2 = 0.9 × 105 M-1 and n = 5 corresponding to external binding. Complementary strand MPE footprinting on a pBR322 restriction fragment showed NETGA binds to 5′-AAAT like netropsin. It causes enhanced cleavage by MPE, particularly at G-C rich sequences and remote from the preferred binding sites. Viscometry measurements provided evidence for biphasic modes of the two binding portions of NETGA. Fluorescence polarization and linear dichroism measurements were in accord with distinct modes of interaction of the acridine (intercalation) and oligopeptide (minor groove binding) portions of NETGA. LD measurments of NETGA indicate that the oligopeptide moiety (netropsin-like) has an orientation typical of minor groove binders, whereas the degree of intercalation of the acridine group is decreased by association of the oligopeptide moiety.
    Additional Material: 13 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030103
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  • 86
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    The formation of mispairs by 8-oxyguanine as a pathway of mutations induced by irradiation and oxygen radicals (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 45-47 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Guanine conversion to 8-oxyguanine (OG) was induced by irradiation and oxygen radicals. The pathways of mutations caused by such DNA damage have been considered. Minima of interaction energies of OG with nucleic acid bases are revealed via classical potential function calculations. The minima exist for OG*:G and OG*:A base pairs, with syn-conformation of OG* and OG:T wobble base pairs. The mutual positions of glycosyl bonds in these base pairs are quite close to those for Watson-Crick pairs, and energies of OG*:G, OG*:A and OG:T mispairs are close to the energy of A:T. The results calculated suggest that these mispairs could arise as intermediates in the transversions C:G to G:C and C:G to A:T, and the transition G:C to A:T.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030105
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  • 87
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    Masthead (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990) 
    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.300030201
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  • 88
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    Conformational constraints: Nonpeptide β-turn mimics (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 55-64 
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    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The β-turn, which has also been referred to as the β-bend, β-loop or reverse turn, has been implicated as an important site for molecular recognition in many biologically active peptides and in globular proteins. This small secondary structure therefore makes an attractive target for mimicry by a conformational constraint, because a peptide which is constrained in a biologically active conformation can display a number of advantages over the parent substrate. The less peptide-like such a constraint is, the more potential there is to maximize these advantages. A decade has passed since the first (and highly successful) attempt to mimic the β-turn with a nonpeptide conformational constraint was disclosed by Freidinger et al. (1980). Since this report, rapidly growing interest in the field of nonpeptide β-turn mimics has seen a variety of experimental approaches and a mixed bag of results. It is attempted in this review, not only to summarize and critically analyse these approaches, but also to touch on the compexities associated with the conformational mimicry of such a diverse structure as the β-turn.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030202
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  • 89
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    Prediction of the secondary structure and functional sites of major histocompatibility complex molecules (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 65-73 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method for the theoretical prediction of the antigenic determinants and the antigen-interactive receptor sites of immunological proteins from their primary structure would constitute a useful tool for their study. Such a method developed in this laboratory uses hydrophilicity, accessibility, flexibility, and recognition profiles, together with the predicted secondary structure (α-helices, β-sheets, and turns). The secondary structure is determined by a modification of the method of Lim (1974), as described below. A study of human and mouse class I and class II major histocompatibility complex (MHC) antigens, central to the regulation of immune responses and to the phenomenon of graft rejection, was carried out using the above method. Comparison of the predictions with some of the available experimental and theoretical information supports the validity and usefulness of the approach.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030203
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  • 90
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    Recognition of the acetylcholine receptor binding site of a long-chain neurotoxin by toxin-specific monoclonal antibodies (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 74-81 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The present paper reports the preparation and characterization of two neutralizing monoclonal antibodies (Mabs), called MST1 and MST2, which bind at the central loop of a long-chain neurotoxin from cobra venom. The central loop is a critical region for the binding of the toxin to the nicotinic acetylcholine receptor. Some of the residues incorporated in the epitopes recognized by MST1 and MST2 have been identified on the basis of competition experiments using a set of ‘chemical mutants’ of the toxin. We show that MST1 and MST2 bind at the base and at the tip of the central loop of the toxin, respectively, however, only MST2 actually overlaps the acetylcholine receptor binding site. Accordingly, only MST2 is capable of recognizing all homologous toxins so far examined. MST2, therefore, mimicks, at least partially, the site by which the nicotinic acetylcholine receptor recognizes a long-chain neurotoxin.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030204
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  • 91
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    Rabies virus binding to an acetylcholine receptor α-subunit peptide (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 82-88 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The binding of 125I-labeled rabies virus to a synthetic peptide comprising residues 173-204 of the α1-subunit of the nicotinic acetylcholine receptor was investigated. Binding of rabies virus to the receptor peptide was dependent on pH, could be competed with by unlabeled homologous virus particles, and was saturable. Synthetic peptides of snake venom, curaremimetic neurotoxins and of the structurally similar segment of the rabies virus glycoprotein, were effective in competing with labeled virus binding to the receptor peptide at micromolar concentrations. Similarly, synthetic peptides of the binding domain on the acetylcholine receptor competed for binding. These findings suggest that both rabies virus and neurotoxins bind to residues 173-204 of the α1-subunit of the acetylcholine receptor. Competition studies with shorter α-subunit peptides within this region indicate that the highest affinity virus binding determinants are located within residues 179-192. A rat nerve α3-subunit peptide, that does not bind α-bungarotoxin, inhibited binding of virus to the α1 peptide, suggesting that rabies binds to neuronal nicotinic acetylcholine receptors. These studies indicate that synthetic peptides of the glycoprotein binding domain and of the receptor binding domain may represent useful antiviral agents by targeting the recognition event between the viral attachment protein and the host cell receptor, and inhibiting attachment of virus to the receptor.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jmr.300030205
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  • 92
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    Enzymatic semisynthesis of human insulin: An update (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 181-186 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Peptide bond formation can be enzymatically catalysed by the reverse reaction of proteases. Application is seen in the industrial production of human insulin. Human insulin derivative can be enzymatically prepared using either porcine insulin or the single chain B(1-29)-A(1-21) insulin precursor as the starting material. This is accomplished by either (1) digesting the starting material at Lys29 with Achromobacter lyticus protease I (Ach) and then coupling with Thr-X (X = blocking residue) (two-step reaction) or (2) subjecting Ala-B30 of procine insulin or Gly-A1 of the single chain insulin precursor to transpeptidation with Thr-X (one-step reaction). Trypsin and Ach can be used for either type of reaction and, in the immobilized form, for the two-step reaction. Since the single chain insulin precursor can be produced by gene technology (yeast), use of immobilized trypsin or Ach and the two-step reaction using the single chain insulin precursor as the starting material ensures the continuous production of human insulin making it a feasible method for industrial manufacture.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030502
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  • 93
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    Masthead (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990) 
    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.300030101
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  • 94
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    Chemical and photochemical probing of DNA complexes (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 1-25 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An overview of the chemical and photochemical probes which over the past ten years have been used in studies of DNA/ligand complexes and of non-B-form DNA conformation is presented with emphasis on the chemical reactions of the probes with DNA and on their present ‘use-profile’. The chemical probes include: dimethyl sulfate, ethyl nitroso urea, diethyl pyrocarbonate, osmium tetroxide, permanganate, aldehydes, methidiumpropyl-EDTA-Fell (MPE), phenanthroline metal complexes and EDTA/FeII. The photochemical probes that have been used include: psoralens, UVB, acridines and uranyl salts. The biological systems analysed by use of these probes are reviewed by tabulation.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030102
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  • 95
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    Sequence-selective, pH-dependent binding to DNA of benzophenanthridine alkaloids (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 48-54 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The sequence selectivity associated with binding to DNA of three alkaloids belonging to the benzophenanthridine family has been analysed by DNase I footprinting, and the results were compared with those obtained from an analysis of the behaviour of the standard intercalator, ethidium bromide. Like the ethidium, the benzophenanthridine compunds appear to bind best to regions of mixed nucleotide sequence, especially those containing alternating purines and pyrimidines, although there are some notable differences in behaviour. There is also a marked lack of binding to sequences such as (AT)n, where n≥3. The binding to DNA of the benzophenanthridines is specifically related to the hydrogen ion concentration of the medium, in that the DNase I footprints are considerably enhanced when the reaction is performed at a pH below 7.0. We discuss these results in terms of a greater preponderance of the intercalating species being present at lower pH.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030106
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    M. A. Vijayalakshmi and O. Bertrand ‘editors’ Protein/Dye interactions: Developments and applications. Elsevier Applied Science, London 1989. 342 pp, $75.50 (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), 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.300030208
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    Purification and characterization of fab fragments from anti-mouse NGF polyclonal antibodies (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 187-191 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A functional role for Nerve Growth Factor (NGF) in the peripheral nervous system is well-documented, but a similar case for NGF in the central nervous system remains to be established. One approach to answering this question would be the availability of high-affinity monospecific Fab fragments obtained against NGF. In the present studies we describe the preparation and characterization of such Fab fragments from anti-mouse NGF polyclonal antibodies. Following their purification by the use of a NGF Sepharose-coupled affinity column, the Fab fragments were examined for biological competence in several ways. In vitro, the anti-Fab fragments blcoked the neuronotrophic activity of NGF, as measured by the survival of chicken embryonic day 8 dorsal root ganglion neurons. In vivo, these Fab fragments, when administered systemically to neonatal rats, produced a decrease of noradrenaline levels in two sympathetically innervated organs, the heart and the spleen. These findings suggest that affinity purified Fab fragments of anti-NGF antibodies can be a useful tool for studying the physiological function of NGF in the nervous system.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030503
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    Binding of the soybean Bowman-Birk proteinase inhibitor and of its chymotrypsin and trypsin inhibiting fragments to bovine α-chymotrypsin and bovine β-trypsin. A thermodynamic study (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 192-196 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The effect of pH and temperature on the apparent association equilibrium constant (Ka) for the binding of the soybean Bowman-Birk proteinase inhibitor (BBI) and of its chymotrypsin and trypsin inhibiting fragments (F-C(p), F-T(p) and F-T(t), respectively) to bovine α-chymotrypsin (α-chymotrypsin) and bovine β-trypsin (β-trypsin) has been investigated. On the basis of Ka values, the proteinase inhibitor affinity can be arranged as follows: β-chymotrypsin: BBI ≈ β-trypsin:BBI ≈ β-trypsin:F-T(t) ≈ β-trypsin:F-T(p) ≫ α-chymotrypsin:F-C(p), F-C(p), F-T(p) and F-T(t) do not inhibit β-trypsin and α-chymotrypsin action, respectively. On lowering the pH from 9.5 to 4.5, values of Ka for BBI, F-C(p), F-T(p) and/or F-T(t) binding to α-chymotrypsin and β-trypsin decrease, thus reflecting the acid-pK shift of the invariant His57 catalytic residue from 7.0, in the free enzymes, to 5.2, in the proteinase:inhibitor complexes. Considering the known molecular models, the observed binding behaviour of BBI, F-C(p), F-T(p) and F-T(t) was related to the inferred stereochemistry of the proteinase:inhibitor contact regions.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030504
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    Specific isolation by anhydrotrypsin-agarose chromatography of a recombinant protein tagged with an affinity tail arginine at the C-terminus (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 204-207 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A characteristic property of anhydrotrypsin, i.e., its ability to strongly bind C-terminal arginine, proved to be useful as a tool for specific enrichment of a recombinant protein. An arginine tail was introduced at the C-terminus, for example, of a human β-galactoside-binding lectin by site-directed mutagenesis. The resulting mutant recombinant lectin, which retained sugar-binding activity as high as the wild-type lectin, became recognizable by anhydrotrypsin. It was adsorbed on an anhydrotrypsin-agarose column and eluted with benzoylglycylarginine. The added arginine tail could be specifically removed by carboxypeptidase B. When E. coli lyzate containing the mutant lectin was applied to the column more than 10-fold enrichment of the mutant lectin was attained. This procedure should be generally applicable and may be advantageous because the addition of a single arginine residue may have minimal effect on the structure and function of the target protein.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030506
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  • 100
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    Effect of modification of enkephalin C-terminal functions on affinity selection of opioid receptors (1990)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 3 (1990), S. 197-203 
    Details
    ISSN: 0952-3499
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Enkephalin analogs with various C-terminal modifications have been synthesized to evaluate the corresponding structural elements in the opioid receptors. The carboxyl group of the C-terminal leucine5 or glycine5 was converted into the mercaptomethyl (-CH2SH) and hydroxymethyl (-CH2OH) groups, starting from leucinthiol or leucinol for Leu5-derivatives and from cysteamine or ethanolamine for Gly5-derivatives. Interactions of synthetic peptides with the opioid receptors were examined by the radioligand receptor binding assays using rat brain and tritiated enkephalin analogs. The data suggest that the C-terminal carboxyl group in enkephalins is important, but not electrostatically, for interaction with delta-opioid receptors. With leucinthiol-enkephalin in biological assays which examine its inhibitory activity for electrically stimulated contractions of isolated smooth muscle, it was found that the reactive thiol group exists in the mu receptors present in the guinea pig ileum. Leucinthiol-enkephalin became bound covalently to this receptor-thiol group via disulfide formation after prolonged incubation.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/jmr.300030505
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